Starting phenix.real_space_refine on Wed May 15 07:28:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xow_38542/05_2024/8xow_38542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xow_38542/05_2024/8xow_38542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xow_38542/05_2024/8xow_38542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xow_38542/05_2024/8xow_38542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xow_38542/05_2024/8xow_38542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xow_38542/05_2024/8xow_38542.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 354 5.16 5 C 38880 2.51 5 N 11172 2.21 5 O 11928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "f GLU 17": "OE1" <-> "OE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f ASP 44": "OD1" <-> "OD2" Residue "f ASP 91": "OD1" <-> "OD2" Residue "f ASP 96": "OD1" <-> "OD2" Residue "W ASP 16": "OD1" <-> "OD2" Residue "w ASP 16": "OD1" <-> "OD2" Residue "w ASP 29": "OD1" <-> "OD2" Residue "w GLU 51": "OE1" <-> "OE2" Residue "U PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "U TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 133": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "b GLU 43": "OE1" <-> "OE2" Residue "b TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 197": "OD1" <-> "OD2" Residue "b ASP 209": "OD1" <-> "OD2" Residue "b GLU 355": "OE1" <-> "OE2" Residue "b GLU 469": "OE1" <-> "OE2" Residue "b TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 485": "OD1" <-> "OD2" Residue "f1 GLU 85": "OE1" <-> "OE2" Residue "f1 GLU 86": "OE1" <-> "OE2" Residue "W1 GLU 5": "OE1" <-> "OE2" Residue "W1 GLU 6": "OE1" <-> "OE2" Residue "W1 ASP 16": "OD1" <-> "OD2" Residue "W1 ASP 29": "OD1" <-> "OD2" Residue "W1 GLU 51": "OE1" <-> "OE2" Residue "w1 GLU 5": "OE1" <-> "OE2" Residue "w1 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U1 GLU 55": "OE1" <-> "OE2" Residue "U1 GLU 68": "OE1" <-> "OE2" Residue "B1 PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 GLU 283": "OE1" <-> "OE2" Residue "B1 GLU 460": "OE1" <-> "OE2" Residue "B1 ASP 485": "OD1" <-> "OD2" Residue "B1 GLU 488": "OE1" <-> "OE2" Residue "b1 ASP 61": "OD1" <-> "OD2" Residue "b1 ASP 79": "OD1" <-> "OD2" Residue "b1 GLU 241": "OE1" <-> "OE2" Residue "b1 ASP 348": "OD1" <-> "OD2" Residue "b1 ASP 446": "OD1" <-> "OD2" Residue "b1 GLU 463": "OE1" <-> "OE2" Residue "b1 GLU 478": "OE1" <-> "OE2" Residue "f2 GLU 86": "OE1" <-> "OE2" Residue "W2 ASP 16": "OD1" <-> "OD2" Residue "W2 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W2 GLU 51": "OE1" <-> "OE2" Residue "W2 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w2 GLU 6": "OE1" <-> "OE2" Residue "w2 ASP 42": "OD1" <-> "OD2" Residue "w2 GLU 49": "OE1" <-> "OE2" Residue "U2 GLU 50": "OE1" <-> "OE2" Residue "U2 GLU 68": "OE1" <-> "OE2" Residue "U2 GLU 79": "OE1" <-> "OE2" Residue "U2 GLU 85": "OE1" <-> "OE2" Residue "U2 TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 150": "OE1" <-> "OE2" Residue "B2 ASP 197": "OD1" <-> "OD2" Residue "B2 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 283": "OE1" <-> "OE2" Residue "b2 ASP 61": "OD1" <-> "OD2" Residue "b2 PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b2 GLU 355": "OE1" <-> "OE2" Residue "f3 GLU 17": "OE1" <-> "OE2" Residue "f3 GLU 47": "OE1" <-> "OE2" Residue "W3 GLU 5": "OE1" <-> "OE2" Residue "W3 ASP 29": "OD1" <-> "OD2" Residue "w3 GLU 6": "OE1" <-> "OE2" Residue "w3 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U3 PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U3 GLU 54": "OE1" <-> "OE2" Residue "U3 GLU 68": "OE1" <-> "OE2" Residue "U3 GLU 85": "OE1" <-> "OE2" Residue "U3 ASP 111": "OD1" <-> "OD2" Residue "B3 GLU 43": "OE1" <-> "OE2" Residue "B3 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 112": "OE1" <-> "OE2" Residue "B3 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 ASP 197": "OD1" <-> "OD2" Residue "B3 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 241": "OE1" <-> "OE2" Residue "B3 ASP 262": "OD1" <-> "OD2" Residue "B3 GLU 285": "OE1" <-> "OE2" Residue "B3 GLU 302": "OE1" <-> "OE2" Residue "B3 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 GLU 460": "OE1" <-> "OE2" Residue "B3 ASP 485": "OD1" <-> "OD2" Residue "B3 GLU 499": "OE1" <-> "OE2" Residue "b3 ASP 62": "OD1" <-> "OD2" Residue "b3 ASP 197": "OD1" <-> "OD2" Residue "b3 ASP 209": "OD1" <-> "OD2" Residue "b3 ASP 348": "OD1" <-> "OD2" Residue "b3 GLU 391": "OE1" <-> "OE2" Residue "b3 ASP 456": "OD1" <-> "OD2" Residue "b3 ASP 485": "OD1" <-> "OD2" Residue "f4 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f4 TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f4 GLU 86": "OE1" <-> "OE2" Residue "W4 GLU 51": "OE1" <-> "OE2" Residue "W4 TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w4 GLU 6": "OE1" <-> "OE2" Residue "w4 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U4 GLU 68": "OE1" <-> "OE2" Residue "B4 GLU 43": "OE1" <-> "OE2" Residue "B4 ASP 61": "OD1" <-> "OD2" Residue "B4 GLU 150": "OE1" <-> "OE2" Residue "B4 PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B4 GLU 371": "OE1" <-> "OE2" Residue "B4 GLU 463": "OE1" <-> "OE2" Residue "b4 ASP 61": "OD1" <-> "OD2" Residue "b4 ASP 242": "OD1" <-> "OD2" Residue "b4 ASP 446": "OD1" <-> "OD2" Residue "b4 TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b4 GLU 478": "OE1" <-> "OE2" Residue "f5 GLU 17": "OE1" <-> "OE2" Residue "f5 GLU 47": "OE1" <-> "OE2" Residue "f5 GLU 85": "OE1" <-> "OE2" Residue "f5 GLU 86": "OE1" <-> "OE2" Residue "W5 ASP 16": "OD1" <-> "OD2" Residue "W5 GLU 34": "OE1" <-> "OE2" Residue "W5 ASP 42": "OD1" <-> "OD2" Residue "W5 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U5 ASP 117": "OD1" <-> "OD2" Residue "B5 GLU 110": "OE1" <-> "OE2" Residue "B5 GLU 112": "OE1" <-> "OE2" Residue "B5 ASP 197": "OD1" <-> "OD2" Residue "B5 GLU 283": "OE1" <-> "OE2" Residue "B5 GLU 285": "OE1" <-> "OE2" Residue "B5 TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b5 ASP 61": "OD1" <-> "OD2" Residue "b5 ASP 337": "OD1" <-> "OD2" Residue "b5 ASP 446": "OD1" <-> "OD2" Residue "b5 GLU 478": "OE1" <-> "OE2" Residue "b5 ASP 485": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 62334 Number of models: 1 Model: "" Number of chains: 36 Chain: "f" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "W" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "w" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "U" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "B" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3727 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3710 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f1" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "W1" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "w1" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "U1" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "B1" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3727 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "b1" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3710 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f2" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "W2" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "w2" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "U2" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "B2" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3727 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "b2" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3710 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f3" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "W3" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "w3" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "U3" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "B3" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3727 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "b3" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3710 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f4" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "W4" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "w4" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "U4" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "B4" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3727 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "b4" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3710 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f5" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "W5" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "w5" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "U5" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "B5" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3727 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "b5" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3710 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 455} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 23.02, per 1000 atoms: 0.37 Number of scatterers: 62334 At special positions: 0 Unit cell: (160.056, 157.907, 222.359, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 354 16.00 O 11928 8.00 N 11172 7.00 C 38880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 123 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS b 123 " - pdb=" SG CYS b 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB1 123 " - pdb=" SG CYSB1 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb1 123 " - pdb=" SG CYSb1 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB2 123 " - pdb=" SG CYSB2 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb2 123 " - pdb=" SG CYSb2 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB3 123 " - pdb=" SG CYSB3 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb3 123 " - pdb=" SG CYSb3 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB4 123 " - pdb=" SG CYSB4 125 " distance=2.04 Simple disulfide: pdb=" SG CYSb4 123 " - pdb=" SG CYSb4 125 " distance=2.03 Simple disulfide: pdb=" SG CYSB5 123 " - pdb=" SG CYSB5 125 " distance=2.03 Simple disulfide: pdb=" SG CYSb5 123 " - pdb=" SG CYSb5 125 " 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=0, symmetry=0 Time building additional restraints: 19.56 Conformation dependent library (CDL) restraints added in 8.3 seconds 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14652 Finding SS restraints... Secondary structure from input PDB file: 286 helices and 73 sheets defined 47.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'f' and resid 8 through 24 Processing helix chain 'f' and resid 68 through 73 Processing helix chain 'W' and resid 3 through 19 Processing helix chain 'W' and resid 40 through 54 removed outlier: 3.515A pdb=" N THR W 54 " --> pdb=" O LEU W 50 " (cutoff:3.500A) Processing helix chain 'w' and resid 3 through 19 Processing helix chain 'w' and resid 39 through 54 removed outlier: 3.920A pdb=" N LEU w 43 " --> pdb=" O SER w 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 20 removed outlier: 3.677A pdb=" N HIS U 20 " --> pdb=" O ALA U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 87 removed outlier: 4.090A pdb=" N LEU U 80 " --> pdb=" O PRO U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 94 removed outlier: 4.392A pdb=" N ASP U 94 " --> pdb=" O VAL U 91 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 102 Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 52 through 66 Processing helix chain 'B' and resid 67 through 82 removed outlier: 3.681A pdb=" N VAL B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 100 through 120 Processing helix chain 'B' and resid 133 through 149 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.692A pdb=" N SER B 253 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 278 removed outlier: 3.858A pdb=" N TYR B 278 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 351 through 367 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 381 through 403 Processing helix chain 'B' and resid 403 through 422 removed outlier: 3.719A pdb=" N GLU B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 485 through 504 Processing helix chain 'b' and resid 44 through 50 Processing helix chain 'b' and resid 52 through 66 Processing helix chain 'b' and resid 67 through 82 Processing helix chain 'b' and resid 93 through 98 removed outlier: 3.806A pdb=" N LEU b 97 " --> pdb=" O SER b 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 120 removed outlier: 3.536A pdb=" N GLU b 120 " --> pdb=" O LYS b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 149 Processing helix chain 'b' and resid 173 through 177 Processing helix chain 'b' and resid 179 through 183 Processing helix chain 'b' and resid 249 through 253 removed outlier: 3.885A pdb=" N SER b 253 " --> pdb=" O VAL b 250 " (cutoff:3.500A) Processing helix chain 'b' and resid 254 through 278 removed outlier: 3.806A pdb=" N TYR b 278 " --> pdb=" O VAL b 274 " (cutoff:3.500A) Processing helix chain 'b' and resid 287 through 295 Processing helix chain 'b' and resid 350 through 367 Processing helix chain 'b' and resid 369 through 375 Processing helix chain 'b' and resid 381 through 403 Processing helix chain 'b' and resid 403 through 422 removed outlier: 3.612A pdb=" N GLU b 418 " --> pdb=" O CYS b 414 " (cutoff:3.500A) Processing helix chain 'b' and resid 438 through 443 Processing helix chain 'b' and resid 457 through 471 Processing helix chain 'b' and resid 474 through 482 Processing helix chain 'b' and resid 485 through 504 Processing helix chain 'f1' and resid 8 through 23 Processing helix chain 'f1' and resid 69 through 73 removed outlier: 3.880A pdb=" N ARGf1 73 " --> pdb=" O ASPf1 70 " (cutoff:3.500A) Processing helix chain 'W1' and resid 3 through 19 Processing helix chain 'W1' and resid 39 through 54 Processing helix chain 'w1' and resid 3 through 19 Processing helix chain 'w1' and resid 40 through 54 Processing helix chain 'U1' and resid 5 through 19 Processing helix chain 'U1' and resid 76 through 85 removed outlier: 3.617A pdb=" N LEUU1 80 " --> pdb=" O PROU1 76 " (cutoff:3.500A) Processing helix chain 'U1' and resid 90 through 94 removed outlier: 4.382A pdb=" N ASPU1 94 " --> pdb=" O VALU1 91 " (cutoff:3.500A) Processing helix chain 'U1' and resid 95 through 102 Processing helix chain 'B1' and resid 44 through 50 Processing helix chain 'B1' and resid 52 through 66 Processing helix chain 'B1' and resid 67 through 82 removed outlier: 3.600A pdb=" N VALB1 82 " --> pdb=" O GLNB1 78 " (cutoff:3.500A) Processing helix chain 'B1' and resid 93 through 98 Processing helix chain 'B1' and resid 100 through 120 removed outlier: 3.888A pdb=" N GLUB1 120 " --> pdb=" O LYSB1 116 " (cutoff:3.500A) Processing helix chain 'B1' and resid 133 through 149 Processing helix chain 'B1' and resid 173 through 177 Processing helix chain 'B1' and resid 179 through 183 Processing helix chain 'B1' and resid 249 through 253 removed outlier: 3.637A pdb=" N SERB1 253 " --> pdb=" O VALB1 250 " (cutoff:3.500A) Processing helix chain 'B1' and resid 254 through 276 removed outlier: 4.056A pdb=" N LEUB1 261 " --> pdb=" O GLNB1 257 " (cutoff:3.500A) Processing helix chain 'B1' and resid 287 through 296 Processing helix chain 'B1' and resid 350 through 367 Processing helix chain 'B1' and resid 369 through 375 Processing helix chain 'B1' and resid 381 through 403 Processing helix chain 'B1' and resid 403 through 422 removed outlier: 3.562A pdb=" N GLUB1 418 " --> pdb=" O CYSB1 414 " (cutoff:3.500A) Processing helix chain 'B1' and resid 438 through 443 Processing helix chain 'B1' and resid 457 through 470 Processing helix chain 'B1' and resid 474 through 482 Processing helix chain 'B1' and resid 485 through 504 removed outlier: 3.529A pdb=" N ILEB1 489 " --> pdb=" O ASPB1 485 " (cutoff:3.500A) Processing helix chain 'b1' and resid 44 through 50 Processing helix chain 'b1' and resid 52 through 67 Processing helix chain 'b1' and resid 67 through 82 removed outlier: 3.515A pdb=" N VALb1 82 " --> pdb=" O GLNb1 78 " (cutoff:3.500A) Processing helix chain 'b1' and resid 93 through 98 Processing helix chain 'b1' and resid 100 through 120 removed outlier: 3.570A pdb=" N GLUb1 120 " --> pdb=" O LYSb1 116 " (cutoff:3.500A) Processing helix chain 'b1' and resid 133 through 149 Processing helix chain 'b1' and resid 173 through 177 Processing helix chain 'b1' and resid 179 through 183 Processing helix chain 'b1' and resid 249 through 253 removed outlier: 3.893A pdb=" N SERb1 253 " --> pdb=" O VALb1 250 " (cutoff:3.500A) Processing helix chain 'b1' and resid 254 through 278 Processing helix chain 'b1' and resid 287 through 295 Processing helix chain 'b1' and resid 350 through 367 Processing helix chain 'b1' and resid 369 through 375 Processing helix chain 'b1' and resid 381 through 403 Processing helix chain 'b1' and resid 403 through 422 removed outlier: 3.780A pdb=" N GLUb1 418 " --> pdb=" O CYSb1 414 " (cutoff:3.500A) Processing helix chain 'b1' and resid 438 through 443 Processing helix chain 'b1' and resid 457 through 470 Processing helix chain 'b1' and resid 474 through 483 Processing helix chain 'b1' and resid 485 through 504 Processing helix chain 'f2' and resid 8 through 23 Processing helix chain 'W2' and resid 3 through 19 Processing helix chain 'W2' and resid 40 through 54 Processing helix chain 'w2' and resid 3 through 19 Processing helix chain 'w2' and resid 39 through 54 removed outlier: 3.531A pdb=" N LEUw2 43 " --> pdb=" O SERw2 39 " (cutoff:3.500A) Processing helix chain 'U2' and resid 5 through 20 removed outlier: 3.694A pdb=" N HISU2 20 " --> pdb=" O ALAU2 16 " (cutoff:3.500A) Processing helix chain 'U2' and resid 76 through 85 removed outlier: 4.129A pdb=" N LEUU2 80 " --> pdb=" O PROU2 76 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLUU2 85 " --> pdb=" O ASPU2 81 " (cutoff:3.500A) Processing helix chain 'U2' and resid 90 through 94 removed outlier: 3.779A pdb=" N ASPU2 94 " --> pdb=" O VALU2 91 " (cutoff:3.500A) Processing helix chain 'U2' and resid 95 through 102 Processing helix chain 'B2' and resid 44 through 50 Processing helix chain 'B2' and resid 52 through 66 Processing helix chain 'B2' and resid 67 through 82 removed outlier: 3.627A pdb=" N VALB2 82 " --> pdb=" O GLNB2 78 " (cutoff:3.500A) Processing helix chain 'B2' and resid 93 through 98 Processing helix chain 'B2' and resid 100 through 120 removed outlier: 3.541A pdb=" N GLUB2 120 " --> pdb=" O LYSB2 116 " (cutoff:3.500A) Processing helix chain 'B2' and resid 133 through 148 Processing helix chain 'B2' and resid 173 through 177 Processing helix chain 'B2' and resid 179 through 183 Processing helix chain 'B2' and resid 249 through 253 removed outlier: 3.707A pdb=" N SERB2 253 " --> pdb=" O VALB2 250 " (cutoff:3.500A) Processing helix chain 'B2' and resid 254 through 278 removed outlier: 3.638A pdb=" N TYRB2 278 " --> pdb=" O VALB2 274 " (cutoff:3.500A) Processing helix chain 'B2' and resid 287 through 296 Processing helix chain 'B2' and resid 350 through 367 Processing helix chain 'B2' and resid 369 through 375 Processing helix chain 'B2' and resid 381 through 403 Processing helix chain 'B2' and resid 403 through 422 removed outlier: 3.532A pdb=" N GLUB2 418 " --> pdb=" O CYSB2 414 " (cutoff:3.500A) Processing helix chain 'B2' and resid 438 through 443 Processing helix chain 'B2' and resid 457 through 471 removed outlier: 3.701A pdb=" N VALB2 461 " --> pdb=" O GLYB2 457 " (cutoff:3.500A) Processing helix chain 'B2' and resid 474 through 482 Processing helix chain 'B2' and resid 485 through 504 removed outlier: 3.742A pdb=" N ILEB2 489 " --> pdb=" O ASPB2 485 " (cutoff:3.500A) Processing helix chain 'b2' and resid 44 through 50 Processing helix chain 'b2' and resid 52 through 67 Processing helix chain 'b2' and resid 67 through 82 Processing helix chain 'b2' and resid 93 through 98 removed outlier: 3.598A pdb=" N LEUb2 97 " --> pdb=" O SERb2 93 " (cutoff:3.500A) Processing helix chain 'b2' and resid 100 through 120 removed outlier: 3.542A pdb=" N GLUb2 120 " --> pdb=" O LYSb2 116 " (cutoff:3.500A) Processing helix chain 'b2' and resid 133 through 149 Processing helix chain 'b2' and resid 173 through 177 Processing helix chain 'b2' and resid 179 through 183 Processing helix chain 'b2' and resid 249 through 253 removed outlier: 3.735A pdb=" N SERb2 253 " --> pdb=" O VALb2 250 " (cutoff:3.500A) Processing helix chain 'b2' and resid 254 through 277 Processing helix chain 'b2' and resid 287 through 295 Processing helix chain 'b2' and resid 350 through 367 Processing helix chain 'b2' and resid 369 through 375 Processing helix chain 'b2' and resid 381 through 403 Processing helix chain 'b2' and resid 403 through 422 removed outlier: 3.650A pdb=" N GLUb2 418 " --> pdb=" O CYSb2 414 " (cutoff:3.500A) Processing helix chain 'b2' and resid 438 through 443 Processing helix chain 'b2' and resid 457 through 471 Processing helix chain 'b2' and resid 474 through 483 Processing helix chain 'b2' and resid 485 through 504 Processing helix chain 'f3' and resid 8 through 23 Processing helix chain 'f3' and resid 70 through 73 removed outlier: 3.516A pdb=" N ARGf3 73 " --> pdb=" O ASPf3 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'f3' and resid 70 through 73' Processing helix chain 'W3' and resid 3 through 19 Processing helix chain 'W3' and resid 39 through 54 Processing helix chain 'w3' and resid 3 through 19 Processing helix chain 'w3' and resid 39 through 54 Processing helix chain 'U3' and resid 5 through 20 removed outlier: 4.008A pdb=" N HISU3 20 " --> pdb=" O ALAU3 16 " (cutoff:3.500A) Processing helix chain 'U3' and resid 76 through 87 removed outlier: 4.184A pdb=" N LEUU3 80 " --> pdb=" O PROU3 76 " (cutoff:3.500A) Processing helix chain 'U3' and resid 88 through 93 Processing helix chain 'U3' and resid 95 through 102 Processing helix chain 'B3' and resid 44 through 50 Processing helix chain 'B3' and resid 52 through 67 Processing helix chain 'B3' and resid 67 through 82 removed outlier: 3.613A pdb=" N VALB3 82 " --> pdb=" O GLNB3 78 " (cutoff:3.500A) Processing helix chain 'B3' and resid 93 through 98 Processing helix chain 'B3' and resid 100 through 120 removed outlier: 3.749A pdb=" N GLUB3 120 " --> pdb=" O LYSB3 116 " (cutoff:3.500A) Processing helix chain 'B3' and resid 133 through 149 Processing helix chain 'B3' and resid 173 through 177 Processing helix chain 'B3' and resid 179 through 183 Processing helix chain 'B3' and resid 249 through 253 removed outlier: 3.694A pdb=" N SERB3 253 " --> pdb=" O VALB3 250 " (cutoff:3.500A) Processing helix chain 'B3' and resid 254 through 278 removed outlier: 3.995A pdb=" N TYRB3 278 " --> pdb=" O VALB3 274 " (cutoff:3.500A) Processing helix chain 'B3' and resid 287 through 296 Processing helix chain 'B3' and resid 350 through 367 Processing helix chain 'B3' and resid 369 through 375 Processing helix chain 'B3' and resid 381 through 403 Processing helix chain 'B3' and resid 403 through 422 removed outlier: 3.622A pdb=" N GLUB3 418 " --> pdb=" O CYSB3 414 " (cutoff:3.500A) Processing helix chain 'B3' and resid 438 through 443 Processing helix chain 'B3' and resid 457 through 471 Processing helix chain 'B3' and resid 474 through 482 Processing helix chain 'B3' and resid 485 through 504 Processing helix chain 'b3' and resid 44 through 50 Processing helix chain 'b3' and resid 52 through 67 Processing helix chain 'b3' and resid 67 through 82 removed outlier: 3.595A pdb=" N VALb3 82 " --> pdb=" O GLNb3 78 " (cutoff:3.500A) Processing helix chain 'b3' and resid 93 through 98 Processing helix chain 'b3' and resid 100 through 120 removed outlier: 3.580A pdb=" N GLUb3 120 " --> pdb=" O LYSb3 116 " (cutoff:3.500A) Processing helix chain 'b3' and resid 133 through 149 Processing helix chain 'b3' and resid 173 through 177 Processing helix chain 'b3' and resid 179 through 183 Processing helix chain 'b3' and resid 249 through 253 removed outlier: 3.895A pdb=" N SERb3 253 " --> pdb=" O VALb3 250 " (cutoff:3.500A) Processing helix chain 'b3' and resid 254 through 277 Processing helix chain 'b3' and resid 287 through 295 Processing helix chain 'b3' and resid 350 through 367 Processing helix chain 'b3' and resid 369 through 375 Processing helix chain 'b3' and resid 381 through 403 Processing helix chain 'b3' and resid 403 through 422 removed outlier: 3.666A pdb=" N GLUb3 418 " --> pdb=" O CYSb3 414 " (cutoff:3.500A) Processing helix chain 'b3' and resid 438 through 443 Processing helix chain 'b3' and resid 457 through 470 Processing helix chain 'b3' and resid 474 through 483 Processing helix chain 'b3' and resid 485 through 504 Processing helix chain 'f4' and resid 8 through 23 Processing helix chain 'f4' and resid 69 through 73 removed outlier: 3.543A pdb=" N ARGf4 73 " --> pdb=" O THRf4 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'f4' and resid 69 through 73' Processing helix chain 'W4' and resid 3 through 20 Processing helix chain 'W4' and resid 40 through 53 Processing helix chain 'w4' and resid 3 through 20 removed outlier: 3.659A pdb=" N GLYw4 20 " --> pdb=" O ASPw4 16 " (cutoff:3.500A) Processing helix chain 'w4' and resid 40 through 54 Processing helix chain 'U4' and resid 5 through 20 removed outlier: 3.845A pdb=" N HISU4 20 " --> pdb=" O ALAU4 16 " (cutoff:3.500A) Processing helix chain 'U4' and resid 76 through 88 Processing helix chain 'U4' and resid 89 through 94 removed outlier: 3.705A pdb=" N METU4 92 " --> pdb=" O TYRU4 89 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASPU4 94 " --> pdb=" O VALU4 91 " (cutoff:3.500A) Processing helix chain 'U4' and resid 95 through 102 Processing helix chain 'B4' and resid 44 through 50 Processing helix chain 'B4' and resid 52 through 66 Processing helix chain 'B4' and resid 67 through 82 removed outlier: 3.651A pdb=" N VALB4 82 " --> pdb=" O GLNB4 78 " (cutoff:3.500A) Processing helix chain 'B4' and resid 93 through 98 Processing helix chain 'B4' and resid 100 through 120 removed outlier: 3.858A pdb=" N GLUB4 120 " --> pdb=" O LYSB4 116 " (cutoff:3.500A) Processing helix chain 'B4' and resid 133 through 148 Processing helix chain 'B4' and resid 173 through 177 Processing helix chain 'B4' and resid 179 through 183 removed outlier: 3.557A pdb=" N THRB4 183 " --> pdb=" O PROB4 180 " (cutoff:3.500A) Processing helix chain 'B4' and resid 249 through 253 removed outlier: 3.572A pdb=" N SERB4 253 " --> pdb=" O VALB4 250 " (cutoff:3.500A) Processing helix chain 'B4' and resid 254 through 276 Processing helix chain 'B4' and resid 287 through 296 Processing helix chain 'B4' and resid 350 through 367 Processing helix chain 'B4' and resid 369 through 375 Processing helix chain 'B4' and resid 381 through 403 Processing helix chain 'B4' and resid 403 through 422 removed outlier: 3.665A pdb=" N GLUB4 418 " --> pdb=" O CYSB4 414 " (cutoff:3.500A) Processing helix chain 'B4' and resid 438 through 443 Processing helix chain 'B4' and resid 457 through 471 Processing helix chain 'B4' and resid 474 through 482 Processing helix chain 'B4' and resid 485 through 504 Processing helix chain 'b4' and resid 44 through 50 Processing helix chain 'b4' and resid 52 through 67 Processing helix chain 'b4' and resid 67 through 82 Processing helix chain 'b4' and resid 93 through 98 Processing helix chain 'b4' and resid 100 through 120 removed outlier: 3.593A pdb=" N GLUb4 120 " --> pdb=" O LYSb4 116 " (cutoff:3.500A) Processing helix chain 'b4' and resid 133 through 149 Processing helix chain 'b4' and resid 173 through 177 Processing helix chain 'b4' and resid 179 through 183 Processing helix chain 'b4' and resid 249 through 253 removed outlier: 3.850A pdb=" N SERb4 253 " --> pdb=" O VALb4 250 " (cutoff:3.500A) Processing helix chain 'b4' and resid 254 through 277 Processing helix chain 'b4' and resid 287 through 295 Processing helix chain 'b4' and resid 350 through 367 Processing helix chain 'b4' and resid 369 through 375 Processing helix chain 'b4' and resid 381 through 403 Processing helix chain 'b4' and resid 403 through 422 removed outlier: 3.667A pdb=" N GLUb4 418 " --> pdb=" O CYSb4 414 " (cutoff:3.500A) Processing helix chain 'b4' and resid 438 through 443 Processing helix chain 'b4' and resid 457 through 470 Processing helix chain 'b4' and resid 474 through 482 Processing helix chain 'b4' and resid 485 through 504 Processing helix chain 'f5' and resid 8 through 23 Processing helix chain 'f5' and resid 69 through 73 removed outlier: 3.937A pdb=" N ARGf5 73 " --> pdb=" O ASPf5 70 " (cutoff:3.500A) Processing helix chain 'W5' and resid 3 through 19 Processing helix chain 'W5' and resid 39 through 54 removed outlier: 3.533A pdb=" N THRW5 54 " --> pdb=" O LEUW5 50 " (cutoff:3.500A) Processing helix chain 'w5' and resid 3 through 20 removed outlier: 3.607A pdb=" N GLYw5 20 " --> pdb=" O ASPw5 16 " (cutoff:3.500A) Processing helix chain 'w5' and resid 39 through 54 Processing helix chain 'U5' and resid 5 through 19 Processing helix chain 'U5' and resid 76 through 87 removed outlier: 3.959A pdb=" N LEUU5 80 " --> pdb=" O PROU5 76 " (cutoff:3.500A) Processing helix chain 'U5' and resid 95 through 102 Processing helix chain 'B5' and resid 44 through 50 Processing helix chain 'B5' and resid 52 through 67 Processing helix chain 'B5' and resid 67 through 82 removed outlier: 3.730A pdb=" N VALB5 82 " --> pdb=" O GLNB5 78 " (cutoff:3.500A) Processing helix chain 'B5' and resid 93 through 98 Processing helix chain 'B5' and resid 100 through 120 removed outlier: 3.642A pdb=" N GLUB5 120 " --> pdb=" O LYSB5 116 " (cutoff:3.500A) Processing helix chain 'B5' and resid 133 through 149 Processing helix chain 'B5' and resid 173 through 177 Processing helix chain 'B5' and resid 179 through 183 Processing helix chain 'B5' and resid 249 through 253 removed outlier: 3.625A pdb=" N SERB5 253 " --> pdb=" O VALB5 250 " (cutoff:3.500A) Processing helix chain 'B5' and resid 254 through 278 removed outlier: 3.888A pdb=" N TYRB5 278 " --> pdb=" O VALB5 274 " (cutoff:3.500A) Processing helix chain 'B5' and resid 287 through 296 Processing helix chain 'B5' and resid 350 through 367 Processing helix chain 'B5' and resid 369 through 375 Processing helix chain 'B5' and resid 381 through 403 Processing helix chain 'B5' and resid 403 through 422 removed outlier: 3.645A pdb=" N GLUB5 418 " --> pdb=" O CYSB5 414 " (cutoff:3.500A) Processing helix chain 'B5' and resid 438 through 443 Processing helix chain 'B5' and resid 457 through 471 Processing helix chain 'B5' and resid 474 through 482 Processing helix chain 'B5' and resid 486 through 504 Processing helix chain 'b5' and resid 44 through 50 Processing helix chain 'b5' and resid 52 through 67 Processing helix chain 'b5' and resid 67 through 82 Processing helix chain 'b5' and resid 93 through 98 Processing helix chain 'b5' and resid 100 through 120 removed outlier: 3.543A pdb=" N GLUb5 120 " --> pdb=" O LYSb5 116 " (cutoff:3.500A) Processing helix chain 'b5' and resid 133 through 149 Processing helix chain 'b5' and resid 173 through 177 Processing helix chain 'b5' and resid 179 through 183 Processing helix chain 'b5' and resid 249 through 253 removed outlier: 3.811A pdb=" N SERb5 253 " --> pdb=" O VALb5 250 " (cutoff:3.500A) Processing helix chain 'b5' and resid 254 through 277 Processing helix chain 'b5' and resid 287 through 295 Processing helix chain 'b5' and resid 350 through 367 Processing helix chain 'b5' and resid 369 through 375 Processing helix chain 'b5' and resid 381 through 403 Processing helix chain 'b5' and resid 403 through 422 removed outlier: 3.755A pdb=" N GLUb5 418 " --> pdb=" O CYSb5 414 " (cutoff:3.500A) Processing helix chain 'b5' and resid 438 through 443 Processing helix chain 'b5' and resid 457 through 469 Processing helix chain 'b5' and resid 474 through 483 Processing helix chain 'b5' and resid 485 through 504 Processing sheet with id=AA1, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.640A pdb=" N ALA f 37 " --> pdb=" O ILE f 29 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TRP f 104 " --> pdb=" O ASP f 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'f' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'W' and resid 23 through 28 removed outlier: 5.798A pdb=" N ALA W 24 " --> pdb=" O PHE W 35 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG W 32 " --> pdb=" O VALw5 26 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VALw5 26 " --> pdb=" O ARG W 32 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU W 34 " --> pdb=" O ALAw5 24 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALAw5 24 " --> pdb=" O PHEw5 35 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARGw5 32 " --> pdb=" O VALW5 26 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VALW5 26 " --> pdb=" O ARGw5 32 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLUw5 34 " --> pdb=" O ALAW5 24 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALAW5 24 " --> pdb=" O PHEW5 35 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ARGW5 32 " --> pdb=" O VALw4 26 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VALw4 26 " --> pdb=" O ARGW5 32 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLUW5 34 " --> pdb=" O ALAw4 24 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALAw4 24 " --> pdb=" O PHEw4 35 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALAW4 24 " --> pdb=" O PHEW4 35 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARGW4 32 " --> pdb=" O VALw3 26 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VALw3 26 " --> pdb=" O ARGW4 32 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLUW4 34 " --> pdb=" O ALAw3 24 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ALAw3 24 " --> pdb=" O PHEw3 35 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARGw3 32 " --> pdb=" O VALW3 26 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VALW3 26 " --> pdb=" O ARGw3 32 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLUw3 34 " --> pdb=" O ALAW3 24 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALAW3 24 " --> pdb=" O PHEW3 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THRw2 25 " --> pdb=" O GLUW3 34 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ALAw2 24 " --> pdb=" O PHEw2 35 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ALAW2 24 " --> pdb=" O PHEW2 35 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARGW2 32 " --> pdb=" O VALw1 26 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VALw1 26 " --> pdb=" O ARGW2 32 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLUW2 34 " --> pdb=" O ALAw1 24 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALAw1 24 " --> pdb=" O PHEw1 35 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARGw1 32 " --> pdb=" O VALW1 26 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VALW1 26 " --> pdb=" O ARGw1 32 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLUw1 34 " --> pdb=" O ALAW1 24 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALAW1 24 " --> pdb=" O PHEW1 35 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARGW1 32 " --> pdb=" O VAL w 26 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL w 26 " --> pdb=" O ARGW1 32 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLUW1 34 " --> pdb=" O ALA w 24 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA w 24 " --> pdb=" O PHE w 35 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG w 32 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL W 26 " --> pdb=" O ARG w 32 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU w 34 " --> pdb=" O ALA W 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 26 through 28 removed outlier: 7.127A pdb=" N PHE U 27 " --> pdb=" O VAL U 44 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LEU U 46 " --> pdb=" O PHE U 27 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN U 62 " --> pdb=" O ALA U 49 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TRP U 121 " --> pdb=" O ARG U 114 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG U 114 " --> pdb=" O TRP U 121 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N SER U 123 " --> pdb=" O TYR U 112 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR U 112 " --> pdb=" O SER U 123 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP U 125 " --> pdb=" O TYR U 110 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR U 110 " --> pdb=" O ASP U 125 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR U 127 " --> pdb=" O SER U 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER U 104 " --> pdb=" O THR U 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AA6, first strand: chain 'B' and resid 167 through 172 removed outlier: 3.922A pdb=" N PHE B 152 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 190 removed outlier: 6.844A pdb=" N GLN B 194 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 338 through 341 removed outlier: 8.370A pdb=" N LEUb5 333 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE B 282 " --> pdb=" O LEUb5 333 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 332 through 333 Processing sheet with id=AB1, first strand: chain 'b' and resid 87 through 90 Processing sheet with id=AB2, first strand: chain 'b' and resid 167 through 172 removed outlier: 4.105A pdb=" N PHE b 152 " --> pdb=" O VAL b 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 189 through 190 removed outlier: 3.526A pdb=" N ARG b 190 " --> pdb=" O VAL b 193 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLN b 194 " --> pdb=" O LEU b 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f1' and resid 37 through 41 removed outlier: 3.611A pdb=" N ALAf1 37 " --> pdb=" O ILEf1 29 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TRPf1 104 " --> pdb=" O ASPf1 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f1' and resid 47 through 48 Processing sheet with id=AB6, first strand: chain 'U1' and resid 41 through 50 removed outlier: 6.203A pdb=" N GLNU1 62 " --> pdb=" O ALAU1 49 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TRPU1 121 " --> pdb=" O ARGU1 114 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARGU1 114 " --> pdb=" O TRPU1 121 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N SERU1 123 " --> pdb=" O TYRU1 112 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYRU1 112 " --> pdb=" O SERU1 123 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASPU1 125 " --> pdb=" O TYRU1 110 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYRU1 110 " --> pdb=" O ASPU1 125 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THRU1 127 " --> pdb=" O SERU1 108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B1' and resid 87 through 90 Processing sheet with id=AB8, first strand: chain 'B1' and resid 167 through 172 removed outlier: 4.012A pdb=" N PHEB1 152 " --> pdb=" O VALB1 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B1' and resid 189 through 190 removed outlier: 3.534A pdb=" N GLYB1 203 " --> pdb=" O GLNB1 194 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B1' and resid 280 through 282 Processing sheet with id=AC2, first strand: chain 'B1' and resid 332 through 333 Processing sheet with id=AC3, first strand: chain 'b1' and resid 87 through 90 Processing sheet with id=AC4, first strand: chain 'b1' and resid 167 through 172 removed outlier: 3.772A pdb=" N PHEb1 152 " --> pdb=" O VALb1 172 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b1' and resid 189 through 190 removed outlier: 3.768A pdb=" N GLYb1 203 " --> pdb=" O GLNb1 194 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f2' and resid 37 through 40 removed outlier: 3.997A pdb=" N ALAf2 37 " --> pdb=" O ILEf2 29 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THRf2 30 " --> pdb=" O THRf2 80 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TRPf2 104 " --> pdb=" O ASPf2 91 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'w2' and resid 66 through 67 Processing sheet with id=AC8, first strand: chain 'U2' and resid 41 through 50 removed outlier: 6.300A pdb=" N GLNU2 62 " --> pdb=" O ALAU2 49 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TRPU2 121 " --> pdb=" O ARGU2 114 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARGU2 114 " --> pdb=" O TRPU2 121 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SERU2 123 " --> pdb=" O TYRU2 112 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYRU2 112 " --> pdb=" O SERU2 123 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASPU2 125 " --> pdb=" O TYRU2 110 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYRU2 110 " --> pdb=" O ASPU2 125 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THRU2 127 " --> pdb=" O SERU2 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B2' and resid 87 through 90 Processing sheet with id=AD1, first strand: chain 'B2' and resid 167 through 172 removed outlier: 4.004A pdb=" N PHEB2 152 " --> pdb=" O VALB2 172 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B2' and resid 189 through 190 removed outlier: 6.862A pdb=" N GLNB2 194 " --> pdb=" O LEUB2 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B2' and resid 281 through 282 Processing sheet with id=AD4, first strand: chain 'B2' and resid 332 through 333 Processing sheet with id=AD5, first strand: chain 'b2' and resid 87 through 90 Processing sheet with id=AD6, first strand: chain 'b2' and resid 167 through 172 removed outlier: 4.010A pdb=" N PHEb2 152 " --> pdb=" O VALb2 172 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b2' and resid 189 through 190 removed outlier: 3.778A pdb=" N GLYb2 203 " --> pdb=" O GLNb2 194 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'f3' and resid 37 through 40 removed outlier: 3.985A pdb=" N ALAf3 37 " --> pdb=" O ILEf3 29 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARGf3 92 " --> pdb=" O TRPf3 104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'f3' and resid 47 through 48 Processing sheet with id=AE1, first strand: chain 'f3' and resid 67 through 68 Processing sheet with id=AE2, first strand: chain 'W3' and resid 65 through 67 Processing sheet with id=AE3, first strand: chain 'w3' and resid 65 through 67 Processing sheet with id=AE4, first strand: chain 'U3' and resid 41 through 50 removed outlier: 6.185A pdb=" N GLNU3 62 " --> pdb=" O ALAU3 49 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TRPU3 121 " --> pdb=" O ARGU3 114 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARGU3 114 " --> pdb=" O TRPU3 121 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N SERU3 123 " --> pdb=" O TYRU3 112 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYRU3 112 " --> pdb=" O SERU3 123 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASPU3 125 " --> pdb=" O TYRU3 110 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYRU3 110 " --> pdb=" O ASPU3 125 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THRU3 127 " --> pdb=" O SERU3 108 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B3' and resid 87 through 90 Processing sheet with id=AE6, first strand: chain 'B3' and resid 167 through 172 removed outlier: 4.057A pdb=" N PHEB3 152 " --> pdb=" O VALB3 172 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B3' and resid 189 through 190 Processing sheet with id=AE8, first strand: chain 'B3' and resid 281 through 282 Processing sheet with id=AE9, first strand: chain 'B3' and resid 332 through 333 Processing sheet with id=AF1, first strand: chain 'b3' and resid 87 through 90 Processing sheet with id=AF2, first strand: chain 'b3' and resid 167 through 172 removed outlier: 3.892A pdb=" N PHEb3 152 " --> pdb=" O VALb3 172 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b3' and resid 189 through 190 removed outlier: 6.753A pdb=" N GLNb3 194 " --> pdb=" O LEUb3 202 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'f4' and resid 37 through 40 removed outlier: 4.053A pdb=" N ALAf4 37 " --> pdb=" O ILEf4 29 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TRPf4 104 " --> pdb=" O ASPf4 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'f4' and resid 67 through 68 Processing sheet with id=AF6, first strand: chain 'w4' and resid 66 through 67 Processing sheet with id=AF7, first strand: chain 'U4' and resid 41 through 50 removed outlier: 6.019A pdb=" N GLNU4 62 " --> pdb=" O ALAU4 49 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N TRPU4 121 " --> pdb=" O ARGU4 114 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARGU4 114 " --> pdb=" O TRPU4 121 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SERU4 123 " --> pdb=" O TYRU4 112 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYRU4 112 " --> pdb=" O SERU4 123 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASPU4 125 " --> pdb=" O TYRU4 110 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYRU4 110 " --> pdb=" O ASPU4 125 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THRU4 127 " --> pdb=" O SERU4 108 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B4' and resid 87 through 90 Processing sheet with id=AF9, first strand: chain 'B4' and resid 167 through 172 removed outlier: 3.960A pdb=" N PHEB4 152 " --> pdb=" O VALB4 172 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B4' and resid 189 through 190 removed outlier: 6.884A pdb=" N GLNB4 194 " --> pdb=" O LEUB4 202 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B4' and resid 280 through 282 Processing sheet with id=AG3, first strand: chain 'B4' and resid 332 through 333 Processing sheet with id=AG4, first strand: chain 'b4' and resid 87 through 90 Processing sheet with id=AG5, first strand: chain 'b4' and resid 167 through 172 removed outlier: 3.973A pdb=" N PHEb4 152 " --> pdb=" O VALb4 172 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b4' and resid 189 through 190 Processing sheet with id=AG7, first strand: chain 'f5' and resid 25 through 29 Processing sheet with id=AG8, first strand: chain 'f5' and resid 47 through 48 Processing sheet with id=AG9, first strand: chain 'f5' and resid 80 through 83 removed outlier: 7.193A pdb=" N TRPf5 104 " --> pdb=" O ASPf5 91 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W5' and resid 65 through 67 Processing sheet with id=AH2, first strand: chain 'U5' and resid 41 through 50 removed outlier: 6.061A pdb=" N GLNU5 62 " --> pdb=" O ALAU5 49 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VALU5 129 " --> pdb=" O ALAU5 107 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ALAU5 107 " --> pdb=" O VALU5 129 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THRU5 131 " --> pdb=" O METU5 105 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N METU5 105 " --> pdb=" O THRU5 131 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B5' and resid 87 through 90 Processing sheet with id=AH4, first strand: chain 'B5' and resid 167 through 172 removed outlier: 3.951A pdb=" N PHEB5 152 " --> pdb=" O VALB5 172 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B5' and resid 189 through 190 removed outlier: 6.929A pdb=" N GLNB5 194 " --> pdb=" O LEUB5 202 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B5' and resid 281 through 282 Processing sheet with id=AH7, first strand: chain 'B5' and resid 332 through 333 Processing sheet with id=AH8, first strand: chain 'b5' and resid 87 through 90 Processing sheet with id=AH9, first strand: chain 'b5' and resid 167 through 172 removed outlier: 3.959A pdb=" N PHEb5 152 " --> pdb=" O VALb5 172 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b5' and resid 189 through 190 removed outlier: 3.789A pdb=" N GLYb5 203 " --> pdb=" O GLNb5 194 " (cutoff:3.500A) 3156 hydrogen bonds defined for protein. 9015 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: 21.47 Time building geometry restraints manager: 21.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 21365 1.34 - 1.46: 14798 1.46 - 1.58: 26864 1.58 - 1.70: 3 1.70 - 1.82: 618 Bond restraints: 63648 Sorted by residual: bond pdb=" CB PROU2 72 " pdb=" CG PROU2 72 " ideal model delta sigma weight residual 1.492 1.609 -0.117 5.00e-02 4.00e+02 5.51e+00 bond pdb=" CB PROU3 72 " pdb=" CG PROU3 72 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.51e+00 bond pdb=" CB PRO U 72 " pdb=" CG PRO U 72 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.44e+00 bond pdb=" CB METB4 397 " pdb=" CG METB4 397 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.78e+00 bond pdb=" CA GLYU1 48 " pdb=" C GLYU1 48 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.40e+00 ... (remaining 63643 not shown) Histogram of bond angle deviations from ideal: 96.78 - 104.22: 911 104.22 - 111.67: 27707 111.67 - 119.12: 22285 119.12 - 126.57: 34081 126.57 - 134.01: 1086 Bond angle restraints: 86070 Sorted by residual: angle pdb=" CA PROU2 72 " pdb=" N PROU2 72 " pdb=" CD PROU2 72 " ideal model delta sigma weight residual 112.00 100.67 11.33 1.40e+00 5.10e-01 6.55e+01 angle pdb=" CA PROU3 72 " pdb=" N PROU3 72 " pdb=" CD PROU3 72 " ideal model delta sigma weight residual 112.00 102.99 9.01 1.40e+00 5.10e-01 4.14e+01 angle pdb=" CA PRO U 72 " pdb=" N PRO U 72 " pdb=" CD PRO U 72 " ideal model delta sigma weight residual 112.00 103.51 8.49 1.40e+00 5.10e-01 3.68e+01 angle pdb=" C THRB5 497 " pdb=" N METB5 498 " pdb=" CA METB5 498 " ideal model delta sigma weight residual 121.58 111.28 10.30 1.95e+00 2.63e-01 2.79e+01 angle pdb=" C ALAB2 320 " pdb=" CA ALAB2 320 " pdb=" CB ALAB2 320 " ideal model delta sigma weight residual 117.23 110.30 6.93 1.36e+00 5.41e-01 2.60e+01 ... (remaining 86065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 31856 18.03 - 36.05: 4614 36.05 - 54.08: 1125 54.08 - 72.10: 227 72.10 - 90.13: 134 Dihedral angle restraints: 37956 sinusoidal: 15126 harmonic: 22830 Sorted by residual: dihedral pdb=" CA PHEU4 39 " pdb=" C PHEU4 39 " pdb=" N PROU4 40 " pdb=" CA PROU4 40 " ideal model delta harmonic sigma weight residual -180.00 -115.96 -64.04 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" CA PHEU3 39 " pdb=" C PHEU3 39 " pdb=" N PROU3 40 " pdb=" CA PROU3 40 " ideal model delta harmonic sigma weight residual -180.00 -116.37 -63.63 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CA PHEU1 39 " pdb=" C PHEU1 39 " pdb=" N PROU1 40 " pdb=" CA PROU1 40 " ideal model delta harmonic sigma weight residual -180.00 -117.22 -62.78 0 5.00e+00 4.00e-02 1.58e+02 ... (remaining 37953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 7848 0.062 - 0.125: 1121 0.125 - 0.187: 81 0.187 - 0.249: 15 0.249 - 0.312: 1 Chirality restraints: 9066 Sorted by residual: chirality pdb=" CG LEU B 413 " pdb=" CB LEU B 413 " pdb=" CD1 LEU B 413 " pdb=" CD2 LEU B 413 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA PROW3 63 " pdb=" N PROW3 63 " pdb=" C PROW3 63 " pdb=" CB PROW3 63 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PROW2 63 " pdb=" N PROW2 63 " pdb=" C PROW2 63 " pdb=" CB PROW2 63 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 9063 not shown) Planarity restraints: 11430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHEU2 39 " 0.108 5.00e-02 4.00e+02 1.66e-01 4.40e+01 pdb=" N PROU2 40 " -0.287 5.00e-02 4.00e+02 pdb=" CA PROU2 40 " 0.098 5.00e-02 4.00e+02 pdb=" CD PROU2 40 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEUU2 71 " -0.099 5.00e-02 4.00e+02 1.41e-01 3.18e+01 pdb=" N PROU2 72 " 0.244 5.00e-02 4.00e+02 pdb=" CA PROU2 72 " -0.073 5.00e-02 4.00e+02 pdb=" CD PROU2 72 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU U 71 " -0.095 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO U 72 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO U 72 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO U 72 " -0.070 5.00e-02 4.00e+02 ... (remaining 11427 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 1853 2.66 - 3.22: 64618 3.22 - 3.78: 107246 3.78 - 4.34: 134752 4.34 - 4.90: 220635 Nonbonded interactions: 529104 Sorted by model distance: nonbonded pdb=" OD1 ASPU1 81 " pdb=" OH TYRU1 112 " model vdw 2.094 2.440 nonbonded pdb=" OH TYRU1 110 " pdb=" OH TYRU1 112 " model vdw 2.117 2.440 nonbonded pdb=" O GLY B 350 " pdb=" OG1 THRb5 347 " model vdw 2.138 2.440 nonbonded pdb=" O VALU4 75 " pdb=" NH2 ARGU5 30 " model vdw 2.139 2.520 nonbonded pdb=" OE2 GLUB1 256 " pdb=" NE2 GLNB1 257 " model vdw 2.141 2.520 ... (remaining 529099 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 'B' and (resid 25 through 302 or resid 318 through 512)) selection = (chain 'B1' and (resid 25 through 302 or resid 318 through 512)) selection = (chain 'B2' and (resid 25 through 302 or resid 318 through 512)) selection = (chain 'B3' and (resid 25 through 302 or resid 318 through 512)) selection = (chain 'B4' and (resid 25 through 302 or resid 318 through 512)) selection = (chain 'B5' and (resid 25 through 302 or resid 318 through 512)) selection = chain 'b' selection = chain 'b1' selection = chain 'b2' selection = chain 'b3' selection = chain 'b4' selection = chain 'b5' } ncs_group { reference = chain 'U' selection = chain 'U1' selection = chain 'U2' selection = chain 'U3' selection = chain 'U4' selection = chain 'U5' } ncs_group { reference = chain 'W' selection = chain 'W1' selection = chain 'W2' selection = chain 'W3' selection = chain 'W4' selection = chain 'W5' selection = chain 'w' selection = chain 'w1' selection = chain 'w2' selection = chain 'w3' selection = chain 'w4' selection = chain 'w5' } ncs_group { reference = chain 'f' selection = chain 'f1' selection = chain 'f2' selection = chain 'f3' selection = chain 'f4' selection = chain 'f5' } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 7.950 Check model and map are aligned: 0.370 Set scattering table: 0.440 Process input model: 122.890 Find NCS groups from input model: 3.520 Set up NCS constraints: 0.430 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:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 63648 Z= 0.260 Angle : 0.780 16.945 86070 Z= 0.387 Chirality : 0.043 0.312 9066 Planarity : 0.006 0.166 11430 Dihedral : 18.344 90.130 23268 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.50 % Favored : 91.01 % Rotamer: Outliers : 0.98 % Allowed : 35.91 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.03 % 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: -0.27 (0.10), residues: 7866 helix: 1.14 (0.09), residues: 3318 sheet: -0.14 (0.16), residues: 1020 loop : -1.51 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRPB5 393 HIS 0.005 0.001 HISb2 332 PHE 0.028 0.001 PHEU5 39 TYR 0.027 0.002 TYRb4 395 ARG 0.018 0.000 ARGb2 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1340 time to evaluate : 5.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLN cc_start: 0.9237 (mm110) cc_final: 0.9018 (mm-40) REVERT: B1 194 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8376 (tp40) REVERT: B1 380 MET cc_start: 0.8602 (mmm) cc_final: 0.8111 (tpp) REVERT: U2 50 GLU cc_start: 0.8383 (pm20) cc_final: 0.7743 (pm20) REVERT: U2 62 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8535 (pp30) REVERT: B2 187 ARG cc_start: 0.9022 (ttm110) cc_final: 0.8719 (ttm110) REVERT: B3 499 GLU cc_start: 0.9355 (tt0) cc_final: 0.9145 (tm-30) REVERT: b3 340 ASN cc_start: 0.9382 (m-40) cc_final: 0.8750 (p0) REVERT: f5 116 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8396 (mpp80) REVERT: U5 134 MET cc_start: 0.8838 (ppp) cc_final: 0.8633 (ppp) REVERT: B5 292 MET cc_start: 0.9270 (mpp) cc_final: 0.8973 (mtm) REVERT: b5 52 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8256 (p0) outliers start: 63 outliers final: 36 residues processed: 1365 average time/residue: 0.5717 time to fit residues: 1315.4557 Evaluate side-chains 1323 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1284 time to evaluate : 5.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain U residue 30 ARG Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain f1 residue 25 THR Chi-restraints excluded: chain f1 residue 29 ILE Chi-restraints excluded: chain f1 residue 83 ILE Chi-restraints excluded: chain f1 residue 109 VAL Chi-restraints excluded: chain W1 residue 51 GLU Chi-restraints excluded: chain w1 residue 51 GLU Chi-restraints excluded: chain w1 residue 53 GLN Chi-restraints excluded: chain U1 residue 110 TYR Chi-restraints excluded: chain B1 residue 25 HIS Chi-restraints excluded: chain B1 residue 167 THR Chi-restraints excluded: chain B1 residue 194 GLN Chi-restraints excluded: chain b1 residue 31 PHE Chi-restraints excluded: chain b1 residue 273 ILE Chi-restraints excluded: chain f2 residue 109 VAL Chi-restraints excluded: chain W2 residue 23 VAL Chi-restraints excluded: chain W2 residue 50 LEU Chi-restraints excluded: chain W2 residue 56 MET Chi-restraints excluded: chain B2 residue 25 HIS Chi-restraints excluded: chain b2 residue 39 ASN Chi-restraints excluded: chain W3 residue 50 LEU Chi-restraints excluded: chain U3 residue 9 LEU Chi-restraints excluded: chain B3 residue 172 VAL Chi-restraints excluded: chain B3 residue 273 ILE Chi-restraints excluded: chain b3 residue 255 MET Chi-restraints excluded: chain f4 residue 82 THR Chi-restraints excluded: chain w4 residue 25 THR Chi-restraints excluded: chain U4 residue 52 THR Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 340 ASN Chi-restraints excluded: chain f5 residue 116 ARG Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 467 LEU Chi-restraints excluded: chain b5 residue 52 ASN Chi-restraints excluded: chain b5 residue 283 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 658 optimal weight: 10.0000 chunk 591 optimal weight: 10.0000 chunk 328 optimal weight: 9.9990 chunk 201 optimal weight: 0.9990 chunk 398 optimal weight: 6.9990 chunk 315 optimal weight: 4.9990 chunk 611 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 371 optimal weight: 20.0000 chunk 455 optimal weight: 4.9990 chunk 708 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS ** b 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 34 GLN ** b1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W2 4 GLN w2 4 GLN w2 53 GLN ** B2 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 342 GLN W3 4 GLN B3 25 HIS ** B3 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 487 GLN ** b3 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w5 58 GLN ** B5 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 356 GLN ** b5 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 342 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 63648 Z= 0.279 Angle : 0.658 11.937 86070 Z= 0.335 Chirality : 0.042 0.249 9066 Planarity : 0.005 0.128 11430 Dihedral : 5.517 66.645 8904 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.26 % Favored : 91.25 % Rotamer: Outliers : 5.86 % Allowed : 30.76 % Favored : 63.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.10), residues: 7866 helix: 1.19 (0.09), residues: 3432 sheet: -0.33 (0.16), residues: 1044 loop : -1.47 (0.11), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPB5 393 HIS 0.006 0.001 HIS b 332 PHE 0.024 0.001 PHE U 39 TYR 0.020 0.001 TYRb4 395 ARG 0.010 0.000 ARGU4 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1705 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 1330 time to evaluate : 5.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: w 51 GLU cc_start: 0.9410 (pt0) cc_final: 0.9017 (pt0) REVERT: B 342 GLN cc_start: 0.9235 (mm110) cc_final: 0.8384 (mp10) REVERT: b 334 MET cc_start: 0.8975 (tpp) cc_final: 0.8589 (tpp) REVERT: b 359 LEU cc_start: 0.9707 (mm) cc_final: 0.9480 (mm) REVERT: W1 56 MET cc_start: 0.8357 (tmm) cc_final: 0.8029 (ppp) REVERT: w1 31 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7294 (mtm-85) REVERT: U1 19 LYS cc_start: 0.9394 (ttpp) cc_final: 0.9133 (ttpp) REVERT: B1 140 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: B1 241 GLU cc_start: 0.8342 (pp20) cc_final: 0.7996 (pp20) REVERT: B1 366 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9431 (mm) REVERT: b1 61 ASP cc_start: 0.8254 (t0) cc_final: 0.8045 (t0) REVERT: b1 82 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.9056 (p) REVERT: b1 437 GLU cc_start: 0.9424 (OUTLIER) cc_final: 0.8889 (pt0) REVERT: U2 62 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8445 (tm-30) REVERT: U2 114 ARG cc_start: 0.8892 (ptp90) cc_final: 0.8524 (ptp90) REVERT: U2 134 MET cc_start: 0.8009 (mtm) cc_final: 0.7749 (ptp) REVERT: B2 346 ASP cc_start: 0.8976 (t0) cc_final: 0.8768 (t0) REVERT: b2 479 CYS cc_start: 0.9426 (m) cc_final: 0.8907 (p) REVERT: f3 34 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8509 (mp10) REVERT: f3 77 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8524 (ttt180) REVERT: U3 50 GLU cc_start: 0.7919 (mp0) cc_final: 0.7573 (mp0) REVERT: U3 62 GLN cc_start: 0.8690 (pp30) cc_final: 0.8273 (pm20) REVERT: B3 463 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8839 (mm-30) REVERT: U4 114 ARG cc_start: 0.8736 (ptp-110) cc_final: 0.8482 (ptp-110) REVERT: B4 35 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9165 (pp) REVERT: B4 366 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9299 (mm) REVERT: b4 359 LEU cc_start: 0.9742 (mm) cc_final: 0.9474 (mm) REVERT: b4 380 MET cc_start: 0.7879 (tpp) cc_final: 0.7660 (tpp) REVERT: b4 469 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8840 (mm-30) REVERT: w5 25 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9169 (p) REVERT: U5 17 LEU cc_start: 0.9583 (tp) cc_final: 0.9347 (tp) REVERT: U5 134 MET cc_start: 0.8919 (ppp) cc_final: 0.8661 (ppp) REVERT: B5 348 ASP cc_start: 0.9208 (t0) cc_final: 0.8908 (t0) REVERT: b5 252 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8488 (t80) REVERT: b5 353 VAL cc_start: 0.9718 (OUTLIER) cc_final: 0.9517 (m) REVERT: b5 466 MET cc_start: 0.9505 (OUTLIER) cc_final: 0.8540 (ppp) outliers start: 375 outliers final: 219 residues processed: 1561 average time/residue: 0.5745 time to fit residues: 1516.0927 Evaluate side-chains 1513 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1281 time to evaluate : 5.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 4 PHE Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain w residue 23 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 42 ASP Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 110 TYR Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain b residue 39 ASN Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 135 THR Chi-restraints excluded: chain b residue 226 LEU Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 255 MET Chi-restraints excluded: chain b residue 273 ILE Chi-restraints excluded: chain b residue 339 LEU Chi-restraints excluded: chain b residue 358 LEU Chi-restraints excluded: chain f1 residue 4 PHE Chi-restraints excluded: chain f1 residue 29 ILE Chi-restraints excluded: chain f1 residue 56 VAL Chi-restraints excluded: chain f1 residue 109 VAL Chi-restraints excluded: chain W1 residue 23 VAL Chi-restraints excluded: chain W1 residue 34 GLU Chi-restraints excluded: chain W1 residue 41 SER Chi-restraints excluded: chain W1 residue 52 VAL Chi-restraints excluded: chain w1 residue 23 VAL Chi-restraints excluded: chain w1 residue 25 THR Chi-restraints excluded: chain w1 residue 29 ASP Chi-restraints excluded: chain w1 residue 31 ARG Chi-restraints excluded: chain w1 residue 33 VAL Chi-restraints excluded: chain w1 residue 38 THR Chi-restraints excluded: chain w1 residue 53 GLN Chi-restraints excluded: chain U1 residue 110 TYR Chi-restraints excluded: chain B1 residue 25 HIS Chi-restraints excluded: chain B1 residue 140 GLU Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 219 TRP Chi-restraints excluded: chain B1 residue 257 GLN Chi-restraints excluded: chain B1 residue 274 VAL Chi-restraints excluded: chain B1 residue 337 ASP Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 461 VAL Chi-restraints excluded: chain B1 residue 497 THR Chi-restraints excluded: chain b1 residue 31 PHE Chi-restraints excluded: chain b1 residue 39 ASN Chi-restraints excluded: chain b1 residue 45 VAL Chi-restraints excluded: chain b1 residue 82 VAL Chi-restraints excluded: chain b1 residue 133 THR Chi-restraints excluded: chain b1 residue 144 MET Chi-restraints excluded: chain b1 residue 185 ASP Chi-restraints excluded: chain b1 residue 226 LEU Chi-restraints excluded: chain b1 residue 358 LEU Chi-restraints excluded: chain b1 residue 425 VAL Chi-restraints excluded: chain b1 residue 437 GLU Chi-restraints excluded: chain b1 residue 439 ARG Chi-restraints excluded: chain b1 residue 463 GLU Chi-restraints excluded: chain f2 residue 7 LEU Chi-restraints excluded: chain f2 residue 56 VAL Chi-restraints excluded: chain f2 residue 65 LEU Chi-restraints excluded: chain f2 residue 67 VAL Chi-restraints excluded: chain f2 residue 109 VAL Chi-restraints excluded: chain W2 residue 23 VAL Chi-restraints excluded: chain W2 residue 34 GLU Chi-restraints excluded: chain W2 residue 42 ASP Chi-restraints excluded: chain W2 residue 50 LEU Chi-restraints excluded: chain w2 residue 19 THR Chi-restraints excluded: chain w2 residue 39 SER Chi-restraints excluded: chain w2 residue 52 VAL Chi-restraints excluded: chain U2 residue 22 THR Chi-restraints excluded: chain U2 residue 33 VAL Chi-restraints excluded: chain U2 residue 42 VAL Chi-restraints excluded: chain U2 residue 110 TYR Chi-restraints excluded: chain U2 residue 123 SER Chi-restraints excluded: chain B2 residue 25 HIS Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 82 VAL Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 195 ILE Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 215 MET Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 341 LEU Chi-restraints excluded: chain B2 residue 358 LEU Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 366 LEU Chi-restraints excluded: chain B2 residue 455 ILE Chi-restraints excluded: chain B2 residue 467 LEU Chi-restraints excluded: chain B2 residue 474 THR Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 109 ARG Chi-restraints excluded: chain b2 residue 132 ARG Chi-restraints excluded: chain b2 residue 171 MET Chi-restraints excluded: chain b2 residue 202 LEU Chi-restraints excluded: chain b2 residue 220 THR Chi-restraints excluded: chain b2 residue 226 LEU Chi-restraints excluded: chain b2 residue 240 VAL Chi-restraints excluded: chain b2 residue 339 LEU Chi-restraints excluded: chain b2 residue 340 ASN Chi-restraints excluded: chain b2 residue 358 LEU Chi-restraints excluded: chain b2 residue 425 VAL Chi-restraints excluded: chain b2 residue 466 MET Chi-restraints excluded: chain f3 residue 4 PHE Chi-restraints excluded: chain f3 residue 25 THR Chi-restraints excluded: chain f3 residue 34 GLN Chi-restraints excluded: chain f3 residue 56 VAL Chi-restraints excluded: chain f3 residue 77 ARG Chi-restraints excluded: chain f3 residue 90 VAL Chi-restraints excluded: chain W3 residue 23 VAL Chi-restraints excluded: chain W3 residue 25 THR Chi-restraints excluded: chain W3 residue 39 SER Chi-restraints excluded: chain W3 residue 50 LEU Chi-restraints excluded: chain w3 residue 23 VAL Chi-restraints excluded: chain w3 residue 25 THR Chi-restraints excluded: chain w3 residue 33 VAL Chi-restraints excluded: chain w3 residue 34 GLU Chi-restraints excluded: chain w3 residue 39 SER Chi-restraints excluded: chain U3 residue 17 LEU Chi-restraints excluded: chain U3 residue 52 THR Chi-restraints excluded: chain U3 residue 110 TYR Chi-restraints excluded: chain U3 residue 117 ASP Chi-restraints excluded: chain U3 residue 122 SER Chi-restraints excluded: chain U3 residue 123 SER Chi-restraints excluded: chain B3 residue 25 HIS Chi-restraints excluded: chain B3 residue 37 SER Chi-restraints excluded: chain B3 residue 50 LEU Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 126 ILE Chi-restraints excluded: chain B3 residue 132 ARG Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 340 ASN Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 446 ASP Chi-restraints excluded: chain B3 residue 474 THR Chi-restraints excluded: chain B3 residue 484 ASP Chi-restraints excluded: chain b3 residue 31 PHE Chi-restraints excluded: chain b3 residue 136 MET Chi-restraints excluded: chain b3 residue 185 ASP Chi-restraints excluded: chain b3 residue 206 VAL Chi-restraints excluded: chain b3 residue 255 MET Chi-restraints excluded: chain b3 residue 337 ASP Chi-restraints excluded: chain b3 residue 358 LEU Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 434 SER Chi-restraints excluded: chain f4 residue 25 THR Chi-restraints excluded: chain f4 residue 56 VAL Chi-restraints excluded: chain f4 residue 58 VAL Chi-restraints excluded: chain f4 residue 69 THR Chi-restraints excluded: chain f4 residue 90 VAL Chi-restraints excluded: chain f4 residue 109 VAL Chi-restraints excluded: chain W4 residue 7 LEU Chi-restraints excluded: chain W4 residue 23 VAL Chi-restraints excluded: chain W4 residue 34 GLU Chi-restraints excluded: chain W4 residue 42 ASP Chi-restraints excluded: chain w4 residue 17 LEU Chi-restraints excluded: chain w4 residue 25 THR Chi-restraints excluded: chain w4 residue 38 THR Chi-restraints excluded: chain w4 residue 42 ASP Chi-restraints excluded: chain U4 residue 52 THR Chi-restraints excluded: chain U4 residue 110 TYR Chi-restraints excluded: chain U4 residue 117 ASP Chi-restraints excluded: chain B4 residue 35 LEU Chi-restraints excluded: chain B4 residue 54 THR Chi-restraints excluded: chain B4 residue 144 MET Chi-restraints excluded: chain B4 residue 188 ASN Chi-restraints excluded: chain B4 residue 206 VAL Chi-restraints excluded: chain B4 residue 287 ASP Chi-restraints excluded: chain B4 residue 340 ASN Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 446 ASP Chi-restraints excluded: chain b4 residue 35 LEU Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 226 LEU Chi-restraints excluded: chain b4 residue 240 VAL Chi-restraints excluded: chain b4 residue 283 GLU Chi-restraints excluded: chain b4 residue 358 LEU Chi-restraints excluded: chain f5 residue 4 PHE Chi-restraints excluded: chain f5 residue 29 ILE Chi-restraints excluded: chain f5 residue 56 VAL Chi-restraints excluded: chain W5 residue 23 VAL Chi-restraints excluded: chain W5 residue 34 GLU Chi-restraints excluded: chain W5 residue 38 THR Chi-restraints excluded: chain W5 residue 39 SER Chi-restraints excluded: chain W5 residue 57 THR Chi-restraints excluded: chain w5 residue 23 VAL Chi-restraints excluded: chain w5 residue 25 THR Chi-restraints excluded: chain w5 residue 39 SER Chi-restraints excluded: chain U5 residue 20 HIS Chi-restraints excluded: chain U5 residue 30 ARG Chi-restraints excluded: chain U5 residue 52 THR Chi-restraints excluded: chain U5 residue 67 ILE Chi-restraints excluded: chain U5 residue 75 VAL Chi-restraints excluded: chain U5 residue 110 TYR Chi-restraints excluded: chain U5 residue 117 ASP Chi-restraints excluded: chain B5 residue 25 HIS Chi-restraints excluded: chain B5 residue 126 ILE Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 252 TYR Chi-restraints excluded: chain B5 residue 284 SER Chi-restraints excluded: chain B5 residue 340 ASN Chi-restraints excluded: chain B5 residue 392 SER Chi-restraints excluded: chain B5 residue 425 VAL Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 144 MET Chi-restraints excluded: chain b5 residue 159 THR Chi-restraints excluded: chain b5 residue 218 LYS Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 337 ASP Chi-restraints excluded: chain b5 residue 340 ASN Chi-restraints excluded: chain b5 residue 353 VAL Chi-restraints excluded: chain b5 residue 358 LEU Chi-restraints excluded: chain b5 residue 425 VAL Chi-restraints excluded: chain b5 residue 463 GLU Chi-restraints excluded: chain b5 residue 466 MET Chi-restraints excluded: chain b5 residue 478 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 393 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 589 optimal weight: 8.9990 chunk 482 optimal weight: 0.8980 chunk 195 optimal weight: 0.0870 chunk 709 optimal weight: 0.9980 chunk 766 optimal weight: 5.9990 chunk 631 optimal weight: 20.0000 chunk 703 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 569 optimal weight: 30.0000 overall best weight: 2.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS ** b 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 342 GLN ** B1 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 372 GLN ** b1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f2 102 HIS ** f2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 53 GLN ** B2 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 342 GLN ** B3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 34 GLN ** b3 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b4 342 GLN w5 58 GLN ** B5 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 356 GLN ** b5 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 342 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 63648 Z= 0.199 Angle : 0.649 12.174 86070 Z= 0.323 Chirality : 0.041 0.236 9066 Planarity : 0.005 0.106 11430 Dihedral : 5.157 65.806 8858 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.17 % Favored : 91.36 % Rotamer: Outliers : 5.98 % Allowed : 31.21 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.10), residues: 7866 helix: 1.30 (0.09), residues: 3414 sheet: -0.31 (0.16), residues: 1056 loop : -1.48 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPB5 393 HIS 0.008 0.001 HISB3 25 PHE 0.024 0.001 PHEB1 147 TYR 0.020 0.001 TYRB3 24 ARG 0.009 0.000 ARGU4 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1828 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 1445 time to evaluate : 5.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 75 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9413 (mp) REVERT: w 51 GLU cc_start: 0.9383 (pt0) cc_final: 0.8977 (pt0) REVERT: U 50 GLU cc_start: 0.8042 (mp0) cc_final: 0.7467 (mp0) REVERT: U 62 GLN cc_start: 0.8929 (pp30) cc_final: 0.8289 (pm20) REVERT: U 84 MET cc_start: 0.8495 (mtp) cc_final: 0.8004 (mtt) REVERT: U 134 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8265 (mtm) REVERT: B 342 GLN cc_start: 0.9177 (mm110) cc_final: 0.8758 (mm-40) REVERT: b 359 LEU cc_start: 0.9706 (mm) cc_final: 0.9427 (mm) REVERT: b 411 MET cc_start: 0.9649 (mtm) cc_final: 0.9384 (mtm) REVERT: W1 45 LYS cc_start: 0.9390 (mtmm) cc_final: 0.9168 (mtmm) REVERT: w1 31 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7217 (mtm-85) REVERT: U1 19 LYS cc_start: 0.9386 (ttpp) cc_final: 0.9109 (ttpp) REVERT: U1 105 MET cc_start: 0.9235 (tpp) cc_final: 0.8687 (tpp) REVERT: B1 241 GLU cc_start: 0.8359 (pp20) cc_final: 0.8001 (pp20) REVERT: B1 252 TYR cc_start: 0.9509 (OUTLIER) cc_final: 0.8277 (t80) REVERT: B1 366 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9409 (mm) REVERT: b1 61 ASP cc_start: 0.8259 (t0) cc_final: 0.7984 (t0) REVERT: b1 82 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.9023 (p) REVERT: b1 489 ILE cc_start: 0.9662 (OUTLIER) cc_final: 0.9444 (tt) REVERT: f2 77 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8345 (ttt-90) REVERT: U2 62 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8439 (tm-30) REVERT: U2 114 ARG cc_start: 0.8873 (ptp90) cc_final: 0.8509 (ptp90) REVERT: B2 342 GLN cc_start: 0.8918 (mp10) cc_final: 0.8421 (mp10) REVERT: B2 346 ASP cc_start: 0.8958 (t0) cc_final: 0.8716 (t0) REVERT: b2 437 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8845 (pt0) REVERT: b2 479 CYS cc_start: 0.9406 (m) cc_final: 0.8917 (p) REVERT: f3 16 ASP cc_start: 0.8931 (t0) cc_final: 0.8604 (t0) REVERT: f3 34 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: f3 77 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8195 (ttt180) REVERT: W3 32 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8056 (ttm-80) REVERT: w3 31 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7627 (mtm-85) REVERT: U3 50 GLU cc_start: 0.7781 (mp0) cc_final: 0.7419 (mp0) REVERT: U3 62 GLN cc_start: 0.8753 (pp30) cc_final: 0.8164 (pm20) REVERT: B3 334 MET cc_start: 0.9019 (mpp) cc_final: 0.8811 (mpp) REVERT: b3 340 ASN cc_start: 0.9348 (m-40) cc_final: 0.8620 (p0) REVERT: b3 498 MET cc_start: 0.9195 (tmm) cc_final: 0.8806 (tmm) REVERT: W4 45 LYS cc_start: 0.9588 (mtpp) cc_final: 0.9344 (mtmm) REVERT: U4 27 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7180 (m-10) REVERT: U4 50 GLU cc_start: 0.8127 (pm20) cc_final: 0.7792 (pm20) REVERT: U4 114 ARG cc_start: 0.8690 (ptp-110) cc_final: 0.8299 (ptp-170) REVERT: B4 35 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9087 (pp) REVERT: B4 218 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8824 (mptt) REVERT: B4 366 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9262 (mm) REVERT: B4 463 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8815 (mm-30) REVERT: b4 61 ASP cc_start: 0.8279 (t0) cc_final: 0.8054 (t0) REVERT: b4 241 GLU cc_start: 0.7575 (pp20) cc_final: 0.7271 (pp20) REVERT: b4 359 LEU cc_start: 0.9784 (mm) cc_final: 0.9422 (mm) REVERT: b4 399 ARG cc_start: 0.9448 (tpp80) cc_final: 0.9025 (tpp80) REVERT: b4 469 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8887 (mm-30) REVERT: b4 477 LYS cc_start: 0.9757 (mtpp) cc_final: 0.9546 (mtpp) REVERT: U5 17 LEU cc_start: 0.9522 (tp) cc_final: 0.9237 (tp) REVERT: U5 134 MET cc_start: 0.8897 (ppp) cc_final: 0.8686 (ppp) REVERT: B5 348 ASP cc_start: 0.9210 (t0) cc_final: 0.8815 (t0) REVERT: b5 137 MET cc_start: 0.9616 (mmm) cc_final: 0.9315 (mmm) REVERT: b5 252 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8426 (t80) REVERT: b5 453 MET cc_start: 0.8708 (ppp) cc_final: 0.7892 (ppp) REVERT: b5 466 MET cc_start: 0.9553 (OUTLIER) cc_final: 0.8203 (ppp) REVERT: b5 469 GLU cc_start: 0.9247 (pp20) cc_final: 0.9025 (pp20) outliers start: 383 outliers final: 236 residues processed: 1660 average time/residue: 0.5797 time to fit residues: 1619.3397 Evaluate side-chains 1590 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1336 time to evaluate : 5.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 4 PHE Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain w residue 23 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 42 ASP Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 110 TYR Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain b residue 39 ASN Chi-restraints excluded: chain b residue 226 LEU Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 255 MET Chi-restraints excluded: chain b residue 337 ASP Chi-restraints excluded: chain b residue 339 LEU Chi-restraints excluded: chain b residue 340 ASN Chi-restraints excluded: chain b residue 358 LEU Chi-restraints excluded: chain b residue 467 LEU Chi-restraints excluded: chain b residue 474 THR Chi-restraints excluded: chain f1 residue 4 PHE Chi-restraints excluded: chain f1 residue 29 ILE Chi-restraints excluded: chain f1 residue 56 VAL Chi-restraints excluded: chain f1 residue 102 HIS Chi-restraints excluded: chain f1 residue 103 LEU Chi-restraints excluded: chain f1 residue 109 VAL Chi-restraints excluded: chain W1 residue 23 VAL Chi-restraints excluded: chain W1 residue 34 GLU Chi-restraints excluded: chain W1 residue 51 GLU Chi-restraints excluded: chain W1 residue 52 VAL Chi-restraints excluded: chain w1 residue 23 VAL Chi-restraints excluded: chain w1 residue 25 THR Chi-restraints excluded: chain w1 residue 31 ARG Chi-restraints excluded: chain w1 residue 33 VAL Chi-restraints excluded: chain w1 residue 38 THR Chi-restraints excluded: chain w1 residue 51 GLU Chi-restraints excluded: chain w1 residue 53 GLN Chi-restraints excluded: chain U1 residue 38 ASP Chi-restraints excluded: chain U1 residue 44 VAL Chi-restraints excluded: chain U1 residue 52 THR Chi-restraints excluded: chain U1 residue 110 TYR Chi-restraints excluded: chain U1 residue 117 ASP Chi-restraints excluded: chain B1 residue 25 HIS Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 219 TRP Chi-restraints excluded: chain B1 residue 252 TYR Chi-restraints excluded: chain B1 residue 257 GLN Chi-restraints excluded: chain B1 residue 261 LEU Chi-restraints excluded: chain B1 residue 337 ASP Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 474 THR Chi-restraints excluded: chain B1 residue 497 THR Chi-restraints excluded: chain b1 residue 31 PHE Chi-restraints excluded: chain b1 residue 39 ASN Chi-restraints excluded: chain b1 residue 45 VAL Chi-restraints excluded: chain b1 residue 82 VAL Chi-restraints excluded: chain b1 residue 133 THR Chi-restraints excluded: chain b1 residue 144 MET Chi-restraints excluded: chain b1 residue 159 THR Chi-restraints excluded: chain b1 residue 185 ASP Chi-restraints excluded: chain b1 residue 186 SER Chi-restraints excluded: chain b1 residue 358 LEU Chi-restraints excluded: chain b1 residue 413 LEU Chi-restraints excluded: chain b1 residue 425 VAL Chi-restraints excluded: chain b1 residue 439 ARG Chi-restraints excluded: chain b1 residue 463 GLU Chi-restraints excluded: chain b1 residue 489 ILE Chi-restraints excluded: chain f2 residue 7 LEU Chi-restraints excluded: chain f2 residue 56 VAL Chi-restraints excluded: chain f2 residue 67 VAL Chi-restraints excluded: chain f2 residue 77 ARG Chi-restraints excluded: chain f2 residue 109 VAL Chi-restraints excluded: chain W2 residue 23 VAL Chi-restraints excluded: chain W2 residue 34 GLU Chi-restraints excluded: chain W2 residue 42 ASP Chi-restraints excluded: chain W2 residue 50 LEU Chi-restraints excluded: chain w2 residue 19 THR Chi-restraints excluded: chain w2 residue 39 SER Chi-restraints excluded: chain w2 residue 52 VAL Chi-restraints excluded: chain U2 residue 30 ARG Chi-restraints excluded: chain U2 residue 33 VAL Chi-restraints excluded: chain U2 residue 42 VAL Chi-restraints excluded: chain U2 residue 52 THR Chi-restraints excluded: chain U2 residue 110 TYR Chi-restraints excluded: chain U2 residue 123 SER Chi-restraints excluded: chain B2 residue 25 HIS Chi-restraints excluded: chain B2 residue 35 LEU Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 82 VAL Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 195 ILE Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 215 MET Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 341 LEU Chi-restraints excluded: chain B2 residue 358 LEU Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 366 LEU Chi-restraints excluded: chain B2 residue 405 SER Chi-restraints excluded: chain B2 residue 425 VAL Chi-restraints excluded: chain B2 residue 474 THR Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 109 ARG Chi-restraints excluded: chain b2 residue 171 MET Chi-restraints excluded: chain b2 residue 202 LEU Chi-restraints excluded: chain b2 residue 226 LEU Chi-restraints excluded: chain b2 residue 240 VAL Chi-restraints excluded: chain b2 residue 339 LEU Chi-restraints excluded: chain b2 residue 358 LEU Chi-restraints excluded: chain b2 residue 425 VAL Chi-restraints excluded: chain b2 residue 437 GLU Chi-restraints excluded: chain b2 residue 466 MET Chi-restraints excluded: chain f3 residue 4 PHE Chi-restraints excluded: chain f3 residue 25 THR Chi-restraints excluded: chain f3 residue 34 GLN Chi-restraints excluded: chain f3 residue 56 VAL Chi-restraints excluded: chain f3 residue 77 ARG Chi-restraints excluded: chain f3 residue 90 VAL Chi-restraints excluded: chain W3 residue 23 VAL Chi-restraints excluded: chain W3 residue 32 ARG Chi-restraints excluded: chain W3 residue 39 SER Chi-restraints excluded: chain W3 residue 50 LEU Chi-restraints excluded: chain w3 residue 23 VAL Chi-restraints excluded: chain w3 residue 25 THR Chi-restraints excluded: chain w3 residue 31 ARG Chi-restraints excluded: chain w3 residue 33 VAL Chi-restraints excluded: chain w3 residue 34 GLU Chi-restraints excluded: chain w3 residue 39 SER Chi-restraints excluded: chain U3 residue 17 LEU Chi-restraints excluded: chain U3 residue 52 THR Chi-restraints excluded: chain U3 residue 74 GLN Chi-restraints excluded: chain U3 residue 110 TYR Chi-restraints excluded: chain U3 residue 117 ASP Chi-restraints excluded: chain U3 residue 122 SER Chi-restraints excluded: chain U3 residue 123 SER Chi-restraints excluded: chain B3 residue 25 HIS Chi-restraints excluded: chain B3 residue 50 LEU Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 125 CYS Chi-restraints excluded: chain B3 residue 126 ILE Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 446 ASP Chi-restraints excluded: chain B3 residue 453 MET Chi-restraints excluded: chain B3 residue 474 THR Chi-restraints excluded: chain b3 residue 31 PHE Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 136 MET Chi-restraints excluded: chain b3 residue 185 ASP Chi-restraints excluded: chain b3 residue 337 ASP Chi-restraints excluded: chain b3 residue 355 GLU Chi-restraints excluded: chain b3 residue 358 LEU Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 434 SER Chi-restraints excluded: chain b3 residue 456 ASP Chi-restraints excluded: chain b3 residue 478 GLU Chi-restraints excluded: chain f4 residue 25 THR Chi-restraints excluded: chain f4 residue 56 VAL Chi-restraints excluded: chain f4 residue 58 VAL Chi-restraints excluded: chain f4 residue 69 THR Chi-restraints excluded: chain f4 residue 90 VAL Chi-restraints excluded: chain W4 residue 7 LEU Chi-restraints excluded: chain W4 residue 23 VAL Chi-restraints excluded: chain W4 residue 34 GLU Chi-restraints excluded: chain W4 residue 42 ASP Chi-restraints excluded: chain w4 residue 25 THR Chi-restraints excluded: chain w4 residue 38 THR Chi-restraints excluded: chain w4 residue 39 SER Chi-restraints excluded: chain U4 residue 27 PHE Chi-restraints excluded: chain U4 residue 52 THR Chi-restraints excluded: chain U4 residue 91 VAL Chi-restraints excluded: chain U4 residue 110 TYR Chi-restraints excluded: chain U4 residue 117 ASP Chi-restraints excluded: chain B4 residue 35 LEU Chi-restraints excluded: chain B4 residue 125 CYS Chi-restraints excluded: chain B4 residue 137 MET Chi-restraints excluded: chain B4 residue 173 SER Chi-restraints excluded: chain B4 residue 188 ASN Chi-restraints excluded: chain B4 residue 206 VAL Chi-restraints excluded: chain B4 residue 269 LEU Chi-restraints excluded: chain B4 residue 287 ASP Chi-restraints excluded: chain B4 residue 340 ASN Chi-restraints excluded: chain B4 residue 341 LEU Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 446 ASP Chi-restraints excluded: chain B4 residue 453 MET Chi-restraints excluded: chain b4 residue 35 LEU Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 226 LEU Chi-restraints excluded: chain b4 residue 240 VAL Chi-restraints excluded: chain b4 residue 283 GLU Chi-restraints excluded: chain b4 residue 460 GLU Chi-restraints excluded: chain f5 residue 4 PHE Chi-restraints excluded: chain f5 residue 29 ILE Chi-restraints excluded: chain f5 residue 42 VAL Chi-restraints excluded: chain f5 residue 56 VAL Chi-restraints excluded: chain W5 residue 23 VAL Chi-restraints excluded: chain W5 residue 38 THR Chi-restraints excluded: chain W5 residue 39 SER Chi-restraints excluded: chain W5 residue 51 GLU Chi-restraints excluded: chain W5 residue 57 THR Chi-restraints excluded: chain w5 residue 23 VAL Chi-restraints excluded: chain w5 residue 39 SER Chi-restraints excluded: chain U5 residue 52 THR Chi-restraints excluded: chain U5 residue 67 ILE Chi-restraints excluded: chain U5 residue 110 TYR Chi-restraints excluded: chain U5 residue 117 ASP Chi-restraints excluded: chain B5 residue 25 HIS Chi-restraints excluded: chain B5 residue 54 THR Chi-restraints excluded: chain B5 residue 126 ILE Chi-restraints excluded: chain B5 residue 252 TYR Chi-restraints excluded: chain B5 residue 269 LEU Chi-restraints excluded: chain B5 residue 284 SER Chi-restraints excluded: chain B5 residue 340 ASN Chi-restraints excluded: chain B5 residue 341 LEU Chi-restraints excluded: chain B5 residue 358 LEU Chi-restraints excluded: chain B5 residue 359 LEU Chi-restraints excluded: chain B5 residue 425 VAL Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 218 LYS Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 269 LEU Chi-restraints excluded: chain b5 residue 340 ASN Chi-restraints excluded: chain b5 residue 355 GLU Chi-restraints excluded: chain b5 residue 357 SER Chi-restraints excluded: chain b5 residue 358 LEU Chi-restraints excluded: chain b5 residue 425 VAL Chi-restraints excluded: chain b5 residue 456 ASP Chi-restraints excluded: chain b5 residue 463 GLU Chi-restraints excluded: chain b5 residue 466 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 701 optimal weight: 8.9990 chunk 533 optimal weight: 7.9990 chunk 368 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 476 optimal weight: 7.9990 chunk 712 optimal weight: 8.9990 chunk 753 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 chunk 674 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** b 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 342 GLN ** B1 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 4 GLN w2 53 GLN B2 235 HIS ** B2 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b2 342 GLN ** f3 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W3 4 GLN B3 25 HIS ** B3 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 356 GLN b3 72 ASN b3 266 ASN ** b3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b3 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 257 GLN ** B4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 356 GLN b4 72 ASN w5 58 GLN B5 182 ASN B5 194 GLN ** B5 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 356 GLN ** b5 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 342 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 63648 Z= 0.388 Angle : 0.702 13.048 86070 Z= 0.359 Chirality : 0.043 0.240 9066 Planarity : 0.006 0.116 11430 Dihedral : 5.303 67.253 8853 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.63 % Favored : 90.88 % Rotamer: Outliers : 7.87 % Allowed : 30.47 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.10), residues: 7866 helix: 1.21 (0.09), residues: 3420 sheet: -0.42 (0.16), residues: 1074 loop : -1.47 (0.11), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPb4 157 HIS 0.008 0.001 HIS b 332 PHE 0.040 0.001 PHEU5 39 TYR 0.021 0.002 TYR U 51 ARG 0.011 0.001 ARGw4 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1822 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 504 poor density : 1318 time to evaluate : 6.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 49 GLU cc_start: 0.9319 (tm-30) cc_final: 0.9105 (tm-30) REVERT: w 51 GLU cc_start: 0.9407 (pt0) cc_final: 0.9015 (pt0) REVERT: U 50 GLU cc_start: 0.8055 (mp0) cc_final: 0.7464 (mp0) REVERT: U 62 GLN cc_start: 0.9006 (pp30) cc_final: 0.8545 (tm-30) REVERT: B 140 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8393 (tm-30) REVERT: B 265 GLN cc_start: 0.9258 (mm110) cc_final: 0.9021 (mm-40) REVERT: B 342 GLN cc_start: 0.9236 (mm110) cc_final: 0.8213 (mp10) REVERT: b 359 LEU cc_start: 0.9774 (mm) cc_final: 0.9534 (mm) REVERT: b 411 MET cc_start: 0.9662 (mtm) cc_final: 0.9392 (mtm) REVERT: w1 31 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7298 (mtm-85) REVERT: w1 49 GLU cc_start: 0.9285 (pm20) cc_final: 0.9059 (pm20) REVERT: B1 241 GLU cc_start: 0.8371 (pp20) cc_final: 0.8014 (pp20) REVERT: B1 366 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9446 (mm) REVERT: B1 386 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8414 (mmm160) REVERT: b1 194 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.9124 (tp40) REVERT: b1 397 MET cc_start: 0.9033 (mmm) cc_final: 0.8826 (mmm) REVERT: b1 439 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8624 (mtt180) REVERT: f2 77 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7953 (ttt90) REVERT: U2 62 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8342 (tm-30) REVERT: U2 113 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8726 (ptm-80) REVERT: U2 114 ARG cc_start: 0.8958 (ptp90) cc_final: 0.8733 (ptp90) REVERT: B2 252 TYR cc_start: 0.9545 (OUTLIER) cc_final: 0.8561 (t80) REVERT: B2 346 ASP cc_start: 0.9003 (t0) cc_final: 0.8784 (t70) REVERT: B2 466 MET cc_start: 0.9526 (ttt) cc_final: 0.9293 (ttp) REVERT: b2 430 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9022 (tptp) REVERT: b2 453 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8475 (ppp) REVERT: b2 460 GLU cc_start: 0.9029 (tp30) cc_final: 0.8728 (tp30) REVERT: b2 479 CYS cc_start: 0.9439 (m) cc_final: 0.8975 (p) REVERT: f3 34 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8612 (mp10) REVERT: f3 77 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8473 (ttt-90) REVERT: U3 50 GLU cc_start: 0.7968 (mp0) cc_final: 0.7560 (mp0) REVERT: U3 62 GLN cc_start: 0.8777 (pp30) cc_final: 0.8135 (pm20) REVERT: U3 64 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8609 (tt0) REVERT: B3 55 ARG cc_start: 0.9526 (OUTLIER) cc_final: 0.8345 (ttp80) REVERT: B3 334 MET cc_start: 0.8974 (mpp) cc_final: 0.8731 (mpp) REVERT: B3 463 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8806 (mm-30) REVERT: b3 339 LEU cc_start: 0.9595 (tp) cc_final: 0.9382 (tp) REVERT: b3 453 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.7904 (ppp) REVERT: b3 498 MET cc_start: 0.9196 (tmm) cc_final: 0.8839 (tmm) REVERT: U4 114 ARG cc_start: 0.8888 (ptp-110) cc_final: 0.8588 (ptp-170) REVERT: B4 35 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9243 (pp) REVERT: B4 131 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8972 (mttt) REVERT: B4 366 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9316 (mm) REVERT: b4 241 GLU cc_start: 0.7812 (pp20) cc_final: 0.7451 (pp20) REVERT: b4 359 LEU cc_start: 0.9817 (mm) cc_final: 0.9482 (mm) REVERT: b4 399 ARG cc_start: 0.9486 (tpp80) cc_final: 0.8902 (tpp80) REVERT: b4 453 MET cc_start: 0.8877 (ppp) cc_final: 0.8192 (ppp) REVERT: b4 469 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8937 (mm-30) REVERT: b4 472 LEU cc_start: 0.9507 (mt) cc_final: 0.9155 (tt) REVERT: b4 477 LYS cc_start: 0.9775 (mtpp) cc_final: 0.9552 (mtpp) REVERT: U5 17 LEU cc_start: 0.9538 (tp) cc_final: 0.9219 (tp) REVERT: U5 134 MET cc_start: 0.8924 (ppp) cc_final: 0.8686 (ppp) REVERT: B5 140 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8556 (tp30) REVERT: B5 342 GLN cc_start: 0.8965 (pm20) cc_final: 0.8692 (pm20) REVERT: B5 397 MET cc_start: 0.9269 (mmm) cc_final: 0.9063 (mmm) REVERT: b5 137 MET cc_start: 0.9638 (OUTLIER) cc_final: 0.9310 (mmm) REVERT: b5 252 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8559 (t80) REVERT: b5 453 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8352 (ppp) REVERT: b5 466 MET cc_start: 0.9529 (OUTLIER) cc_final: 0.8589 (ppp) outliers start: 504 outliers final: 355 residues processed: 1636 average time/residue: 0.5703 time to fit residues: 1576.2222 Evaluate side-chains 1622 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1244 time to evaluate : 5.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 4 PHE Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain w residue 23 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 42 ASP Chi-restraints excluded: chain w residue 47 ILE Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 56 MET Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 110 TYR Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain b residue 25 HIS Chi-restraints excluded: chain b residue 31 PHE Chi-restraints excluded: chain b residue 39 ASN Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 127 ASP Chi-restraints excluded: chain b residue 135 THR Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain b residue 218 LYS Chi-restraints excluded: chain b residue 226 LEU Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 273 ILE Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 337 ASP Chi-restraints excluded: chain b residue 339 LEU Chi-restraints excluded: chain b residue 358 LEU Chi-restraints excluded: chain b residue 434 SER Chi-restraints excluded: chain b residue 467 LEU Chi-restraints excluded: chain b residue 474 THR Chi-restraints excluded: chain b residue 484 ASP Chi-restraints excluded: chain f1 residue 4 PHE Chi-restraints excluded: chain f1 residue 25 THR Chi-restraints excluded: chain f1 residue 28 THR Chi-restraints excluded: chain f1 residue 29 ILE Chi-restraints excluded: chain f1 residue 30 THR Chi-restraints excluded: chain f1 residue 56 VAL Chi-restraints excluded: chain f1 residue 58 VAL Chi-restraints excluded: chain f1 residue 109 VAL Chi-restraints excluded: chain W1 residue 23 VAL Chi-restraints excluded: chain W1 residue 34 GLU Chi-restraints excluded: chain W1 residue 52 VAL Chi-restraints excluded: chain w1 residue 23 VAL Chi-restraints excluded: chain w1 residue 25 THR Chi-restraints excluded: chain w1 residue 29 ASP Chi-restraints excluded: chain w1 residue 31 ARG Chi-restraints excluded: chain w1 residue 33 VAL Chi-restraints excluded: chain w1 residue 38 THR Chi-restraints excluded: chain w1 residue 42 ASP Chi-restraints excluded: chain w1 residue 51 GLU Chi-restraints excluded: chain w1 residue 53 GLN Chi-restraints excluded: chain U1 residue 44 VAL Chi-restraints excluded: chain U1 residue 52 THR Chi-restraints excluded: chain U1 residue 110 TYR Chi-restraints excluded: chain B1 residue 54 THR Chi-restraints excluded: chain B1 residue 181 ASN Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 219 TRP Chi-restraints excluded: chain B1 residue 240 VAL Chi-restraints excluded: chain B1 residue 257 GLN Chi-restraints excluded: chain B1 residue 261 LEU Chi-restraints excluded: chain B1 residue 269 LEU Chi-restraints excluded: chain B1 residue 333 LEU Chi-restraints excluded: chain B1 residue 337 ASP Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 381 SER Chi-restraints excluded: chain B1 residue 386 ARG Chi-restraints excluded: chain B1 residue 468 ILE Chi-restraints excluded: chain B1 residue 474 THR Chi-restraints excluded: chain B1 residue 497 THR Chi-restraints excluded: chain b1 residue 31 PHE Chi-restraints excluded: chain b1 residue 39 ASN Chi-restraints excluded: chain b1 residue 45 VAL Chi-restraints excluded: chain b1 residue 133 THR Chi-restraints excluded: chain b1 residue 144 MET Chi-restraints excluded: chain b1 residue 159 THR Chi-restraints excluded: chain b1 residue 185 ASP Chi-restraints excluded: chain b1 residue 186 SER Chi-restraints excluded: chain b1 residue 194 GLN Chi-restraints excluded: chain b1 residue 226 LEU Chi-restraints excluded: chain b1 residue 337 ASP Chi-restraints excluded: chain b1 residue 357 SER Chi-restraints excluded: chain b1 residue 358 LEU Chi-restraints excluded: chain b1 residue 368 VAL Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 413 LEU Chi-restraints excluded: chain b1 residue 425 VAL Chi-restraints excluded: chain b1 residue 439 ARG Chi-restraints excluded: chain b1 residue 463 GLU Chi-restraints excluded: chain b1 residue 478 GLU Chi-restraints excluded: chain f2 residue 4 PHE Chi-restraints excluded: chain f2 residue 7 LEU Chi-restraints excluded: chain f2 residue 19 ILE Chi-restraints excluded: chain f2 residue 56 VAL Chi-restraints excluded: chain f2 residue 67 VAL Chi-restraints excluded: chain f2 residue 77 ARG Chi-restraints excluded: chain f2 residue 109 VAL Chi-restraints excluded: chain W2 residue 7 LEU Chi-restraints excluded: chain W2 residue 23 VAL Chi-restraints excluded: chain W2 residue 34 GLU Chi-restraints excluded: chain W2 residue 42 ASP Chi-restraints excluded: chain W2 residue 47 ILE Chi-restraints excluded: chain W2 residue 50 LEU Chi-restraints excluded: chain W2 residue 57 THR Chi-restraints excluded: chain W2 residue 68 VAL Chi-restraints excluded: chain w2 residue 19 THR Chi-restraints excluded: chain w2 residue 23 VAL Chi-restraints excluded: chain w2 residue 39 SER Chi-restraints excluded: chain w2 residue 52 VAL Chi-restraints excluded: chain U2 residue 22 THR Chi-restraints excluded: chain U2 residue 30 ARG Chi-restraints excluded: chain U2 residue 33 VAL Chi-restraints excluded: chain U2 residue 42 VAL Chi-restraints excluded: chain U2 residue 52 THR Chi-restraints excluded: chain U2 residue 74 GLN Chi-restraints excluded: chain U2 residue 106 VAL Chi-restraints excluded: chain U2 residue 110 TYR Chi-restraints excluded: chain U2 residue 113 ARG Chi-restraints excluded: chain U2 residue 123 SER Chi-restraints excluded: chain B2 residue 25 HIS Chi-restraints excluded: chain B2 residue 43 GLU Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 82 VAL Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 215 MET Chi-restraints excluded: chain B2 residue 252 TYR Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 341 LEU Chi-restraints excluded: chain B2 residue 349 ASN Chi-restraints excluded: chain B2 residue 358 LEU Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 366 LEU Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain B2 residue 405 SER Chi-restraints excluded: chain B2 residue 425 VAL Chi-restraints excluded: chain B2 residue 455 ILE Chi-restraints excluded: chain B2 residue 474 THR Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 109 ARG Chi-restraints excluded: chain b2 residue 132 ARG Chi-restraints excluded: chain b2 residue 171 MET Chi-restraints excluded: chain b2 residue 195 ILE Chi-restraints excluded: chain b2 residue 202 LEU Chi-restraints excluded: chain b2 residue 220 THR Chi-restraints excluded: chain b2 residue 226 LEU Chi-restraints excluded: chain b2 residue 240 VAL Chi-restraints excluded: chain b2 residue 269 LEU Chi-restraints excluded: chain b2 residue 283 GLU Chi-restraints excluded: chain b2 residue 339 LEU Chi-restraints excluded: chain b2 residue 358 LEU Chi-restraints excluded: chain b2 residue 425 VAL Chi-restraints excluded: chain b2 residue 430 LYS Chi-restraints excluded: chain b2 residue 453 MET Chi-restraints excluded: chain b2 residue 466 MET Chi-restraints excluded: chain b2 residue 484 ASP Chi-restraints excluded: chain f3 residue 4 PHE Chi-restraints excluded: chain f3 residue 25 THR Chi-restraints excluded: chain f3 residue 33 GLU Chi-restraints excluded: chain f3 residue 34 GLN Chi-restraints excluded: chain f3 residue 56 VAL Chi-restraints excluded: chain f3 residue 69 THR Chi-restraints excluded: chain f3 residue 77 ARG Chi-restraints excluded: chain f3 residue 79 ASP Chi-restraints excluded: chain f3 residue 109 VAL Chi-restraints excluded: chain W3 residue 23 VAL Chi-restraints excluded: chain W3 residue 39 SER Chi-restraints excluded: chain w3 residue 23 VAL Chi-restraints excluded: chain w3 residue 25 THR Chi-restraints excluded: chain w3 residue 33 VAL Chi-restraints excluded: chain w3 residue 34 GLU Chi-restraints excluded: chain w3 residue 39 SER Chi-restraints excluded: chain w3 residue 58 GLN Chi-restraints excluded: chain U3 residue 9 LEU Chi-restraints excluded: chain U3 residue 22 THR Chi-restraints excluded: chain U3 residue 52 THR Chi-restraints excluded: chain U3 residue 110 TYR Chi-restraints excluded: chain U3 residue 117 ASP Chi-restraints excluded: chain U3 residue 122 SER Chi-restraints excluded: chain U3 residue 123 SER Chi-restraints excluded: chain B3 residue 25 HIS Chi-restraints excluded: chain B3 residue 37 SER Chi-restraints excluded: chain B3 residue 50 LEU Chi-restraints excluded: chain B3 residue 55 ARG Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 121 ASP Chi-restraints excluded: chain B3 residue 125 CYS Chi-restraints excluded: chain B3 residue 126 ILE Chi-restraints excluded: chain B3 residue 132 ARG Chi-restraints excluded: chain B3 residue 172 VAL Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 258 MET Chi-restraints excluded: chain B3 residue 273 ILE Chi-restraints excluded: chain B3 residue 274 VAL Chi-restraints excluded: chain B3 residue 283 GLU Chi-restraints excluded: chain B3 residue 292 MET Chi-restraints excluded: chain B3 residue 325 LEU Chi-restraints excluded: chain B3 residue 340 ASN Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 446 ASP Chi-restraints excluded: chain B3 residue 467 LEU Chi-restraints excluded: chain B3 residue 474 THR Chi-restraints excluded: chain B3 residue 484 ASP Chi-restraints excluded: chain b3 residue 31 PHE Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 133 THR Chi-restraints excluded: chain b3 residue 136 MET Chi-restraints excluded: chain b3 residue 159 THR Chi-restraints excluded: chain b3 residue 185 ASP Chi-restraints excluded: chain b3 residue 195 ILE Chi-restraints excluded: chain b3 residue 206 VAL Chi-restraints excluded: chain b3 residue 215 MET Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 337 ASP Chi-restraints excluded: chain b3 residue 358 LEU Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 434 SER Chi-restraints excluded: chain b3 residue 453 MET Chi-restraints excluded: chain b3 residue 456 ASP Chi-restraints excluded: chain f4 residue 25 THR Chi-restraints excluded: chain f4 residue 29 ILE Chi-restraints excluded: chain f4 residue 42 VAL Chi-restraints excluded: chain f4 residue 56 VAL Chi-restraints excluded: chain f4 residue 62 SER Chi-restraints excluded: chain f4 residue 64 SER Chi-restraints excluded: chain f4 residue 67 VAL Chi-restraints excluded: chain f4 residue 69 THR Chi-restraints excluded: chain f4 residue 90 VAL Chi-restraints excluded: chain f4 residue 109 VAL Chi-restraints excluded: chain W4 residue 7 LEU Chi-restraints excluded: chain W4 residue 23 VAL Chi-restraints excluded: chain W4 residue 34 GLU Chi-restraints excluded: chain W4 residue 39 SER Chi-restraints excluded: chain W4 residue 42 ASP Chi-restraints excluded: chain w4 residue 17 LEU Chi-restraints excluded: chain w4 residue 23 VAL Chi-restraints excluded: chain w4 residue 25 THR Chi-restraints excluded: chain w4 residue 33 VAL Chi-restraints excluded: chain w4 residue 38 THR Chi-restraints excluded: chain w4 residue 39 SER Chi-restraints excluded: chain w4 residue 42 ASP Chi-restraints excluded: chain U4 residue 19 LYS Chi-restraints excluded: chain U4 residue 22 THR Chi-restraints excluded: chain U4 residue 47 THR Chi-restraints excluded: chain U4 residue 52 THR Chi-restraints excluded: chain U4 residue 91 VAL Chi-restraints excluded: chain U4 residue 92 MET Chi-restraints excluded: chain U4 residue 110 TYR Chi-restraints excluded: chain U4 residue 117 ASP Chi-restraints excluded: chain B4 residue 35 LEU Chi-restraints excluded: chain B4 residue 54 THR Chi-restraints excluded: chain B4 residue 82 VAL Chi-restraints excluded: chain B4 residue 125 CYS Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 137 MET Chi-restraints excluded: chain B4 residue 144 MET Chi-restraints excluded: chain B4 residue 173 SER Chi-restraints excluded: chain B4 residue 188 ASN Chi-restraints excluded: chain B4 residue 206 VAL Chi-restraints excluded: chain B4 residue 262 ASP Chi-restraints excluded: chain B4 residue 287 ASP Chi-restraints excluded: chain B4 residue 292 MET Chi-restraints excluded: chain B4 residue 340 ASN Chi-restraints excluded: chain B4 residue 341 LEU Chi-restraints excluded: chain B4 residue 355 GLU Chi-restraints excluded: chain B4 residue 357 SER Chi-restraints excluded: chain B4 residue 358 LEU Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 381 SER Chi-restraints excluded: chain B4 residue 453 MET Chi-restraints excluded: chain B4 residue 455 ILE Chi-restraints excluded: chain B4 residue 474 THR Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 127 ASP Chi-restraints excluded: chain b4 residue 132 ARG Chi-restraints excluded: chain b4 residue 226 LEU Chi-restraints excluded: chain b4 residue 240 VAL Chi-restraints excluded: chain b4 residue 273 ILE Chi-restraints excluded: chain b4 residue 283 GLU Chi-restraints excluded: chain b4 residue 337 ASP Chi-restraints excluded: chain b4 residue 340 ASN Chi-restraints excluded: chain b4 residue 358 LEU Chi-restraints excluded: chain b4 residue 484 ASP Chi-restraints excluded: chain f5 residue 4 PHE Chi-restraints excluded: chain f5 residue 29 ILE Chi-restraints excluded: chain f5 residue 30 THR Chi-restraints excluded: chain f5 residue 42 VAL Chi-restraints excluded: chain f5 residue 56 VAL Chi-restraints excluded: chain f5 residue 109 VAL Chi-restraints excluded: chain W5 residue 23 VAL Chi-restraints excluded: chain W5 residue 38 THR Chi-restraints excluded: chain W5 residue 39 SER Chi-restraints excluded: chain W5 residue 50 LEU Chi-restraints excluded: chain W5 residue 51 GLU Chi-restraints excluded: chain W5 residue 57 THR Chi-restraints excluded: chain w5 residue 23 VAL Chi-restraints excluded: chain w5 residue 39 SER Chi-restraints excluded: chain U5 residue 20 HIS Chi-restraints excluded: chain U5 residue 30 ARG Chi-restraints excluded: chain U5 residue 52 THR Chi-restraints excluded: chain U5 residue 67 ILE Chi-restraints excluded: chain U5 residue 106 VAL Chi-restraints excluded: chain U5 residue 110 TYR Chi-restraints excluded: chain U5 residue 117 ASP Chi-restraints excluded: chain B5 residue 25 HIS Chi-restraints excluded: chain B5 residue 35 LEU Chi-restraints excluded: chain B5 residue 54 THR Chi-restraints excluded: chain B5 residue 82 VAL Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 126 ILE Chi-restraints excluded: chain B5 residue 140 GLU Chi-restraints excluded: chain B5 residue 202 LEU Chi-restraints excluded: chain B5 residue 206 VAL Chi-restraints excluded: chain B5 residue 252 TYR Chi-restraints excluded: chain B5 residue 261 LEU Chi-restraints excluded: chain B5 residue 269 LEU Chi-restraints excluded: chain B5 residue 284 SER Chi-restraints excluded: chain B5 residue 340 ASN Chi-restraints excluded: chain B5 residue 358 LEU Chi-restraints excluded: chain B5 residue 359 LEU Chi-restraints excluded: chain B5 residue 425 VAL Chi-restraints excluded: chain B5 residue 474 THR Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 137 MET Chi-restraints excluded: chain b5 residue 159 THR Chi-restraints excluded: chain b5 residue 218 LYS Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 254 VAL Chi-restraints excluded: chain b5 residue 269 LEU Chi-restraints excluded: chain b5 residue 333 LEU Chi-restraints excluded: chain b5 residue 357 SER Chi-restraints excluded: chain b5 residue 358 LEU Chi-restraints excluded: chain b5 residue 362 ILE Chi-restraints excluded: chain b5 residue 425 VAL Chi-restraints excluded: chain b5 residue 453 MET Chi-restraints excluded: chain b5 residue 463 GLU Chi-restraints excluded: chain b5 residue 466 MET Chi-restraints excluded: chain b5 residue 478 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 627 optimal weight: 2.9990 chunk 427 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 561 optimal weight: 0.8980 chunk 311 optimal weight: 4.9990 chunk 643 optimal weight: 10.0000 chunk 521 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 384 optimal weight: 20.0000 chunk 676 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f1 87 ASN B1 194 GLN ** B1 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 53 GLN ** B2 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 342 GLN W3 4 GLN ** B3 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 265 GLN ** B3 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b3 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 266 ASN ** B4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b4 342 GLN w5 58 GLN U5 66 HIS B5 194 GLN ** B5 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 342 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 63648 Z= 0.221 Angle : 0.676 13.437 86070 Z= 0.334 Chirality : 0.042 0.236 9066 Planarity : 0.005 0.104 11430 Dihedral : 5.188 67.361 8849 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.26 % Favored : 91.25 % Rotamer: Outliers : 6.89 % Allowed : 31.85 % Favored : 61.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.10), residues: 7866 helix: 1.26 (0.09), residues: 3420 sheet: -0.29 (0.16), residues: 1050 loop : -1.49 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPb4 157 HIS 0.006 0.001 HISB3 25 PHE 0.025 0.001 PHEB1 147 TYR 0.017 0.001 TYRU2 128 ARG 0.008 0.000 ARGw1 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1826 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 441 poor density : 1385 time to evaluate : 5.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 34 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: W 49 GLU cc_start: 0.9324 (tm-30) cc_final: 0.9101 (tm-30) REVERT: w 51 GLU cc_start: 0.9399 (pt0) cc_final: 0.8973 (pt0) REVERT: U 50 GLU cc_start: 0.7958 (mp0) cc_final: 0.7439 (mp0) REVERT: U 62 GLN cc_start: 0.9007 (pp30) cc_final: 0.8710 (tm-30) REVERT: B 140 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: B 342 GLN cc_start: 0.9215 (mm110) cc_final: 0.8236 (mp10) REVERT: B 393 TRP cc_start: 0.9220 (t60) cc_final: 0.8687 (t-100) REVERT: B 463 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8657 (mm-30) REVERT: b 348 ASP cc_start: 0.9089 (t0) cc_final: 0.8877 (t0) REVERT: b 356 GLN cc_start: 0.9336 (mm-40) cc_final: 0.9055 (mm-40) REVERT: b 359 LEU cc_start: 0.9764 (mm) cc_final: 0.9464 (mm) REVERT: b 411 MET cc_start: 0.9642 (mtm) cc_final: 0.9348 (mtm) REVERT: b 469 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8855 (mm-30) REVERT: W1 45 LYS cc_start: 0.9462 (mtmm) cc_final: 0.9185 (mtmm) REVERT: w1 31 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7376 (mtm-85) REVERT: w1 49 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8979 (pm20) REVERT: B1 241 GLU cc_start: 0.8401 (pp20) cc_final: 0.7793 (pp20) REVERT: B1 302 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: B1 366 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9402 (mm) REVERT: B1 380 MET cc_start: 0.8659 (mmm) cc_final: 0.8361 (mmm) REVERT: B1 386 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8345 (mmm160) REVERT: b1 61 ASP cc_start: 0.8309 (t0) cc_final: 0.8030 (t0) REVERT: b1 194 GLN cc_start: 0.9507 (OUTLIER) cc_final: 0.9124 (tp40) REVERT: w2 16 ASP cc_start: 0.9332 (t70) cc_final: 0.8999 (t70) REVERT: U2 62 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8296 (tm-30) REVERT: U2 114 ARG cc_start: 0.8814 (ptp90) cc_final: 0.8612 (ptp90) REVERT: B2 187 ARG cc_start: 0.9179 (ttm110) cc_final: 0.8884 (ttm110) REVERT: B2 346 ASP cc_start: 0.8936 (t0) cc_final: 0.8720 (t0) REVERT: B2 466 MET cc_start: 0.9541 (ttt) cc_final: 0.9332 (ttp) REVERT: b2 137 MET cc_start: 0.9618 (mmm) cc_final: 0.9276 (mmm) REVERT: b2 356 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8998 (mm-40) REVERT: b2 453 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8442 (ppp) REVERT: b2 479 CYS cc_start: 0.9387 (m) cc_final: 0.8924 (p) REVERT: f3 16 ASP cc_start: 0.8938 (t0) cc_final: 0.8645 (t0) REVERT: f3 34 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8434 (mp10) REVERT: w3 31 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7688 (mtm-85) REVERT: U3 50 GLU cc_start: 0.7903 (mp0) cc_final: 0.7393 (mp0) REVERT: U3 62 GLN cc_start: 0.8789 (pp30) cc_final: 0.8233 (pm20) REVERT: U3 64 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8603 (tt0) REVERT: B3 55 ARG cc_start: 0.9465 (OUTLIER) cc_final: 0.8254 (ttp80) REVERT: B3 334 MET cc_start: 0.9104 (mpp) cc_final: 0.8869 (mpp) REVERT: b3 339 LEU cc_start: 0.9594 (tp) cc_final: 0.9372 (tp) REVERT: b3 379 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8535 (pm20) REVERT: b3 453 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.7827 (ppp) REVERT: b3 498 MET cc_start: 0.9174 (tmm) cc_final: 0.8888 (tmm) REVERT: W4 45 LYS cc_start: 0.9594 (mtpp) cc_final: 0.9348 (mtmm) REVERT: U4 27 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7159 (m-10) REVERT: U4 50 GLU cc_start: 0.8247 (pm20) cc_final: 0.7959 (pm20) REVERT: U4 114 ARG cc_start: 0.8799 (ptp-110) cc_final: 0.8468 (ptp-110) REVERT: B4 35 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9177 (pp) REVERT: B4 131 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8925 (mttt) REVERT: B4 366 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9254 (mm) REVERT: b4 241 GLU cc_start: 0.7821 (pp20) cc_final: 0.7524 (pp20) REVERT: b4 359 LEU cc_start: 0.9815 (OUTLIER) cc_final: 0.9489 (mm) REVERT: b4 453 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8430 (ppp) REVERT: b4 469 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8878 (mm-30) REVERT: b4 477 LYS cc_start: 0.9761 (mtpp) cc_final: 0.9537 (mtpp) REVERT: U5 17 LEU cc_start: 0.9505 (tp) cc_final: 0.9165 (tp) REVERT: B5 136 MET cc_start: 0.9087 (ptm) cc_final: 0.8282 (ppp) REVERT: B5 241 GLU cc_start: 0.8448 (pp20) cc_final: 0.8235 (pp20) REVERT: B5 397 MET cc_start: 0.9280 (mmm) cc_final: 0.9040 (mmm) REVERT: b5 137 MET cc_start: 0.9589 (OUTLIER) cc_final: 0.9254 (mmm) REVERT: b5 252 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8431 (t80) REVERT: b5 453 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8153 (ppp) REVERT: b5 466 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.8154 (ppp) outliers start: 441 outliers final: 305 residues processed: 1653 average time/residue: 0.5709 time to fit residues: 1589.8009 Evaluate side-chains 1638 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1309 time to evaluate : 5.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 4 PHE Chi-restraints excluded: chain f residue 34 GLN Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain w residue 23 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 42 ASP Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 56 MET Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 110 TYR Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 134 MET Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain b residue 25 HIS Chi-restraints excluded: chain b residue 39 ASN Chi-restraints excluded: chain b residue 132 ARG Chi-restraints excluded: chain b residue 135 THR Chi-restraints excluded: chain b residue 226 LEU Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 337 ASP Chi-restraints excluded: chain b residue 339 LEU Chi-restraints excluded: chain b residue 340 ASN Chi-restraints excluded: chain b residue 358 LEU Chi-restraints excluded: chain b residue 434 SER Chi-restraints excluded: chain b residue 467 LEU Chi-restraints excluded: chain b residue 474 THR Chi-restraints excluded: chain f1 residue 4 PHE Chi-restraints excluded: chain f1 residue 28 THR Chi-restraints excluded: chain f1 residue 29 ILE Chi-restraints excluded: chain f1 residue 30 THR Chi-restraints excluded: chain f1 residue 56 VAL Chi-restraints excluded: chain f1 residue 103 LEU Chi-restraints excluded: chain f1 residue 109 VAL Chi-restraints excluded: chain W1 residue 23 VAL Chi-restraints excluded: chain W1 residue 34 GLU Chi-restraints excluded: chain W1 residue 52 VAL Chi-restraints excluded: chain w1 residue 23 VAL Chi-restraints excluded: chain w1 residue 25 THR Chi-restraints excluded: chain w1 residue 29 ASP Chi-restraints excluded: chain w1 residue 31 ARG Chi-restraints excluded: chain w1 residue 33 VAL Chi-restraints excluded: chain w1 residue 38 THR Chi-restraints excluded: chain w1 residue 49 GLU Chi-restraints excluded: chain w1 residue 51 GLU Chi-restraints excluded: chain w1 residue 53 GLN Chi-restraints excluded: chain U1 residue 44 VAL Chi-restraints excluded: chain U1 residue 52 THR Chi-restraints excluded: chain U1 residue 110 TYR Chi-restraints excluded: chain U1 residue 117 ASP Chi-restraints excluded: chain B1 residue 25 HIS Chi-restraints excluded: chain B1 residue 54 THR Chi-restraints excluded: chain B1 residue 76 LEU Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 219 TRP Chi-restraints excluded: chain B1 residue 269 LEU Chi-restraints excluded: chain B1 residue 302 GLU Chi-restraints excluded: chain B1 residue 325 LEU Chi-restraints excluded: chain B1 residue 333 LEU Chi-restraints excluded: chain B1 residue 337 ASP Chi-restraints excluded: chain B1 residue 355 GLU Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 386 ARG Chi-restraints excluded: chain B1 residue 461 VAL Chi-restraints excluded: chain B1 residue 474 THR Chi-restraints excluded: chain B1 residue 497 THR Chi-restraints excluded: chain b1 residue 31 PHE Chi-restraints excluded: chain b1 residue 39 ASN Chi-restraints excluded: chain b1 residue 45 VAL Chi-restraints excluded: chain b1 residue 133 THR Chi-restraints excluded: chain b1 residue 159 THR Chi-restraints excluded: chain b1 residue 185 ASP Chi-restraints excluded: chain b1 residue 186 SER Chi-restraints excluded: chain b1 residue 194 GLN Chi-restraints excluded: chain b1 residue 226 LEU Chi-restraints excluded: chain b1 residue 269 LEU Chi-restraints excluded: chain b1 residue 273 ILE Chi-restraints excluded: chain b1 residue 357 SER Chi-restraints excluded: chain b1 residue 358 LEU Chi-restraints excluded: chain b1 residue 413 LEU Chi-restraints excluded: chain b1 residue 425 VAL Chi-restraints excluded: chain b1 residue 463 GLU Chi-restraints excluded: chain b1 residue 478 GLU Chi-restraints excluded: chain f2 residue 4 PHE Chi-restraints excluded: chain f2 residue 7 LEU Chi-restraints excluded: chain f2 residue 42 VAL Chi-restraints excluded: chain f2 residue 56 VAL Chi-restraints excluded: chain f2 residue 67 VAL Chi-restraints excluded: chain f2 residue 109 VAL Chi-restraints excluded: chain W2 residue 7 LEU Chi-restraints excluded: chain W2 residue 23 VAL Chi-restraints excluded: chain W2 residue 34 GLU Chi-restraints excluded: chain W2 residue 41 SER Chi-restraints excluded: chain W2 residue 42 ASP Chi-restraints excluded: chain W2 residue 50 LEU Chi-restraints excluded: chain w2 residue 19 THR Chi-restraints excluded: chain w2 residue 23 VAL Chi-restraints excluded: chain w2 residue 39 SER Chi-restraints excluded: chain w2 residue 52 VAL Chi-restraints excluded: chain U2 residue 4 MET Chi-restraints excluded: chain U2 residue 22 THR Chi-restraints excluded: chain U2 residue 30 ARG Chi-restraints excluded: chain U2 residue 33 VAL Chi-restraints excluded: chain U2 residue 42 VAL Chi-restraints excluded: chain U2 residue 52 THR Chi-restraints excluded: chain U2 residue 106 VAL Chi-restraints excluded: chain U2 residue 110 TYR Chi-restraints excluded: chain U2 residue 123 SER Chi-restraints excluded: chain B2 residue 25 HIS Chi-restraints excluded: chain B2 residue 35 LEU Chi-restraints excluded: chain B2 residue 43 GLU Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 82 VAL Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 215 MET Chi-restraints excluded: chain B2 residue 252 TYR Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 341 LEU Chi-restraints excluded: chain B2 residue 358 LEU Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 366 LEU Chi-restraints excluded: chain B2 residue 405 SER Chi-restraints excluded: chain B2 residue 425 VAL Chi-restraints excluded: chain B2 residue 455 ILE Chi-restraints excluded: chain B2 residue 467 LEU Chi-restraints excluded: chain B2 residue 474 THR Chi-restraints excluded: chain b2 residue 25 HIS Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 109 ARG Chi-restraints excluded: chain b2 residue 132 ARG Chi-restraints excluded: chain b2 residue 171 MET Chi-restraints excluded: chain b2 residue 202 LEU Chi-restraints excluded: chain b2 residue 226 LEU Chi-restraints excluded: chain b2 residue 240 VAL Chi-restraints excluded: chain b2 residue 269 LEU Chi-restraints excluded: chain b2 residue 339 LEU Chi-restraints excluded: chain b2 residue 340 ASN Chi-restraints excluded: chain b2 residue 358 LEU Chi-restraints excluded: chain b2 residue 425 VAL Chi-restraints excluded: chain b2 residue 453 MET Chi-restraints excluded: chain b2 residue 456 ASP Chi-restraints excluded: chain b2 residue 466 MET Chi-restraints excluded: chain f3 residue 4 PHE Chi-restraints excluded: chain f3 residue 25 THR Chi-restraints excluded: chain f3 residue 28 THR Chi-restraints excluded: chain f3 residue 34 GLN Chi-restraints excluded: chain f3 residue 56 VAL Chi-restraints excluded: chain f3 residue 69 THR Chi-restraints excluded: chain f3 residue 77 ARG Chi-restraints excluded: chain f3 residue 79 ASP Chi-restraints excluded: chain W3 residue 23 VAL Chi-restraints excluded: chain W3 residue 26 VAL Chi-restraints excluded: chain W3 residue 39 SER Chi-restraints excluded: chain w3 residue 23 VAL Chi-restraints excluded: chain w3 residue 25 THR Chi-restraints excluded: chain w3 residue 31 ARG Chi-restraints excluded: chain w3 residue 33 VAL Chi-restraints excluded: chain w3 residue 39 SER Chi-restraints excluded: chain U3 residue 9 LEU Chi-restraints excluded: chain U3 residue 17 LEU Chi-restraints excluded: chain U3 residue 52 THR Chi-restraints excluded: chain U3 residue 74 GLN Chi-restraints excluded: chain U3 residue 110 TYR Chi-restraints excluded: chain U3 residue 117 ASP Chi-restraints excluded: chain U3 residue 122 SER Chi-restraints excluded: chain U3 residue 123 SER Chi-restraints excluded: chain B3 residue 50 LEU Chi-restraints excluded: chain B3 residue 55 ARG Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 121 ASP Chi-restraints excluded: chain B3 residue 123 CYS Chi-restraints excluded: chain B3 residue 125 CYS Chi-restraints excluded: chain B3 residue 126 ILE Chi-restraints excluded: chain B3 residue 132 ARG Chi-restraints excluded: chain B3 residue 172 VAL Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 258 MET Chi-restraints excluded: chain B3 residue 283 GLU Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 446 ASP Chi-restraints excluded: chain B3 residue 474 THR Chi-restraints excluded: chain b3 residue 39 ASN Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 133 THR Chi-restraints excluded: chain b3 residue 194 GLN Chi-restraints excluded: chain b3 residue 195 ILE Chi-restraints excluded: chain b3 residue 215 MET Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 337 ASP Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 358 LEU Chi-restraints excluded: chain b3 residue 379 GLN Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 425 VAL Chi-restraints excluded: chain b3 residue 434 SER Chi-restraints excluded: chain b3 residue 453 MET Chi-restraints excluded: chain b3 residue 456 ASP Chi-restraints excluded: chain b3 residue 478 GLU Chi-restraints excluded: chain f4 residue 25 THR Chi-restraints excluded: chain f4 residue 28 THR Chi-restraints excluded: chain f4 residue 56 VAL Chi-restraints excluded: chain f4 residue 58 VAL Chi-restraints excluded: chain f4 residue 67 VAL Chi-restraints excluded: chain f4 residue 69 THR Chi-restraints excluded: chain f4 residue 90 VAL Chi-restraints excluded: chain f4 residue 109 VAL Chi-restraints excluded: chain W4 residue 7 LEU Chi-restraints excluded: chain W4 residue 23 VAL Chi-restraints excluded: chain W4 residue 34 GLU Chi-restraints excluded: chain W4 residue 42 ASP Chi-restraints excluded: chain w4 residue 25 THR Chi-restraints excluded: chain w4 residue 38 THR Chi-restraints excluded: chain w4 residue 39 SER Chi-restraints excluded: chain U4 residue 27 PHE Chi-restraints excluded: chain U4 residue 42 VAL Chi-restraints excluded: chain U4 residue 52 THR Chi-restraints excluded: chain U4 residue 69 VAL Chi-restraints excluded: chain U4 residue 91 VAL Chi-restraints excluded: chain U4 residue 110 TYR Chi-restraints excluded: chain U4 residue 117 ASP Chi-restraints excluded: chain U4 residue 122 SER Chi-restraints excluded: chain B4 residue 35 LEU Chi-restraints excluded: chain B4 residue 54 THR Chi-restraints excluded: chain B4 residue 82 VAL Chi-restraints excluded: chain B4 residue 125 CYS Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 173 SER Chi-restraints excluded: chain B4 residue 188 ASN Chi-restraints excluded: chain B4 residue 206 VAL Chi-restraints excluded: chain B4 residue 262 ASP Chi-restraints excluded: chain B4 residue 287 ASP Chi-restraints excluded: chain B4 residue 292 MET Chi-restraints excluded: chain B4 residue 340 ASN Chi-restraints excluded: chain B4 residue 341 LEU Chi-restraints excluded: chain B4 residue 358 LEU Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 453 MET Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 226 LEU Chi-restraints excluded: chain b4 residue 240 VAL Chi-restraints excluded: chain b4 residue 273 ILE Chi-restraints excluded: chain b4 residue 359 LEU Chi-restraints excluded: chain b4 residue 453 MET Chi-restraints excluded: chain f5 residue 4 PHE Chi-restraints excluded: chain f5 residue 29 ILE Chi-restraints excluded: chain f5 residue 42 VAL Chi-restraints excluded: chain f5 residue 56 VAL Chi-restraints excluded: chain f5 residue 69 THR Chi-restraints excluded: chain f5 residue 109 VAL Chi-restraints excluded: chain W5 residue 23 VAL Chi-restraints excluded: chain W5 residue 38 THR Chi-restraints excluded: chain W5 residue 39 SER Chi-restraints excluded: chain W5 residue 51 GLU Chi-restraints excluded: chain w5 residue 23 VAL Chi-restraints excluded: chain w5 residue 39 SER Chi-restraints excluded: chain U5 residue 20 HIS Chi-restraints excluded: chain U5 residue 30 ARG Chi-restraints excluded: chain U5 residue 52 THR Chi-restraints excluded: chain U5 residue 67 ILE Chi-restraints excluded: chain U5 residue 110 TYR Chi-restraints excluded: chain U5 residue 117 ASP Chi-restraints excluded: chain U5 residue 122 SER Chi-restraints excluded: chain B5 residue 25 HIS Chi-restraints excluded: chain B5 residue 35 LEU Chi-restraints excluded: chain B5 residue 54 THR Chi-restraints excluded: chain B5 residue 126 ILE Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 206 VAL Chi-restraints excluded: chain B5 residue 252 TYR Chi-restraints excluded: chain B5 residue 269 LEU Chi-restraints excluded: chain B5 residue 284 SER Chi-restraints excluded: chain B5 residue 340 ASN Chi-restraints excluded: chain B5 residue 343 THR Chi-restraints excluded: chain B5 residue 358 LEU Chi-restraints excluded: chain B5 residue 359 LEU Chi-restraints excluded: chain B5 residue 425 VAL Chi-restraints excluded: chain B5 residue 434 SER Chi-restraints excluded: chain B5 residue 467 LEU Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 137 MET Chi-restraints excluded: chain b5 residue 202 LEU Chi-restraints excluded: chain b5 residue 206 VAL Chi-restraints excluded: chain b5 residue 218 LYS Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 254 VAL Chi-restraints excluded: chain b5 residue 269 LEU Chi-restraints excluded: chain b5 residue 333 LEU Chi-restraints excluded: chain b5 residue 355 GLU Chi-restraints excluded: chain b5 residue 357 SER Chi-restraints excluded: chain b5 residue 358 LEU Chi-restraints excluded: chain b5 residue 362 ILE Chi-restraints excluded: chain b5 residue 425 VAL Chi-restraints excluded: chain b5 residue 453 MET Chi-restraints excluded: chain b5 residue 456 ASP Chi-restraints excluded: chain b5 residue 463 GLU Chi-restraints excluded: chain b5 residue 466 MET Chi-restraints excluded: chain b5 residue 478 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 253 optimal weight: 7.9990 chunk 678 optimal weight: 30.0000 chunk 149 optimal weight: 9.9990 chunk 442 optimal weight: 7.9990 chunk 186 optimal weight: 0.0980 chunk 754 optimal weight: 8.9990 chunk 626 optimal weight: 10.0000 chunk 349 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 396 optimal weight: 20.0000 overall best weight: 6.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 265 GLN ** b 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w1 53 GLN B1 342 GLN ** B1 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 356 GLN ** b1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 492 GLN ** f2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 53 GLN ** B2 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 342 GLN ** W3 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 25 HIS ** B3 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b3 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b3 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b3 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 342 GLN U4 20 HIS B4 57 ASN ** B4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b4 145 HIS b4 342 GLN w5 58 GLN ** B5 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 342 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 63648 Z= 0.348 Angle : 0.713 13.309 86070 Z= 0.359 Chirality : 0.043 0.243 9066 Planarity : 0.005 0.105 11430 Dihedral : 5.265 71.880 8849 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.66 % Favored : 90.87 % Rotamer: Outliers : 7.89 % Allowed : 31.83 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.10), residues: 7866 helix: 1.18 (0.09), residues: 3420 sheet: -0.30 (0.16), residues: 1044 loop : -1.54 (0.11), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRPB5 393 HIS 0.007 0.001 HIS b 332 PHE 0.029 0.001 PHEU4 39 TYR 0.021 0.002 TYRU2 128 ARG 0.011 0.000 ARGB5 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1803 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 505 poor density : 1298 time to evaluate : 5.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 34 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: W 49 GLU cc_start: 0.9325 (tm-30) cc_final: 0.9109 (tm-30) REVERT: w 51 GLU cc_start: 0.9430 (pt0) cc_final: 0.9022 (pt0) REVERT: U 50 GLU cc_start: 0.8129 (mp0) cc_final: 0.7611 (mp0) REVERT: U 62 GLN cc_start: 0.9056 (pp30) cc_final: 0.8751 (tm-30) REVERT: B 140 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: B 265 GLN cc_start: 0.9234 (mm110) cc_final: 0.9033 (mm-40) REVERT: B 463 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8750 (mm-30) REVERT: b 359 LEU cc_start: 0.9786 (mm) cc_final: 0.9516 (mm) REVERT: b 469 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8870 (mm-30) REVERT: w1 31 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7299 (mtm-85) REVERT: w1 49 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8975 (pm20) REVERT: B1 140 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8588 (tp30) REVERT: B1 241 GLU cc_start: 0.8361 (pp20) cc_final: 0.7754 (pp20) REVERT: B1 302 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: B1 366 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9433 (mm) REVERT: B1 380 MET cc_start: 0.8747 (mmm) cc_final: 0.8429 (mmm) REVERT: b1 61 ASP cc_start: 0.8304 (t0) cc_final: 0.8000 (t0) REVERT: b1 194 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.9015 (tp40) REVERT: b1 397 MET cc_start: 0.9069 (mmm) cc_final: 0.8818 (mmm) REVERT: b1 439 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8615 (mtt180) REVERT: w2 16 ASP cc_start: 0.9366 (t70) cc_final: 0.9133 (t0) REVERT: U2 62 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: B2 187 ARG cc_start: 0.9225 (ttm110) cc_final: 0.8914 (ttm110) REVERT: B2 346 ASP cc_start: 0.8979 (t0) cc_final: 0.8762 (t70) REVERT: B2 466 MET cc_start: 0.9564 (ttt) cc_final: 0.9360 (ttp) REVERT: b2 137 MET cc_start: 0.9646 (mmm) cc_final: 0.9277 (mmm) REVERT: b2 356 GLN cc_start: 0.9391 (mm-40) cc_final: 0.8991 (mm-40) REVERT: b2 411 MET cc_start: 0.9689 (mtt) cc_final: 0.9434 (mtp) REVERT: b2 453 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8621 (ppp) REVERT: b2 460 GLU cc_start: 0.9023 (tp30) cc_final: 0.8696 (tp30) REVERT: b2 479 CYS cc_start: 0.9399 (m) cc_final: 0.8937 (p) REVERT: f3 16 ASP cc_start: 0.8921 (t0) cc_final: 0.8655 (t0) REVERT: f3 34 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8359 (mp10) REVERT: U3 50 GLU cc_start: 0.8004 (mp0) cc_final: 0.7484 (mp0) REVERT: U3 62 GLN cc_start: 0.8832 (pp30) cc_final: 0.8245 (pm20) REVERT: U3 64 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8621 (tt0) REVERT: U3 120 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9335 (mm) REVERT: B3 55 ARG cc_start: 0.9532 (OUTLIER) cc_final: 0.8359 (ttp80) REVERT: B3 217 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: B3 393 TRP cc_start: 0.9222 (t60) cc_final: 0.8649 (t-100) REVERT: b3 242 ASP cc_start: 0.8329 (t70) cc_final: 0.8125 (p0) REVERT: b3 339 LEU cc_start: 0.9590 (tp) cc_final: 0.9369 (tp) REVERT: b3 379 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8593 (pm20) REVERT: b3 453 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7853 (ppp) REVERT: b3 498 MET cc_start: 0.9204 (tmm) cc_final: 0.8924 (tmm) REVERT: W4 21 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.8869 (mmmm) REVERT: U4 114 ARG cc_start: 0.8775 (ptp-110) cc_final: 0.8496 (ptp-110) REVERT: B4 35 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9268 (pp) REVERT: B4 131 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8965 (mttt) REVERT: B4 366 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9269 (mm) REVERT: B4 463 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8797 (mm-30) REVERT: b4 61 ASP cc_start: 0.8334 (t0) cc_final: 0.8128 (t0) REVERT: b4 157 TRP cc_start: 0.8055 (OUTLIER) cc_final: 0.7804 (m100) REVERT: b4 241 GLU cc_start: 0.7966 (pp20) cc_final: 0.7611 (pp20) REVERT: b4 469 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8903 (mm-30) REVERT: b4 472 LEU cc_start: 0.9517 (mt) cc_final: 0.9197 (tt) REVERT: b4 477 LYS cc_start: 0.9779 (mtpp) cc_final: 0.9534 (mtpp) REVERT: W5 3 ARG cc_start: 0.9329 (mmp80) cc_final: 0.9036 (mmp80) REVERT: U5 64 GLU cc_start: 0.8993 (tt0) cc_final: 0.8571 (tt0) REVERT: B5 241 GLU cc_start: 0.8460 (pp20) cc_final: 0.8119 (pp20) REVERT: B5 397 MET cc_start: 0.9307 (mmm) cc_final: 0.9102 (mmm) REVERT: b5 55 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7549 (ttp80) REVERT: b5 137 MET cc_start: 0.9624 (OUTLIER) cc_final: 0.9287 (mmm) REVERT: b5 252 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8544 (t80) REVERT: b5 466 MET cc_start: 0.9470 (OUTLIER) cc_final: 0.8538 (ppp) outliers start: 505 outliers final: 373 residues processed: 1618 average time/residue: 0.5730 time to fit residues: 1569.5887 Evaluate side-chains 1668 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 399 poor density : 1269 time to evaluate : 5.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 4 PHE Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 34 GLN Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 51 GLU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain w residue 23 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 42 ASP Chi-restraints excluded: chain w residue 47 ILE Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 56 MET Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 110 TYR Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain b residue 25 HIS Chi-restraints excluded: chain b residue 39 ASN Chi-restraints excluded: chain b residue 132 ARG Chi-restraints excluded: chain b residue 135 THR Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 218 LYS Chi-restraints excluded: chain b residue 226 LEU Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 255 MET Chi-restraints excluded: chain b residue 273 ILE Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 337 ASP Chi-restraints excluded: chain b residue 339 LEU Chi-restraints excluded: chain b residue 358 LEU Chi-restraints excluded: chain b residue 467 LEU Chi-restraints excluded: chain b residue 474 THR Chi-restraints excluded: chain b residue 478 GLU Chi-restraints excluded: chain f1 residue 4 PHE Chi-restraints excluded: chain f1 residue 9 ASP Chi-restraints excluded: chain f1 residue 25 THR Chi-restraints excluded: chain f1 residue 28 THR Chi-restraints excluded: chain f1 residue 29 ILE Chi-restraints excluded: chain f1 residue 30 THR Chi-restraints excluded: chain f1 residue 56 VAL Chi-restraints excluded: chain f1 residue 58 VAL Chi-restraints excluded: chain f1 residue 70 ASP Chi-restraints excluded: chain f1 residue 103 LEU Chi-restraints excluded: chain f1 residue 109 VAL Chi-restraints excluded: chain W1 residue 23 VAL Chi-restraints excluded: chain W1 residue 34 GLU Chi-restraints excluded: chain W1 residue 39 SER Chi-restraints excluded: chain W1 residue 52 VAL Chi-restraints excluded: chain w1 residue 23 VAL Chi-restraints excluded: chain w1 residue 25 THR Chi-restraints excluded: chain w1 residue 29 ASP Chi-restraints excluded: chain w1 residue 31 ARG Chi-restraints excluded: chain w1 residue 33 VAL Chi-restraints excluded: chain w1 residue 38 THR Chi-restraints excluded: chain w1 residue 39 SER Chi-restraints excluded: chain w1 residue 49 GLU Chi-restraints excluded: chain w1 residue 51 GLU Chi-restraints excluded: chain w1 residue 53 GLN Chi-restraints excluded: chain U1 residue 44 VAL Chi-restraints excluded: chain U1 residue 52 THR Chi-restraints excluded: chain U1 residue 110 TYR Chi-restraints excluded: chain B1 residue 25 HIS Chi-restraints excluded: chain B1 residue 54 THR Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 140 GLU Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 219 TRP Chi-restraints excluded: chain B1 residue 269 LEU Chi-restraints excluded: chain B1 residue 302 GLU Chi-restraints excluded: chain B1 residue 325 LEU Chi-restraints excluded: chain B1 residue 333 LEU Chi-restraints excluded: chain B1 residue 337 ASP Chi-restraints excluded: chain B1 residue 355 GLU Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 386 ARG Chi-restraints excluded: chain B1 residue 468 ILE Chi-restraints excluded: chain B1 residue 474 THR Chi-restraints excluded: chain B1 residue 497 THR Chi-restraints excluded: chain b1 residue 31 PHE Chi-restraints excluded: chain b1 residue 39 ASN Chi-restraints excluded: chain b1 residue 45 VAL Chi-restraints excluded: chain b1 residue 50 LEU Chi-restraints excluded: chain b1 residue 133 THR Chi-restraints excluded: chain b1 residue 144 MET Chi-restraints excluded: chain b1 residue 159 THR Chi-restraints excluded: chain b1 residue 173 SER Chi-restraints excluded: chain b1 residue 185 ASP Chi-restraints excluded: chain b1 residue 186 SER Chi-restraints excluded: chain b1 residue 194 GLN Chi-restraints excluded: chain b1 residue 195 ILE Chi-restraints excluded: chain b1 residue 226 LEU Chi-restraints excluded: chain b1 residue 269 LEU Chi-restraints excluded: chain b1 residue 337 ASP Chi-restraints excluded: chain b1 residue 357 SER Chi-restraints excluded: chain b1 residue 358 LEU Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 413 LEU Chi-restraints excluded: chain b1 residue 425 VAL Chi-restraints excluded: chain b1 residue 439 ARG Chi-restraints excluded: chain b1 residue 463 GLU Chi-restraints excluded: chain b1 residue 478 GLU Chi-restraints excluded: chain f2 residue 4 PHE Chi-restraints excluded: chain f2 residue 7 LEU Chi-restraints excluded: chain f2 residue 19 ILE Chi-restraints excluded: chain f2 residue 56 VAL Chi-restraints excluded: chain f2 residue 67 VAL Chi-restraints excluded: chain f2 residue 109 VAL Chi-restraints excluded: chain W2 residue 23 VAL Chi-restraints excluded: chain W2 residue 34 GLU Chi-restraints excluded: chain W2 residue 42 ASP Chi-restraints excluded: chain W2 residue 47 ILE Chi-restraints excluded: chain W2 residue 50 LEU Chi-restraints excluded: chain W2 residue 51 GLU Chi-restraints excluded: chain w2 residue 19 THR Chi-restraints excluded: chain w2 residue 23 VAL Chi-restraints excluded: chain w2 residue 39 SER Chi-restraints excluded: chain w2 residue 52 VAL Chi-restraints excluded: chain w2 residue 57 THR Chi-restraints excluded: chain U2 residue 4 MET Chi-restraints excluded: chain U2 residue 22 THR Chi-restraints excluded: chain U2 residue 30 ARG Chi-restraints excluded: chain U2 residue 33 VAL Chi-restraints excluded: chain U2 residue 42 VAL Chi-restraints excluded: chain U2 residue 52 THR Chi-restraints excluded: chain U2 residue 62 GLN Chi-restraints excluded: chain U2 residue 74 GLN Chi-restraints excluded: chain U2 residue 106 VAL Chi-restraints excluded: chain U2 residue 110 TYR Chi-restraints excluded: chain U2 residue 114 ARG Chi-restraints excluded: chain U2 residue 122 SER Chi-restraints excluded: chain U2 residue 123 SER Chi-restraints excluded: chain B2 residue 25 HIS Chi-restraints excluded: chain B2 residue 43 GLU Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 76 LEU Chi-restraints excluded: chain B2 residue 82 VAL Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 215 MET Chi-restraints excluded: chain B2 residue 252 TYR Chi-restraints excluded: chain B2 residue 340 ASN Chi-restraints excluded: chain B2 residue 341 LEU Chi-restraints excluded: chain B2 residue 358 LEU Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 366 LEU Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain B2 residue 405 SER Chi-restraints excluded: chain B2 residue 425 VAL Chi-restraints excluded: chain B2 residue 455 ILE Chi-restraints excluded: chain B2 residue 467 LEU Chi-restraints excluded: chain B2 residue 474 THR Chi-restraints excluded: chain B2 residue 484 ASP Chi-restraints excluded: chain b2 residue 25 HIS Chi-restraints excluded: chain b2 residue 39 ASN Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 109 ARG Chi-restraints excluded: chain b2 residue 132 ARG Chi-restraints excluded: chain b2 residue 171 MET Chi-restraints excluded: chain b2 residue 195 ILE Chi-restraints excluded: chain b2 residue 202 LEU Chi-restraints excluded: chain b2 residue 226 LEU Chi-restraints excluded: chain b2 residue 240 VAL Chi-restraints excluded: chain b2 residue 269 LEU Chi-restraints excluded: chain b2 residue 339 LEU Chi-restraints excluded: chain b2 residue 358 LEU Chi-restraints excluded: chain b2 residue 425 VAL Chi-restraints excluded: chain b2 residue 453 MET Chi-restraints excluded: chain b2 residue 456 ASP Chi-restraints excluded: chain b2 residue 466 MET Chi-restraints excluded: chain f3 residue 4 PHE Chi-restraints excluded: chain f3 residue 25 THR Chi-restraints excluded: chain f3 residue 28 THR Chi-restraints excluded: chain f3 residue 34 GLN Chi-restraints excluded: chain f3 residue 56 VAL Chi-restraints excluded: chain f3 residue 69 THR Chi-restraints excluded: chain f3 residue 77 ARG Chi-restraints excluded: chain f3 residue 79 ASP Chi-restraints excluded: chain f3 residue 109 VAL Chi-restraints excluded: chain W3 residue 23 VAL Chi-restraints excluded: chain W3 residue 26 VAL Chi-restraints excluded: chain W3 residue 39 SER Chi-restraints excluded: chain w3 residue 23 VAL Chi-restraints excluded: chain w3 residue 25 THR Chi-restraints excluded: chain w3 residue 33 VAL Chi-restraints excluded: chain w3 residue 34 GLU Chi-restraints excluded: chain w3 residue 39 SER Chi-restraints excluded: chain U3 residue 17 LEU Chi-restraints excluded: chain U3 residue 20 HIS Chi-restraints excluded: chain U3 residue 52 THR Chi-restraints excluded: chain U3 residue 74 GLN Chi-restraints excluded: chain U3 residue 110 TYR Chi-restraints excluded: chain U3 residue 120 LEU Chi-restraints excluded: chain U3 residue 122 SER Chi-restraints excluded: chain U3 residue 123 SER Chi-restraints excluded: chain B3 residue 25 HIS Chi-restraints excluded: chain B3 residue 50 LEU Chi-restraints excluded: chain B3 residue 55 ARG Chi-restraints excluded: chain B3 residue 63 LEU Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 84 SER Chi-restraints excluded: chain B3 residue 121 ASP Chi-restraints excluded: chain B3 residue 123 CYS Chi-restraints excluded: chain B3 residue 125 CYS Chi-restraints excluded: chain B3 residue 126 ILE Chi-restraints excluded: chain B3 residue 132 ARG Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 217 GLN Chi-restraints excluded: chain B3 residue 274 VAL Chi-restraints excluded: chain B3 residue 283 GLU Chi-restraints excluded: chain B3 residue 340 ASN Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 446 ASP Chi-restraints excluded: chain B3 residue 474 THR Chi-restraints excluded: chain B3 residue 484 ASP Chi-restraints excluded: chain b3 residue 39 ASN Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 50 LEU Chi-restraints excluded: chain b3 residue 133 THR Chi-restraints excluded: chain b3 residue 136 MET Chi-restraints excluded: chain b3 residue 159 THR Chi-restraints excluded: chain b3 residue 194 GLN Chi-restraints excluded: chain b3 residue 195 ILE Chi-restraints excluded: chain b3 residue 206 VAL Chi-restraints excluded: chain b3 residue 215 MET Chi-restraints excluded: chain b3 residue 218 LYS Chi-restraints excluded: chain b3 residue 255 MET Chi-restraints excluded: chain b3 residue 337 ASP Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 358 LEU Chi-restraints excluded: chain b3 residue 379 GLN Chi-restraints excluded: chain b3 residue 381 SER Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 425 VAL Chi-restraints excluded: chain b3 residue 453 MET Chi-restraints excluded: chain b3 residue 456 ASP Chi-restraints excluded: chain b3 residue 463 GLU Chi-restraints excluded: chain b3 residue 478 GLU Chi-restraints excluded: chain f4 residue 19 ILE Chi-restraints excluded: chain f4 residue 25 THR Chi-restraints excluded: chain f4 residue 29 ILE Chi-restraints excluded: chain f4 residue 33 GLU Chi-restraints excluded: chain f4 residue 56 VAL Chi-restraints excluded: chain f4 residue 58 VAL Chi-restraints excluded: chain f4 residue 64 SER Chi-restraints excluded: chain f4 residue 67 VAL Chi-restraints excluded: chain f4 residue 69 THR Chi-restraints excluded: chain f4 residue 90 VAL Chi-restraints excluded: chain f4 residue 109 VAL Chi-restraints excluded: chain W4 residue 7 LEU Chi-restraints excluded: chain W4 residue 21 LYS Chi-restraints excluded: chain W4 residue 23 VAL Chi-restraints excluded: chain W4 residue 34 GLU Chi-restraints excluded: chain W4 residue 39 SER Chi-restraints excluded: chain W4 residue 42 ASP Chi-restraints excluded: chain w4 residue 17 LEU Chi-restraints excluded: chain w4 residue 23 VAL Chi-restraints excluded: chain w4 residue 25 THR Chi-restraints excluded: chain w4 residue 38 THR Chi-restraints excluded: chain w4 residue 39 SER Chi-restraints excluded: chain U4 residue 19 LYS Chi-restraints excluded: chain U4 residue 20 HIS Chi-restraints excluded: chain U4 residue 22 THR Chi-restraints excluded: chain U4 residue 42 VAL Chi-restraints excluded: chain U4 residue 52 THR Chi-restraints excluded: chain U4 residue 69 VAL Chi-restraints excluded: chain U4 residue 91 VAL Chi-restraints excluded: chain U4 residue 92 MET Chi-restraints excluded: chain U4 residue 110 TYR Chi-restraints excluded: chain U4 residue 117 ASP Chi-restraints excluded: chain U4 residue 122 SER Chi-restraints excluded: chain B4 residue 35 LEU Chi-restraints excluded: chain B4 residue 50 LEU Chi-restraints excluded: chain B4 residue 54 THR Chi-restraints excluded: chain B4 residue 82 VAL Chi-restraints excluded: chain B4 residue 125 CYS Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 144 MET Chi-restraints excluded: chain B4 residue 173 SER Chi-restraints excluded: chain B4 residue 188 ASN Chi-restraints excluded: chain B4 residue 206 VAL Chi-restraints excluded: chain B4 residue 269 LEU Chi-restraints excluded: chain B4 residue 287 ASP Chi-restraints excluded: chain B4 residue 292 MET Chi-restraints excluded: chain B4 residue 340 ASN Chi-restraints excluded: chain B4 residue 341 LEU Chi-restraints excluded: chain B4 residue 355 GLU Chi-restraints excluded: chain B4 residue 357 SER Chi-restraints excluded: chain B4 residue 358 LEU Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 381 SER Chi-restraints excluded: chain B4 residue 392 SER Chi-restraints excluded: chain B4 residue 448 ILE Chi-restraints excluded: chain B4 residue 453 MET Chi-restraints excluded: chain B4 residue 455 ILE Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 132 ARG Chi-restraints excluded: chain b4 residue 157 TRP Chi-restraints excluded: chain b4 residue 226 LEU Chi-restraints excluded: chain b4 residue 240 VAL Chi-restraints excluded: chain b4 residue 273 ILE Chi-restraints excluded: chain b4 residue 337 ASP Chi-restraints excluded: chain b4 residue 340 ASN Chi-restraints excluded: chain f5 residue 4 PHE Chi-restraints excluded: chain f5 residue 29 ILE Chi-restraints excluded: chain f5 residue 30 THR Chi-restraints excluded: chain f5 residue 42 VAL Chi-restraints excluded: chain f5 residue 56 VAL Chi-restraints excluded: chain f5 residue 69 THR Chi-restraints excluded: chain f5 residue 109 VAL Chi-restraints excluded: chain W5 residue 23 VAL Chi-restraints excluded: chain W5 residue 38 THR Chi-restraints excluded: chain W5 residue 39 SER Chi-restraints excluded: chain W5 residue 51 GLU Chi-restraints excluded: chain W5 residue 57 THR Chi-restraints excluded: chain w5 residue 23 VAL Chi-restraints excluded: chain w5 residue 39 SER Chi-restraints excluded: chain U5 residue 20 HIS Chi-restraints excluded: chain U5 residue 30 ARG Chi-restraints excluded: chain U5 residue 38 ASP Chi-restraints excluded: chain U5 residue 52 THR Chi-restraints excluded: chain U5 residue 67 ILE Chi-restraints excluded: chain U5 residue 75 VAL Chi-restraints excluded: chain U5 residue 110 TYR Chi-restraints excluded: chain U5 residue 117 ASP Chi-restraints excluded: chain U5 residue 122 SER Chi-restraints excluded: chain B5 residue 25 HIS Chi-restraints excluded: chain B5 residue 35 LEU Chi-restraints excluded: chain B5 residue 54 THR Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 126 ILE Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 202 LEU Chi-restraints excluded: chain B5 residue 206 VAL Chi-restraints excluded: chain B5 residue 252 TYR Chi-restraints excluded: chain B5 residue 269 LEU Chi-restraints excluded: chain B5 residue 284 SER Chi-restraints excluded: chain B5 residue 340 ASN Chi-restraints excluded: chain B5 residue 358 LEU Chi-restraints excluded: chain B5 residue 359 LEU Chi-restraints excluded: chain B5 residue 425 VAL Chi-restraints excluded: chain B5 residue 434 SER Chi-restraints excluded: chain B5 residue 455 ILE Chi-restraints excluded: chain B5 residue 467 LEU Chi-restraints excluded: chain B5 residue 474 THR Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 55 ARG Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 137 MET Chi-restraints excluded: chain b5 residue 159 THR Chi-restraints excluded: chain b5 residue 202 LEU Chi-restraints excluded: chain b5 residue 206 VAL Chi-restraints excluded: chain b5 residue 218 LYS Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 254 VAL Chi-restraints excluded: chain b5 residue 269 LEU Chi-restraints excluded: chain b5 residue 333 LEU Chi-restraints excluded: chain b5 residue 355 GLU Chi-restraints excluded: chain b5 residue 357 SER Chi-restraints excluded: chain b5 residue 358 LEU Chi-restraints excluded: chain b5 residue 362 ILE Chi-restraints excluded: chain b5 residue 424 VAL Chi-restraints excluded: chain b5 residue 425 VAL Chi-restraints excluded: chain b5 residue 456 ASP Chi-restraints excluded: chain b5 residue 466 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 727 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 429 optimal weight: 9.9990 chunk 551 optimal weight: 0.9980 chunk 427 optimal weight: 0.7980 chunk 635 optimal weight: 10.0000 chunk 421 optimal weight: 10.0000 chunk 751 optimal weight: 8.9990 chunk 470 optimal weight: 10.0000 chunk 458 optimal weight: 0.7980 chunk 347 optimal weight: 0.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN b 52 ASN b 299 ASN ** W1 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 342 GLN ** B1 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f2 102 HIS ** f2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 53 GLN ** B2 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 342 GLN w3 4 GLN B3 25 HIS ** B3 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 289 GLN ** B3 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b3 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 266 ASN b3 342 GLN B4 57 ASN B4 257 GLN ** B4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b4 342 GLN w5 58 GLN ** B5 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 342 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 63648 Z= 0.196 Angle : 0.706 14.106 86070 Z= 0.344 Chirality : 0.042 0.233 9066 Planarity : 0.005 0.104 11430 Dihedral : 5.189 69.782 8849 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.30 % Favored : 91.24 % Rotamer: Outliers : 6.53 % Allowed : 33.01 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.10), residues: 7866 helix: 1.24 (0.09), residues: 3420 sheet: -0.29 (0.16), residues: 1050 loop : -1.48 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPB5 393 HIS 0.023 0.001 HISU4 20 PHE 0.027 0.001 PHEB1 147 TYR 0.021 0.001 TYRU5 110 ARG 0.009 0.000 ARG W 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1825 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 418 poor density : 1407 time to evaluate : 5.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 34 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: w 18 MET cc_start: 0.9304 (mmm) cc_final: 0.8968 (mmm) REVERT: w 51 GLU cc_start: 0.9438 (pt0) cc_final: 0.9057 (pt0) REVERT: B 140 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8262 (tm-30) REVERT: B 342 GLN cc_start: 0.9364 (mm110) cc_final: 0.8417 (mp10) REVERT: B 463 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8720 (mm-30) REVERT: b 252 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8231 (t80) REVERT: b 356 GLN cc_start: 0.9324 (mm-40) cc_final: 0.9018 (mm-40) REVERT: b 359 LEU cc_start: 0.9787 (OUTLIER) cc_final: 0.9470 (mm) REVERT: b 469 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8900 (mm-30) REVERT: b 478 GLU cc_start: 0.9624 (OUTLIER) cc_final: 0.9322 (mm-30) REVERT: w1 49 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8952 (pm20) REVERT: B1 35 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9395 (pp) REVERT: B1 241 GLU cc_start: 0.8310 (pp20) cc_final: 0.7693 (pp20) REVERT: B1 252 TYR cc_start: 0.9493 (OUTLIER) cc_final: 0.8251 (t80) REVERT: B1 302 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: B1 366 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9386 (mm) REVERT: B1 380 MET cc_start: 0.8685 (mmm) cc_final: 0.8423 (mmm) REVERT: B1 386 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8627 (mmm-85) REVERT: B1 463 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8898 (mm-30) REVERT: b1 61 ASP cc_start: 0.8200 (t0) cc_final: 0.7932 (t0) REVERT: b1 78 GLN cc_start: 0.9348 (mt0) cc_final: 0.8688 (mt0) REVERT: b1 194 GLN cc_start: 0.9502 (OUTLIER) cc_final: 0.8981 (tp40) REVERT: b1 397 MET cc_start: 0.9085 (mmm) cc_final: 0.8830 (mmm) REVERT: f2 34 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: f2 86 GLU cc_start: 0.9094 (tp30) cc_final: 0.8648 (tm-30) REVERT: w2 16 ASP cc_start: 0.9332 (t70) cc_final: 0.9037 (t70) REVERT: w2 51 GLU cc_start: 0.9196 (pt0) cc_final: 0.8918 (pt0) REVERT: U2 62 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8256 (tm-30) REVERT: U2 114 ARG cc_start: 0.8812 (ptp90) cc_final: 0.8600 (ptp90) REVERT: B2 187 ARG cc_start: 0.9235 (ttm110) cc_final: 0.8811 (ttm110) REVERT: B2 346 ASP cc_start: 0.8916 (t0) cc_final: 0.8694 (t0) REVERT: B2 463 GLU cc_start: 0.9460 (mt-10) cc_final: 0.8822 (mm-30) REVERT: B2 466 MET cc_start: 0.9561 (ttt) cc_final: 0.9078 (ttp) REVERT: b2 356 GLN cc_start: 0.9338 (mm-40) cc_final: 0.8950 (mm-40) REVERT: b2 453 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8453 (ppp) REVERT: b2 479 CYS cc_start: 0.9368 (m) cc_final: 0.8881 (p) REVERT: f3 16 ASP cc_start: 0.8928 (t0) cc_final: 0.8649 (t0) REVERT: W3 3 ARG cc_start: 0.9501 (mmp80) cc_final: 0.9293 (mmp80) REVERT: w3 31 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7664 (mtm-85) REVERT: U3 38 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7957 (t0) REVERT: U3 50 GLU cc_start: 0.7894 (mp0) cc_final: 0.7315 (mp0) REVERT: U3 62 GLN cc_start: 0.8732 (pp30) cc_final: 0.7965 (pm20) REVERT: U3 64 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8596 (tt0) REVERT: U3 120 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9404 (mm) REVERT: B3 55 ARG cc_start: 0.9460 (OUTLIER) cc_final: 0.8246 (ttp80) REVERT: B3 463 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8744 (mm-30) REVERT: b3 379 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8550 (pm20) REVERT: b3 453 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7763 (ppp) REVERT: b3 498 MET cc_start: 0.9202 (tmm) cc_final: 0.8940 (tmm) REVERT: W4 21 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8754 (mmmm) REVERT: W4 45 LYS cc_start: 0.9590 (mtpp) cc_final: 0.9346 (mtmm) REVERT: U4 27 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7051 (m-10) REVERT: U4 114 ARG cc_start: 0.8639 (ptp-110) cc_final: 0.8307 (ptp-110) REVERT: B4 35 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9120 (pp) REVERT: B4 366 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9234 (mm) REVERT: B4 463 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8788 (mm-30) REVERT: b4 359 LEU cc_start: 0.9753 (mm) cc_final: 0.9550 (mm) REVERT: b4 469 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8871 (mm-30) REVERT: b4 477 LYS cc_start: 0.9768 (mtpp) cc_final: 0.9531 (mtpp) REVERT: W5 3 ARG cc_start: 0.9285 (mmp80) cc_final: 0.9022 (mmp80) REVERT: U5 62 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8610 (tm-30) REVERT: B5 241 GLU cc_start: 0.8446 (pp20) cc_final: 0.8039 (pp20) REVERT: B5 397 MET cc_start: 0.9300 (mmm) cc_final: 0.9080 (mmm) REVERT: b5 109 ARG cc_start: 0.9466 (OUTLIER) cc_final: 0.9077 (ptp-110) REVERT: b5 252 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.8419 (t80) REVERT: b5 466 MET cc_start: 0.9464 (OUTLIER) cc_final: 0.8535 (ppp) outliers start: 418 outliers final: 309 residues processed: 1653 average time/residue: 0.5767 time to fit residues: 1610.4515 Evaluate side-chains 1665 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1329 time to evaluate : 5.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 4 PHE Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 34 GLN Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain w residue 23 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 42 ASP Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 56 MET Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 110 TYR Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 34 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain b residue 25 HIS Chi-restraints excluded: chain b residue 39 ASN Chi-restraints excluded: chain b residue 132 ARG Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain b residue 226 LEU Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 252 TYR Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 337 ASP Chi-restraints excluded: chain b residue 339 LEU Chi-restraints excluded: chain b residue 358 LEU Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 456 ASP Chi-restraints excluded: chain b residue 466 MET Chi-restraints excluded: chain b residue 474 THR Chi-restraints excluded: chain b residue 478 GLU Chi-restraints excluded: chain f1 residue 4 PHE Chi-restraints excluded: chain f1 residue 25 THR Chi-restraints excluded: chain f1 residue 28 THR Chi-restraints excluded: chain f1 residue 29 ILE Chi-restraints excluded: chain f1 residue 56 VAL Chi-restraints excluded: chain f1 residue 103 LEU Chi-restraints excluded: chain f1 residue 109 VAL Chi-restraints excluded: chain W1 residue 23 VAL Chi-restraints excluded: chain W1 residue 34 GLU Chi-restraints excluded: chain W1 residue 39 SER Chi-restraints excluded: chain W1 residue 52 VAL Chi-restraints excluded: chain w1 residue 25 THR Chi-restraints excluded: chain w1 residue 31 ARG Chi-restraints excluded: chain w1 residue 33 VAL Chi-restraints excluded: chain w1 residue 38 THR Chi-restraints excluded: chain w1 residue 39 SER Chi-restraints excluded: chain w1 residue 49 GLU Chi-restraints excluded: chain w1 residue 53 GLN Chi-restraints excluded: chain U1 residue 44 VAL Chi-restraints excluded: chain U1 residue 52 THR Chi-restraints excluded: chain U1 residue 110 TYR Chi-restraints excluded: chain U1 residue 117 ASP Chi-restraints excluded: chain B1 residue 25 HIS Chi-restraints excluded: chain B1 residue 35 LEU Chi-restraints excluded: chain B1 residue 54 THR Chi-restraints excluded: chain B1 residue 76 LEU Chi-restraints excluded: chain B1 residue 91 ARG Chi-restraints excluded: chain B1 residue 125 CYS Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 219 TRP Chi-restraints excluded: chain B1 residue 252 TYR Chi-restraints excluded: chain B1 residue 269 LEU Chi-restraints excluded: chain B1 residue 302 GLU Chi-restraints excluded: chain B1 residue 325 LEU Chi-restraints excluded: chain B1 residue 333 LEU Chi-restraints excluded: chain B1 residue 337 ASP Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 386 ARG Chi-restraints excluded: chain B1 residue 461 VAL Chi-restraints excluded: chain B1 residue 468 ILE Chi-restraints excluded: chain B1 residue 474 THR Chi-restraints excluded: chain b1 residue 31 PHE Chi-restraints excluded: chain b1 residue 39 ASN Chi-restraints excluded: chain b1 residue 50 LEU Chi-restraints excluded: chain b1 residue 144 MET Chi-restraints excluded: chain b1 residue 159 THR Chi-restraints excluded: chain b1 residue 185 ASP Chi-restraints excluded: chain b1 residue 194 GLN Chi-restraints excluded: chain b1 residue 226 LEU Chi-restraints excluded: chain b1 residue 269 LEU Chi-restraints excluded: chain b1 residue 357 SER Chi-restraints excluded: chain b1 residue 358 LEU Chi-restraints excluded: chain b1 residue 381 SER Chi-restraints excluded: chain b1 residue 413 LEU Chi-restraints excluded: chain b1 residue 425 VAL Chi-restraints excluded: chain b1 residue 439 ARG Chi-restraints excluded: chain b1 residue 463 GLU Chi-restraints excluded: chain b1 residue 474 THR Chi-restraints excluded: chain b1 residue 478 GLU Chi-restraints excluded: chain f2 residue 7 LEU Chi-restraints excluded: chain f2 residue 34 GLN Chi-restraints excluded: chain f2 residue 56 VAL Chi-restraints excluded: chain f2 residue 67 VAL Chi-restraints excluded: chain f2 residue 109 VAL Chi-restraints excluded: chain W2 residue 23 VAL Chi-restraints excluded: chain W2 residue 34 GLU Chi-restraints excluded: chain W2 residue 50 LEU Chi-restraints excluded: chain W2 residue 51 GLU Chi-restraints excluded: chain w2 residue 19 THR Chi-restraints excluded: chain w2 residue 23 VAL Chi-restraints excluded: chain w2 residue 39 SER Chi-restraints excluded: chain w2 residue 52 VAL Chi-restraints excluded: chain U2 residue 4 MET Chi-restraints excluded: chain U2 residue 9 LEU Chi-restraints excluded: chain U2 residue 22 THR Chi-restraints excluded: chain U2 residue 30 ARG Chi-restraints excluded: chain U2 residue 33 VAL Chi-restraints excluded: chain U2 residue 42 VAL Chi-restraints excluded: chain U2 residue 52 THR Chi-restraints excluded: chain U2 residue 106 VAL Chi-restraints excluded: chain U2 residue 110 TYR Chi-restraints excluded: chain U2 residue 122 SER Chi-restraints excluded: chain U2 residue 123 SER Chi-restraints excluded: chain B2 residue 25 HIS Chi-restraints excluded: chain B2 residue 35 LEU Chi-restraints excluded: chain B2 residue 43 GLU Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 76 LEU Chi-restraints excluded: chain B2 residue 82 VAL Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 215 MET Chi-restraints excluded: chain B2 residue 252 TYR Chi-restraints excluded: chain B2 residue 341 LEU Chi-restraints excluded: chain B2 residue 349 ASN Chi-restraints excluded: chain B2 residue 358 LEU Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 366 LEU Chi-restraints excluded: chain B2 residue 425 VAL Chi-restraints excluded: chain B2 residue 467 LEU Chi-restraints excluded: chain B2 residue 474 THR Chi-restraints excluded: chain b2 residue 25 HIS Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 109 ARG Chi-restraints excluded: chain b2 residue 171 MET Chi-restraints excluded: chain b2 residue 202 LEU Chi-restraints excluded: chain b2 residue 226 LEU Chi-restraints excluded: chain b2 residue 240 VAL Chi-restraints excluded: chain b2 residue 339 LEU Chi-restraints excluded: chain b2 residue 340 ASN Chi-restraints excluded: chain b2 residue 358 LEU Chi-restraints excluded: chain b2 residue 425 VAL Chi-restraints excluded: chain b2 residue 453 MET Chi-restraints excluded: chain b2 residue 456 ASP Chi-restraints excluded: chain b2 residue 466 MET Chi-restraints excluded: chain f3 residue 4 PHE Chi-restraints excluded: chain f3 residue 25 THR Chi-restraints excluded: chain f3 residue 28 THR Chi-restraints excluded: chain f3 residue 56 VAL Chi-restraints excluded: chain f3 residue 69 THR Chi-restraints excluded: chain f3 residue 77 ARG Chi-restraints excluded: chain f3 residue 79 ASP Chi-restraints excluded: chain f3 residue 109 VAL Chi-restraints excluded: chain W3 residue 23 VAL Chi-restraints excluded: chain W3 residue 39 SER Chi-restraints excluded: chain W3 residue 56 MET Chi-restraints excluded: chain w3 residue 23 VAL Chi-restraints excluded: chain w3 residue 25 THR Chi-restraints excluded: chain w3 residue 31 ARG Chi-restraints excluded: chain w3 residue 33 VAL Chi-restraints excluded: chain w3 residue 39 SER Chi-restraints excluded: chain U3 residue 9 LEU Chi-restraints excluded: chain U3 residue 17 LEU Chi-restraints excluded: chain U3 residue 38 ASP Chi-restraints excluded: chain U3 residue 52 THR Chi-restraints excluded: chain U3 residue 74 GLN Chi-restraints excluded: chain U3 residue 92 MET Chi-restraints excluded: chain U3 residue 102 ILE Chi-restraints excluded: chain U3 residue 110 TYR Chi-restraints excluded: chain U3 residue 120 LEU Chi-restraints excluded: chain U3 residue 122 SER Chi-restraints excluded: chain B3 residue 50 LEU Chi-restraints excluded: chain B3 residue 55 ARG Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 84 SER Chi-restraints excluded: chain B3 residue 121 ASP Chi-restraints excluded: chain B3 residue 123 CYS Chi-restraints excluded: chain B3 residue 125 CYS Chi-restraints excluded: chain B3 residue 126 ILE Chi-restraints excluded: chain B3 residue 132 ARG Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 273 ILE Chi-restraints excluded: chain B3 residue 283 GLU Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 446 ASP Chi-restraints excluded: chain B3 residue 474 THR Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 133 THR Chi-restraints excluded: chain b3 residue 195 ILE Chi-restraints excluded: chain b3 residue 215 MET Chi-restraints excluded: chain b3 residue 255 MET Chi-restraints excluded: chain b3 residue 337 ASP Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 358 LEU Chi-restraints excluded: chain b3 residue 379 GLN Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 425 VAL Chi-restraints excluded: chain b3 residue 453 MET Chi-restraints excluded: chain b3 residue 456 ASP Chi-restraints excluded: chain b3 residue 478 GLU Chi-restraints excluded: chain b3 residue 489 ILE Chi-restraints excluded: chain f4 residue 25 THR Chi-restraints excluded: chain f4 residue 28 THR Chi-restraints excluded: chain f4 residue 33 GLU Chi-restraints excluded: chain f4 residue 56 VAL Chi-restraints excluded: chain f4 residue 58 VAL Chi-restraints excluded: chain f4 residue 64 SER Chi-restraints excluded: chain f4 residue 69 THR Chi-restraints excluded: chain f4 residue 90 VAL Chi-restraints excluded: chain f4 residue 109 VAL Chi-restraints excluded: chain W4 residue 7 LEU Chi-restraints excluded: chain W4 residue 21 LYS Chi-restraints excluded: chain W4 residue 23 VAL Chi-restraints excluded: chain W4 residue 34 GLU Chi-restraints excluded: chain W4 residue 39 SER Chi-restraints excluded: chain w4 residue 17 LEU Chi-restraints excluded: chain w4 residue 23 VAL Chi-restraints excluded: chain w4 residue 25 THR Chi-restraints excluded: chain w4 residue 38 THR Chi-restraints excluded: chain w4 residue 39 SER Chi-restraints excluded: chain U4 residue 22 THR Chi-restraints excluded: chain U4 residue 27 PHE Chi-restraints excluded: chain U4 residue 42 VAL Chi-restraints excluded: chain U4 residue 52 THR Chi-restraints excluded: chain U4 residue 91 VAL Chi-restraints excluded: chain U4 residue 110 TYR Chi-restraints excluded: chain U4 residue 117 ASP Chi-restraints excluded: chain U4 residue 122 SER Chi-restraints excluded: chain U4 residue 130 ILE Chi-restraints excluded: chain B4 residue 35 LEU Chi-restraints excluded: chain B4 residue 50 LEU Chi-restraints excluded: chain B4 residue 82 VAL Chi-restraints excluded: chain B4 residue 116 LYS Chi-restraints excluded: chain B4 residue 125 CYS Chi-restraints excluded: chain B4 residue 206 VAL Chi-restraints excluded: chain B4 residue 269 LEU Chi-restraints excluded: chain B4 residue 287 ASP Chi-restraints excluded: chain B4 residue 340 ASN Chi-restraints excluded: chain B4 residue 341 LEU Chi-restraints excluded: chain B4 residue 355 GLU Chi-restraints excluded: chain B4 residue 357 SER Chi-restraints excluded: chain B4 residue 358 LEU Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 381 SER Chi-restraints excluded: chain B4 residue 392 SER Chi-restraints excluded: chain B4 residue 453 MET Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 132 ARG Chi-restraints excluded: chain b4 residue 215 MET Chi-restraints excluded: chain b4 residue 226 LEU Chi-restraints excluded: chain b4 residue 240 VAL Chi-restraints excluded: chain b4 residue 273 ILE Chi-restraints excluded: chain b4 residue 358 LEU Chi-restraints excluded: chain f5 residue 4 PHE Chi-restraints excluded: chain f5 residue 29 ILE Chi-restraints excluded: chain f5 residue 42 VAL Chi-restraints excluded: chain f5 residue 56 VAL Chi-restraints excluded: chain f5 residue 69 THR Chi-restraints excluded: chain f5 residue 109 VAL Chi-restraints excluded: chain W5 residue 23 VAL Chi-restraints excluded: chain W5 residue 38 THR Chi-restraints excluded: chain W5 residue 39 SER Chi-restraints excluded: chain W5 residue 51 GLU Chi-restraints excluded: chain w5 residue 23 VAL Chi-restraints excluded: chain w5 residue 39 SER Chi-restraints excluded: chain w5 residue 40 VAL Chi-restraints excluded: chain w5 residue 43 LEU Chi-restraints excluded: chain U5 residue 20 HIS Chi-restraints excluded: chain U5 residue 30 ARG Chi-restraints excluded: chain U5 residue 38 ASP Chi-restraints excluded: chain U5 residue 52 THR Chi-restraints excluded: chain U5 residue 58 SER Chi-restraints excluded: chain U5 residue 67 ILE Chi-restraints excluded: chain U5 residue 75 VAL Chi-restraints excluded: chain U5 residue 110 TYR Chi-restraints excluded: chain U5 residue 117 ASP Chi-restraints excluded: chain U5 residue 122 SER Chi-restraints excluded: chain B5 residue 25 HIS Chi-restraints excluded: chain B5 residue 35 LEU Chi-restraints excluded: chain B5 residue 42 SER Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 126 ILE Chi-restraints excluded: chain B5 residue 206 VAL Chi-restraints excluded: chain B5 residue 252 TYR Chi-restraints excluded: chain B5 residue 269 LEU Chi-restraints excluded: chain B5 residue 284 SER Chi-restraints excluded: chain B5 residue 358 LEU Chi-restraints excluded: chain B5 residue 359 LEU Chi-restraints excluded: chain B5 residue 425 VAL Chi-restraints excluded: chain B5 residue 434 SER Chi-restraints excluded: chain B5 residue 467 LEU Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 109 ARG Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 159 THR Chi-restraints excluded: chain b5 residue 164 LEU Chi-restraints excluded: chain b5 residue 186 SER Chi-restraints excluded: chain b5 residue 202 LEU Chi-restraints excluded: chain b5 residue 206 VAL Chi-restraints excluded: chain b5 residue 218 LYS Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 269 LEU Chi-restraints excluded: chain b5 residue 333 LEU Chi-restraints excluded: chain b5 residue 355 GLU Chi-restraints excluded: chain b5 residue 357 SER Chi-restraints excluded: chain b5 residue 358 LEU Chi-restraints excluded: chain b5 residue 362 ILE Chi-restraints excluded: chain b5 residue 392 SER Chi-restraints excluded: chain b5 residue 466 MET Chi-restraints excluded: chain b5 residue 478 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 465 optimal weight: 8.9990 chunk 300 optimal weight: 6.9990 chunk 449 optimal weight: 3.9990 chunk 226 optimal weight: 30.0000 chunk 147 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 477 optimal weight: 6.9990 chunk 512 optimal weight: 0.9980 chunk 371 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 590 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 53 GLN B2 182 ASN ** B2 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 342 GLN B3 182 ASN ** B3 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 34 GLN b3 376 ASN U4 20 HIS ** B4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w5 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 194 GLN ** B5 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 342 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 63648 Z= 0.254 Angle : 0.727 14.396 86070 Z= 0.357 Chirality : 0.043 0.311 9066 Planarity : 0.005 0.117 11430 Dihedral : 5.177 71.239 8849 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.34 % Favored : 91.20 % Rotamer: Outliers : 6.75 % Allowed : 33.05 % Favored : 60.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.10), residues: 7866 helix: 1.20 (0.09), residues: 3426 sheet: -0.27 (0.16), residues: 1050 loop : -1.50 (0.11), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRPB5 393 HIS 0.005 0.001 HIS b 332 PHE 0.026 0.001 PHEU5 39 TYR 0.019 0.001 TYRU2 128 ARG 0.014 0.000 ARGb2 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1780 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 432 poor density : 1348 time to evaluate : 5.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 34 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: w 51 GLU cc_start: 0.9415 (pt0) cc_final: 0.8971 (pt0) REVERT: B 140 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: B 453 MET cc_start: 0.8384 (ppp) cc_final: 0.8051 (ppp) REVERT: b 359 LEU cc_start: 0.9792 (OUTLIER) cc_final: 0.9506 (mm) REVERT: b 411 MET cc_start: 0.9641 (mtm) cc_final: 0.9389 (mtm) REVERT: b 469 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8939 (mm-30) REVERT: w1 31 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7287 (mtm-85) REVERT: w1 45 LYS cc_start: 0.9292 (ptpp) cc_final: 0.9049 (ptpp) REVERT: w1 49 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8969 (pm20) REVERT: B1 241 GLU cc_start: 0.8356 (pp20) cc_final: 0.7690 (pp20) REVERT: B1 302 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: B1 366 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9423 (mm) REVERT: B1 380 MET cc_start: 0.8670 (mmm) cc_final: 0.8391 (mmm) REVERT: B1 463 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8917 (mm-30) REVERT: b1 439 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8539 (mtt180) REVERT: w2 16 ASP cc_start: 0.9352 (t70) cc_final: 0.9053 (t70) REVERT: w2 51 GLU cc_start: 0.9211 (pt0) cc_final: 0.8934 (pt0) REVERT: U2 62 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B2 187 ARG cc_start: 0.9253 (ttm110) cc_final: 0.8806 (ttm110) REVERT: B2 346 ASP cc_start: 0.8922 (t0) cc_final: 0.8670 (t70) REVERT: B2 463 GLU cc_start: 0.9480 (OUTLIER) cc_final: 0.8894 (mm-30) REVERT: B2 466 MET cc_start: 0.9563 (ttt) cc_final: 0.9255 (ttp) REVERT: b2 137 MET cc_start: 0.9613 (mmm) cc_final: 0.9374 (mmm) REVERT: b2 356 GLN cc_start: 0.9358 (mm-40) cc_final: 0.8957 (mm-40) REVERT: b2 411 MET cc_start: 0.9676 (mtt) cc_final: 0.9415 (mtp) REVERT: b2 453 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8462 (ppp) REVERT: b2 460 GLU cc_start: 0.8961 (tp30) cc_final: 0.8654 (tp30) REVERT: b2 479 CYS cc_start: 0.9365 (m) cc_final: 0.8871 (p) REVERT: f3 16 ASP cc_start: 0.8894 (t0) cc_final: 0.8617 (t0) REVERT: f3 17 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8605 (mm-30) REVERT: w3 31 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7693 (mtm-85) REVERT: U3 50 GLU cc_start: 0.7894 (mp0) cc_final: 0.7289 (mp0) REVERT: U3 62 GLN cc_start: 0.8738 (pp30) cc_final: 0.7962 (pm20) REVERT: U3 64 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8750 (tt0) REVERT: U3 120 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9403 (mm) REVERT: B3 55 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.8270 (ttp80) REVERT: B3 463 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8682 (mm-30) REVERT: b3 379 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8524 (pm20) REVERT: b3 453 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7732 (ppp) REVERT: b3 498 MET cc_start: 0.9212 (tmm) cc_final: 0.8957 (tmm) REVERT: W4 21 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8778 (mmmm) REVERT: W4 45 LYS cc_start: 0.9597 (mtpp) cc_final: 0.9350 (mtmm) REVERT: U4 114 ARG cc_start: 0.8688 (ptp-110) cc_final: 0.8415 (ptp-170) REVERT: B4 35 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9176 (pp) REVERT: B4 131 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8784 (mttt) REVERT: B4 366 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9232 (mm) REVERT: b4 359 LEU cc_start: 0.9763 (mm) cc_final: 0.9546 (mm) REVERT: b4 469 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8918 (mm-30) REVERT: b4 472 LEU cc_start: 0.9462 (mt) cc_final: 0.9238 (tt) REVERT: U5 134 MET cc_start: 0.8997 (ppp) cc_final: 0.8763 (ppp) REVERT: B5 112 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9208 (mm-30) REVERT: B5 150 GLU cc_start: 0.8569 (pt0) cc_final: 0.8348 (pt0) REVERT: B5 241 GLU cc_start: 0.8448 (pp20) cc_final: 0.8059 (pp20) REVERT: B5 277 MET cc_start: 0.9157 (ttm) cc_final: 0.8938 (ttt) REVERT: b5 109 ARG cc_start: 0.9466 (OUTLIER) cc_final: 0.9068 (ptp-110) REVERT: b5 137 MET cc_start: 0.9608 (mmm) cc_final: 0.9408 (mmm) REVERT: b5 194 GLN cc_start: 0.9495 (OUTLIER) cc_final: 0.9113 (tp40) REVERT: b5 252 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8466 (t80) REVERT: b5 466 MET cc_start: 0.9485 (OUTLIER) cc_final: 0.8539 (ppp) outliers start: 432 outliers final: 342 residues processed: 1606 average time/residue: 0.5918 time to fit residues: 1607.5155 Evaluate side-chains 1673 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1308 time to evaluate : 5.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 4 PHE Chi-restraints excluded: chain f residue 6 ASN Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 34 GLN Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain w residue 23 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 42 ASP Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 56 MET Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 110 TYR Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain b residue 25 HIS Chi-restraints excluded: chain b residue 31 PHE Chi-restraints excluded: chain b residue 39 ASN Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain b residue 218 LYS Chi-restraints excluded: chain b residue 226 LEU Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 255 MET Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 337 ASP Chi-restraints excluded: chain b residue 339 LEU Chi-restraints excluded: chain b residue 358 LEU Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 456 ASP Chi-restraints excluded: chain b residue 474 THR Chi-restraints excluded: chain f1 residue 4 PHE Chi-restraints excluded: chain f1 residue 25 THR Chi-restraints excluded: chain f1 residue 29 ILE Chi-restraints excluded: chain f1 residue 56 VAL Chi-restraints excluded: chain f1 residue 103 LEU Chi-restraints excluded: chain f1 residue 109 VAL Chi-restraints excluded: chain W1 residue 23 VAL Chi-restraints excluded: chain W1 residue 34 GLU Chi-restraints excluded: chain W1 residue 39 SER Chi-restraints excluded: chain W1 residue 52 VAL Chi-restraints excluded: chain w1 residue 23 VAL Chi-restraints excluded: chain w1 residue 25 THR Chi-restraints excluded: chain w1 residue 29 ASP Chi-restraints excluded: chain w1 residue 31 ARG Chi-restraints excluded: chain w1 residue 33 VAL Chi-restraints excluded: chain w1 residue 38 THR Chi-restraints excluded: chain w1 residue 39 SER Chi-restraints excluded: chain w1 residue 49 GLU Chi-restraints excluded: chain w1 residue 53 GLN Chi-restraints excluded: chain U1 residue 44 VAL Chi-restraints excluded: chain U1 residue 110 TYR Chi-restraints excluded: chain U1 residue 117 ASP Chi-restraints excluded: chain B1 residue 25 HIS Chi-restraints excluded: chain B1 residue 54 THR Chi-restraints excluded: chain B1 residue 125 CYS Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 219 TRP Chi-restraints excluded: chain B1 residue 269 LEU Chi-restraints excluded: chain B1 residue 302 GLU Chi-restraints excluded: chain B1 residue 325 LEU Chi-restraints excluded: chain B1 residue 333 LEU Chi-restraints excluded: chain B1 residue 337 ASP Chi-restraints excluded: chain B1 residue 340 ASN Chi-restraints excluded: chain B1 residue 355 GLU Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 386 ARG Chi-restraints excluded: chain B1 residue 461 VAL Chi-restraints excluded: chain B1 residue 468 ILE Chi-restraints excluded: chain B1 residue 474 THR Chi-restraints excluded: chain b1 residue 31 PHE Chi-restraints excluded: chain b1 residue 39 ASN Chi-restraints excluded: chain b1 residue 50 LEU Chi-restraints excluded: chain b1 residue 144 MET Chi-restraints excluded: chain b1 residue 159 THR Chi-restraints excluded: chain b1 residue 185 ASP Chi-restraints excluded: chain b1 residue 186 SER Chi-restraints excluded: chain b1 residue 226 LEU Chi-restraints excluded: chain b1 residue 269 LEU Chi-restraints excluded: chain b1 residue 358 LEU Chi-restraints excluded: chain b1 residue 413 LEU Chi-restraints excluded: chain b1 residue 425 VAL Chi-restraints excluded: chain b1 residue 439 ARG Chi-restraints excluded: chain b1 residue 463 GLU Chi-restraints excluded: chain b1 residue 474 THR Chi-restraints excluded: chain b1 residue 478 GLU Chi-restraints excluded: chain f2 residue 7 LEU Chi-restraints excluded: chain f2 residue 56 VAL Chi-restraints excluded: chain f2 residue 67 VAL Chi-restraints excluded: chain f2 residue 109 VAL Chi-restraints excluded: chain W2 residue 23 VAL Chi-restraints excluded: chain W2 residue 34 GLU Chi-restraints excluded: chain W2 residue 47 ILE Chi-restraints excluded: chain W2 residue 50 LEU Chi-restraints excluded: chain W2 residue 51 GLU Chi-restraints excluded: chain w2 residue 19 THR Chi-restraints excluded: chain w2 residue 23 VAL Chi-restraints excluded: chain w2 residue 39 SER Chi-restraints excluded: chain w2 residue 52 VAL Chi-restraints excluded: chain U2 residue 9 LEU Chi-restraints excluded: chain U2 residue 22 THR Chi-restraints excluded: chain U2 residue 33 VAL Chi-restraints excluded: chain U2 residue 42 VAL Chi-restraints excluded: chain U2 residue 52 THR Chi-restraints excluded: chain U2 residue 74 GLN Chi-restraints excluded: chain U2 residue 106 VAL Chi-restraints excluded: chain U2 residue 110 TYR Chi-restraints excluded: chain U2 residue 122 SER Chi-restraints excluded: chain U2 residue 123 SER Chi-restraints excluded: chain B2 residue 35 LEU Chi-restraints excluded: chain B2 residue 43 GLU Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 82 VAL Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 215 MET Chi-restraints excluded: chain B2 residue 252 TYR Chi-restraints excluded: chain B2 residue 341 LEU Chi-restraints excluded: chain B2 residue 349 ASN Chi-restraints excluded: chain B2 residue 358 LEU Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 366 LEU Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain B2 residue 425 VAL Chi-restraints excluded: chain B2 residue 455 ILE Chi-restraints excluded: chain B2 residue 463 GLU Chi-restraints excluded: chain B2 residue 467 LEU Chi-restraints excluded: chain B2 residue 474 THR Chi-restraints excluded: chain B2 residue 489 ILE Chi-restraints excluded: chain b2 residue 25 HIS Chi-restraints excluded: chain b2 residue 39 ASN Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 109 ARG Chi-restraints excluded: chain b2 residue 171 MET Chi-restraints excluded: chain b2 residue 202 LEU Chi-restraints excluded: chain b2 residue 226 LEU Chi-restraints excluded: chain b2 residue 240 VAL Chi-restraints excluded: chain b2 residue 269 LEU Chi-restraints excluded: chain b2 residue 283 GLU Chi-restraints excluded: chain b2 residue 340 ASN Chi-restraints excluded: chain b2 residue 358 LEU Chi-restraints excluded: chain b2 residue 425 VAL Chi-restraints excluded: chain b2 residue 453 MET Chi-restraints excluded: chain b2 residue 456 ASP Chi-restraints excluded: chain b2 residue 466 MET Chi-restraints excluded: chain f3 residue 4 PHE Chi-restraints excluded: chain f3 residue 25 THR Chi-restraints excluded: chain f3 residue 28 THR Chi-restraints excluded: chain f3 residue 56 VAL Chi-restraints excluded: chain f3 residue 69 THR Chi-restraints excluded: chain f3 residue 77 ARG Chi-restraints excluded: chain f3 residue 79 ASP Chi-restraints excluded: chain f3 residue 109 VAL Chi-restraints excluded: chain W3 residue 23 VAL Chi-restraints excluded: chain W3 residue 26 VAL Chi-restraints excluded: chain W3 residue 39 SER Chi-restraints excluded: chain w3 residue 23 VAL Chi-restraints excluded: chain w3 residue 25 THR Chi-restraints excluded: chain w3 residue 31 ARG Chi-restraints excluded: chain w3 residue 33 VAL Chi-restraints excluded: chain w3 residue 39 SER Chi-restraints excluded: chain U3 residue 9 LEU Chi-restraints excluded: chain U3 residue 17 LEU Chi-restraints excluded: chain U3 residue 52 THR Chi-restraints excluded: chain U3 residue 74 GLN Chi-restraints excluded: chain U3 residue 92 MET Chi-restraints excluded: chain U3 residue 102 ILE Chi-restraints excluded: chain U3 residue 110 TYR Chi-restraints excluded: chain U3 residue 120 LEU Chi-restraints excluded: chain U3 residue 122 SER Chi-restraints excluded: chain B3 residue 25 HIS Chi-restraints excluded: chain B3 residue 37 SER Chi-restraints excluded: chain B3 residue 50 LEU Chi-restraints excluded: chain B3 residue 55 ARG Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 84 SER Chi-restraints excluded: chain B3 residue 121 ASP Chi-restraints excluded: chain B3 residue 123 CYS Chi-restraints excluded: chain B3 residue 125 CYS Chi-restraints excluded: chain B3 residue 126 ILE Chi-restraints excluded: chain B3 residue 132 ARG Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 258 MET Chi-restraints excluded: chain B3 residue 283 GLU Chi-restraints excluded: chain B3 residue 340 ASN Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 434 SER Chi-restraints excluded: chain B3 residue 446 ASP Chi-restraints excluded: chain B3 residue 474 THR Chi-restraints excluded: chain B3 residue 484 ASP Chi-restraints excluded: chain b3 residue 31 PHE Chi-restraints excluded: chain b3 residue 39 ASN Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 50 LEU Chi-restraints excluded: chain b3 residue 133 THR Chi-restraints excluded: chain b3 residue 159 THR Chi-restraints excluded: chain b3 residue 186 SER Chi-restraints excluded: chain b3 residue 194 GLN Chi-restraints excluded: chain b3 residue 195 ILE Chi-restraints excluded: chain b3 residue 215 MET Chi-restraints excluded: chain b3 residue 255 MET Chi-restraints excluded: chain b3 residue 337 ASP Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 358 LEU Chi-restraints excluded: chain b3 residue 376 ASN Chi-restraints excluded: chain b3 residue 379 GLN Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 425 VAL Chi-restraints excluded: chain b3 residue 453 MET Chi-restraints excluded: chain b3 residue 456 ASP Chi-restraints excluded: chain b3 residue 478 GLU Chi-restraints excluded: chain b3 residue 489 ILE Chi-restraints excluded: chain f4 residue 25 THR Chi-restraints excluded: chain f4 residue 28 THR Chi-restraints excluded: chain f4 residue 29 ILE Chi-restraints excluded: chain f4 residue 33 GLU Chi-restraints excluded: chain f4 residue 56 VAL Chi-restraints excluded: chain f4 residue 58 VAL Chi-restraints excluded: chain f4 residue 64 SER Chi-restraints excluded: chain f4 residue 67 VAL Chi-restraints excluded: chain f4 residue 69 THR Chi-restraints excluded: chain f4 residue 90 VAL Chi-restraints excluded: chain f4 residue 109 VAL Chi-restraints excluded: chain W4 residue 7 LEU Chi-restraints excluded: chain W4 residue 21 LYS Chi-restraints excluded: chain W4 residue 23 VAL Chi-restraints excluded: chain W4 residue 34 GLU Chi-restraints excluded: chain W4 residue 39 SER Chi-restraints excluded: chain W4 residue 42 ASP Chi-restraints excluded: chain w4 residue 17 LEU Chi-restraints excluded: chain w4 residue 23 VAL Chi-restraints excluded: chain w4 residue 25 THR Chi-restraints excluded: chain w4 residue 38 THR Chi-restraints excluded: chain w4 residue 39 SER Chi-restraints excluded: chain U4 residue 19 LYS Chi-restraints excluded: chain U4 residue 20 HIS Chi-restraints excluded: chain U4 residue 22 THR Chi-restraints excluded: chain U4 residue 42 VAL Chi-restraints excluded: chain U4 residue 52 THR Chi-restraints excluded: chain U4 residue 91 VAL Chi-restraints excluded: chain U4 residue 92 MET Chi-restraints excluded: chain U4 residue 110 TYR Chi-restraints excluded: chain U4 residue 117 ASP Chi-restraints excluded: chain U4 residue 122 SER Chi-restraints excluded: chain U4 residue 126 LEU Chi-restraints excluded: chain B4 residue 35 LEU Chi-restraints excluded: chain B4 residue 50 LEU Chi-restraints excluded: chain B4 residue 54 THR Chi-restraints excluded: chain B4 residue 82 VAL Chi-restraints excluded: chain B4 residue 125 CYS Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 173 SER Chi-restraints excluded: chain B4 residue 188 ASN Chi-restraints excluded: chain B4 residue 206 VAL Chi-restraints excluded: chain B4 residue 287 ASP Chi-restraints excluded: chain B4 residue 292 MET Chi-restraints excluded: chain B4 residue 337 ASP Chi-restraints excluded: chain B4 residue 340 ASN Chi-restraints excluded: chain B4 residue 341 LEU Chi-restraints excluded: chain B4 residue 355 GLU Chi-restraints excluded: chain B4 residue 357 SER Chi-restraints excluded: chain B4 residue 358 LEU Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 381 SER Chi-restraints excluded: chain B4 residue 392 SER Chi-restraints excluded: chain B4 residue 453 MET Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 132 ARG Chi-restraints excluded: chain b4 residue 215 MET Chi-restraints excluded: chain b4 residue 226 LEU Chi-restraints excluded: chain b4 residue 240 VAL Chi-restraints excluded: chain b4 residue 273 ILE Chi-restraints excluded: chain b4 residue 283 GLU Chi-restraints excluded: chain b4 residue 358 LEU Chi-restraints excluded: chain b4 residue 413 LEU Chi-restraints excluded: chain f5 residue 4 PHE Chi-restraints excluded: chain f5 residue 29 ILE Chi-restraints excluded: chain f5 residue 42 VAL Chi-restraints excluded: chain f5 residue 56 VAL Chi-restraints excluded: chain f5 residue 69 THR Chi-restraints excluded: chain f5 residue 109 VAL Chi-restraints excluded: chain W5 residue 23 VAL Chi-restraints excluded: chain W5 residue 38 THR Chi-restraints excluded: chain W5 residue 39 SER Chi-restraints excluded: chain W5 residue 51 GLU Chi-restraints excluded: chain w5 residue 23 VAL Chi-restraints excluded: chain w5 residue 39 SER Chi-restraints excluded: chain w5 residue 40 VAL Chi-restraints excluded: chain w5 residue 43 LEU Chi-restraints excluded: chain w5 residue 68 VAL Chi-restraints excluded: chain U5 residue 20 HIS Chi-restraints excluded: chain U5 residue 30 ARG Chi-restraints excluded: chain U5 residue 52 THR Chi-restraints excluded: chain U5 residue 58 SER Chi-restraints excluded: chain U5 residue 67 ILE Chi-restraints excluded: chain U5 residue 75 VAL Chi-restraints excluded: chain U5 residue 110 TYR Chi-restraints excluded: chain U5 residue 117 ASP Chi-restraints excluded: chain U5 residue 122 SER Chi-restraints excluded: chain B5 residue 25 HIS Chi-restraints excluded: chain B5 residue 42 SER Chi-restraints excluded: chain B5 residue 54 THR Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 126 ILE Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 202 LEU Chi-restraints excluded: chain B5 residue 206 VAL Chi-restraints excluded: chain B5 residue 252 TYR Chi-restraints excluded: chain B5 residue 269 LEU Chi-restraints excluded: chain B5 residue 284 SER Chi-restraints excluded: chain B5 residue 337 ASP Chi-restraints excluded: chain B5 residue 358 LEU Chi-restraints excluded: chain B5 residue 359 LEU Chi-restraints excluded: chain B5 residue 425 VAL Chi-restraints excluded: chain B5 residue 434 SER Chi-restraints excluded: chain B5 residue 455 ILE Chi-restraints excluded: chain B5 residue 467 LEU Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 109 ARG Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 159 THR Chi-restraints excluded: chain b5 residue 186 SER Chi-restraints excluded: chain b5 residue 194 GLN Chi-restraints excluded: chain b5 residue 206 VAL Chi-restraints excluded: chain b5 residue 218 LYS Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 254 VAL Chi-restraints excluded: chain b5 residue 269 LEU Chi-restraints excluded: chain b5 residue 333 LEU Chi-restraints excluded: chain b5 residue 355 GLU Chi-restraints excluded: chain b5 residue 358 LEU Chi-restraints excluded: chain b5 residue 362 ILE Chi-restraints excluded: chain b5 residue 392 SER Chi-restraints excluded: chain b5 residue 425 VAL Chi-restraints excluded: chain b5 residue 466 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 683 optimal weight: 6.9990 chunk 720 optimal weight: 8.9990 chunk 657 optimal weight: 0.0980 chunk 700 optimal weight: 3.9990 chunk 421 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 550 optimal weight: 5.9990 chunk 214 optimal weight: 0.0370 chunk 633 optimal weight: 5.9990 chunk 662 optimal weight: 6.9990 chunk 698 optimal weight: 5.9990 overall best weight: 3.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 53 GLN ** B2 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 342 GLN w3 4 GLN ** B3 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 376 ASN ** B4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b4 342 GLN b4 492 GLN ** w5 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 194 GLN ** B5 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 342 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 63648 Z= 0.234 Angle : 0.743 15.363 86070 Z= 0.362 Chirality : 0.043 0.265 9066 Planarity : 0.005 0.117 11430 Dihedral : 5.168 70.689 8847 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.39 % Favored : 91.16 % Rotamer: Outliers : 6.59 % Allowed : 33.35 % Favored : 60.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.10), residues: 7866 helix: 1.18 (0.09), residues: 3420 sheet: -0.35 (0.16), residues: 1062 loop : -1.49 (0.11), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRPB5 393 HIS 0.005 0.001 HISU4 20 PHE 0.027 0.001 PHEU5 39 TYR 0.019 0.001 TYRB4 211 ARG 0.011 0.000 ARGb2 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1776 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 422 poor density : 1354 time to evaluate : 5.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 34 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8031 (mp10) REVERT: W 49 GLU cc_start: 0.9332 (tm-30) cc_final: 0.9113 (tm-30) REVERT: w 51 GLU cc_start: 0.9409 (pt0) cc_final: 0.8958 (pt0) REVERT: U 4 MET cc_start: 0.5617 (mmp) cc_final: 0.5193 (mmp) REVERT: B 140 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: B 144 MET cc_start: 0.9240 (tpt) cc_final: 0.8966 (tpt) REVERT: B 366 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9361 (mm) REVERT: B 453 MET cc_start: 0.8346 (ppp) cc_final: 0.8018 (ppp) REVERT: B 463 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8570 (mm-30) REVERT: b 252 TYR cc_start: 0.9290 (OUTLIER) cc_final: 0.8239 (t80) REVERT: b 359 LEU cc_start: 0.9792 (OUTLIER) cc_final: 0.9486 (mm) REVERT: b 469 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8931 (mm-30) REVERT: w1 31 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7371 (mtm-85) REVERT: w1 49 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8961 (pm20) REVERT: B1 140 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8581 (tp30) REVERT: B1 241 GLU cc_start: 0.8321 (pp20) cc_final: 0.7714 (pp20) REVERT: B1 302 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: B1 366 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9415 (mm) REVERT: B1 380 MET cc_start: 0.8662 (mmm) cc_final: 0.8405 (mmm) REVERT: B1 463 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8887 (mm-30) REVERT: b1 62 ASP cc_start: 0.9541 (t0) cc_final: 0.9282 (t0) REVERT: b1 175 LYS cc_start: 0.9676 (OUTLIER) cc_final: 0.9300 (tttt) REVERT: b1 439 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8523 (mtt180) REVERT: w2 16 ASP cc_start: 0.9340 (t70) cc_final: 0.9029 (t70) REVERT: w2 51 GLU cc_start: 0.9205 (pt0) cc_final: 0.8922 (pt0) REVERT: U2 62 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B2 187 ARG cc_start: 0.9238 (ttm110) cc_final: 0.8786 (ttm110) REVERT: B2 346 ASP cc_start: 0.8909 (t0) cc_final: 0.8685 (t0) REVERT: B2 463 GLU cc_start: 0.9477 (OUTLIER) cc_final: 0.8907 (mm-30) REVERT: B2 466 MET cc_start: 0.9556 (ttt) cc_final: 0.9282 (ttp) REVERT: b2 137 MET cc_start: 0.9595 (mmm) cc_final: 0.9350 (mmm) REVERT: b2 356 GLN cc_start: 0.9329 (mm-40) cc_final: 0.8961 (mm-40) REVERT: b2 411 MET cc_start: 0.9683 (mtt) cc_final: 0.9429 (mtp) REVERT: b2 453 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8407 (ppp) REVERT: b2 460 GLU cc_start: 0.8945 (tp30) cc_final: 0.8650 (tp30) REVERT: b2 479 CYS cc_start: 0.9349 (m) cc_final: 0.8857 (p) REVERT: f3 16 ASP cc_start: 0.8884 (t0) cc_final: 0.8597 (t0) REVERT: f3 17 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8603 (mm-30) REVERT: f3 77 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8481 (ttt180) REVERT: w3 31 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7678 (mtm-85) REVERT: U3 50 GLU cc_start: 0.7875 (mp0) cc_final: 0.7328 (mp0) REVERT: U3 62 GLN cc_start: 0.8617 (pp30) cc_final: 0.7830 (pm20) REVERT: U3 64 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8749 (tt0) REVERT: U3 120 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9420 (mm) REVERT: B3 55 ARG cc_start: 0.9464 (OUTLIER) cc_final: 0.8251 (ttp80) REVERT: B3 140 GLU cc_start: 0.9173 (tp30) cc_final: 0.8836 (tt0) REVERT: B3 463 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8678 (mm-30) REVERT: b3 379 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: b3 453 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7729 (ppp) REVERT: b3 498 MET cc_start: 0.9208 (tmm) cc_final: 0.8953 (tmm) REVERT: W4 21 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8747 (mmmm) REVERT: W4 45 LYS cc_start: 0.9599 (mtpp) cc_final: 0.9344 (mtmm) REVERT: U4 27 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7047 (m-10) REVERT: U4 114 ARG cc_start: 0.8618 (ptp-110) cc_final: 0.8370 (ptp-170) REVERT: B4 35 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9150 (pp) REVERT: B4 131 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8925 (mttt) REVERT: B4 252 TYR cc_start: 0.9511 (OUTLIER) cc_final: 0.8430 (t80) REVERT: B4 283 GLU cc_start: 0.8967 (tp30) cc_final: 0.8563 (tp30) REVERT: B4 366 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9217 (mm) REVERT: b4 359 LEU cc_start: 0.9751 (mm) cc_final: 0.9522 (mm) REVERT: b4 399 ARG cc_start: 0.9363 (mmm-85) cc_final: 0.8829 (tpp80) REVERT: b4 469 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8908 (mm-30) REVERT: b4 472 LEU cc_start: 0.9447 (mt) cc_final: 0.9232 (tt) REVERT: U5 62 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8605 (tm-30) REVERT: B5 112 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9202 (mm-30) REVERT: B5 150 GLU cc_start: 0.8585 (pt0) cc_final: 0.8360 (pt0) REVERT: B5 241 GLU cc_start: 0.8418 (pp20) cc_final: 0.8053 (pp20) REVERT: B5 277 MET cc_start: 0.9150 (ttm) cc_final: 0.8930 (ttt) REVERT: B5 463 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8493 (mm-30) REVERT: b5 109 ARG cc_start: 0.9463 (OUTLIER) cc_final: 0.9063 (ptp-110) REVERT: b5 137 MET cc_start: 0.9604 (mmm) cc_final: 0.9401 (mmm) REVERT: b5 194 GLN cc_start: 0.9494 (OUTLIER) cc_final: 0.9112 (tp40) REVERT: b5 252 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8447 (t80) REVERT: b5 466 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.8540 (ppp) outliers start: 422 outliers final: 342 residues processed: 1612 average time/residue: 0.5675 time to fit residues: 1550.5820 Evaluate side-chains 1697 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 1325 time to evaluate : 5.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 4 PHE Chi-restraints excluded: chain f residue 6 ASN Chi-restraints excluded: chain f residue 12 ILE Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 34 GLN Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain w residue 23 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 42 ASP Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 56 MET Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 110 TYR Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain b residue 25 HIS Chi-restraints excluded: chain b residue 31 PHE Chi-restraints excluded: chain b residue 39 ASN Chi-restraints excluded: chain b residue 135 THR Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain b residue 226 LEU Chi-restraints excluded: chain b residue 240 VAL Chi-restraints excluded: chain b residue 252 TYR Chi-restraints excluded: chain b residue 255 MET Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 337 ASP Chi-restraints excluded: chain b residue 339 LEU Chi-restraints excluded: chain b residue 358 LEU Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 456 ASP Chi-restraints excluded: chain b residue 474 THR Chi-restraints excluded: chain f1 residue 4 PHE Chi-restraints excluded: chain f1 residue 25 THR Chi-restraints excluded: chain f1 residue 29 ILE Chi-restraints excluded: chain f1 residue 30 THR Chi-restraints excluded: chain f1 residue 56 VAL Chi-restraints excluded: chain f1 residue 58 VAL Chi-restraints excluded: chain f1 residue 109 VAL Chi-restraints excluded: chain W1 residue 23 VAL Chi-restraints excluded: chain W1 residue 39 SER Chi-restraints excluded: chain W1 residue 52 VAL Chi-restraints excluded: chain w1 residue 23 VAL Chi-restraints excluded: chain w1 residue 25 THR Chi-restraints excluded: chain w1 residue 29 ASP Chi-restraints excluded: chain w1 residue 31 ARG Chi-restraints excluded: chain w1 residue 33 VAL Chi-restraints excluded: chain w1 residue 38 THR Chi-restraints excluded: chain w1 residue 39 SER Chi-restraints excluded: chain w1 residue 49 GLU Chi-restraints excluded: chain w1 residue 53 GLN Chi-restraints excluded: chain U1 residue 14 LEU Chi-restraints excluded: chain U1 residue 44 VAL Chi-restraints excluded: chain U1 residue 110 TYR Chi-restraints excluded: chain U1 residue 117 ASP Chi-restraints excluded: chain U1 residue 126 LEU Chi-restraints excluded: chain B1 residue 25 HIS Chi-restraints excluded: chain B1 residue 54 THR Chi-restraints excluded: chain B1 residue 76 LEU Chi-restraints excluded: chain B1 residue 125 CYS Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 140 GLU Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 302 GLU Chi-restraints excluded: chain B1 residue 325 LEU Chi-restraints excluded: chain B1 residue 333 LEU Chi-restraints excluded: chain B1 residue 337 ASP Chi-restraints excluded: chain B1 residue 355 GLU Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 386 ARG Chi-restraints excluded: chain B1 residue 461 VAL Chi-restraints excluded: chain B1 residue 468 ILE Chi-restraints excluded: chain B1 residue 474 THR Chi-restraints excluded: chain b1 residue 31 PHE Chi-restraints excluded: chain b1 residue 39 ASN Chi-restraints excluded: chain b1 residue 45 VAL Chi-restraints excluded: chain b1 residue 50 LEU Chi-restraints excluded: chain b1 residue 144 MET Chi-restraints excluded: chain b1 residue 159 THR Chi-restraints excluded: chain b1 residue 175 LYS Chi-restraints excluded: chain b1 residue 185 ASP Chi-restraints excluded: chain b1 residue 186 SER Chi-restraints excluded: chain b1 residue 226 LEU Chi-restraints excluded: chain b1 residue 269 LEU Chi-restraints excluded: chain b1 residue 358 LEU Chi-restraints excluded: chain b1 residue 413 LEU Chi-restraints excluded: chain b1 residue 425 VAL Chi-restraints excluded: chain b1 residue 439 ARG Chi-restraints excluded: chain b1 residue 463 GLU Chi-restraints excluded: chain b1 residue 474 THR Chi-restraints excluded: chain b1 residue 478 GLU Chi-restraints excluded: chain f2 residue 7 LEU Chi-restraints excluded: chain f2 residue 56 VAL Chi-restraints excluded: chain f2 residue 67 VAL Chi-restraints excluded: chain f2 residue 109 VAL Chi-restraints excluded: chain W2 residue 23 VAL Chi-restraints excluded: chain W2 residue 34 GLU Chi-restraints excluded: chain W2 residue 39 SER Chi-restraints excluded: chain W2 residue 47 ILE Chi-restraints excluded: chain W2 residue 50 LEU Chi-restraints excluded: chain W2 residue 51 GLU Chi-restraints excluded: chain w2 residue 23 VAL Chi-restraints excluded: chain w2 residue 39 SER Chi-restraints excluded: chain w2 residue 52 VAL Chi-restraints excluded: chain U2 residue 9 LEU Chi-restraints excluded: chain U2 residue 22 THR Chi-restraints excluded: chain U2 residue 33 VAL Chi-restraints excluded: chain U2 residue 42 VAL Chi-restraints excluded: chain U2 residue 52 THR Chi-restraints excluded: chain U2 residue 74 GLN Chi-restraints excluded: chain U2 residue 106 VAL Chi-restraints excluded: chain U2 residue 110 TYR Chi-restraints excluded: chain U2 residue 114 ARG Chi-restraints excluded: chain U2 residue 122 SER Chi-restraints excluded: chain U2 residue 123 SER Chi-restraints excluded: chain B2 residue 25 HIS Chi-restraints excluded: chain B2 residue 35 LEU Chi-restraints excluded: chain B2 residue 43 GLU Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 82 VAL Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 215 MET Chi-restraints excluded: chain B2 residue 252 TYR Chi-restraints excluded: chain B2 residue 341 LEU Chi-restraints excluded: chain B2 residue 349 ASN Chi-restraints excluded: chain B2 residue 358 LEU Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 366 LEU Chi-restraints excluded: chain B2 residue 381 SER Chi-restraints excluded: chain B2 residue 425 VAL Chi-restraints excluded: chain B2 residue 455 ILE Chi-restraints excluded: chain B2 residue 463 GLU Chi-restraints excluded: chain B2 residue 467 LEU Chi-restraints excluded: chain B2 residue 474 THR Chi-restraints excluded: chain b2 residue 25 HIS Chi-restraints excluded: chain b2 residue 39 ASN Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 109 ARG Chi-restraints excluded: chain b2 residue 132 ARG Chi-restraints excluded: chain b2 residue 171 MET Chi-restraints excluded: chain b2 residue 202 LEU Chi-restraints excluded: chain b2 residue 226 LEU Chi-restraints excluded: chain b2 residue 240 VAL Chi-restraints excluded: chain b2 residue 269 LEU Chi-restraints excluded: chain b2 residue 283 GLU Chi-restraints excluded: chain b2 residue 340 ASN Chi-restraints excluded: chain b2 residue 358 LEU Chi-restraints excluded: chain b2 residue 425 VAL Chi-restraints excluded: chain b2 residue 453 MET Chi-restraints excluded: chain b2 residue 456 ASP Chi-restraints excluded: chain b2 residue 466 MET Chi-restraints excluded: chain b2 residue 474 THR Chi-restraints excluded: chain f3 residue 4 PHE Chi-restraints excluded: chain f3 residue 25 THR Chi-restraints excluded: chain f3 residue 56 VAL Chi-restraints excluded: chain f3 residue 69 THR Chi-restraints excluded: chain f3 residue 77 ARG Chi-restraints excluded: chain f3 residue 109 VAL Chi-restraints excluded: chain W3 residue 23 VAL Chi-restraints excluded: chain W3 residue 26 VAL Chi-restraints excluded: chain W3 residue 39 SER Chi-restraints excluded: chain w3 residue 23 VAL Chi-restraints excluded: chain w3 residue 25 THR Chi-restraints excluded: chain w3 residue 31 ARG Chi-restraints excluded: chain w3 residue 33 VAL Chi-restraints excluded: chain w3 residue 39 SER Chi-restraints excluded: chain U3 residue 9 LEU Chi-restraints excluded: chain U3 residue 17 LEU Chi-restraints excluded: chain U3 residue 52 THR Chi-restraints excluded: chain U3 residue 74 GLN Chi-restraints excluded: chain U3 residue 92 MET Chi-restraints excluded: chain U3 residue 102 ILE Chi-restraints excluded: chain U3 residue 110 TYR Chi-restraints excluded: chain U3 residue 120 LEU Chi-restraints excluded: chain U3 residue 122 SER Chi-restraints excluded: chain B3 residue 25 HIS Chi-restraints excluded: chain B3 residue 37 SER Chi-restraints excluded: chain B3 residue 50 LEU Chi-restraints excluded: chain B3 residue 55 ARG Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 84 SER Chi-restraints excluded: chain B3 residue 121 ASP Chi-restraints excluded: chain B3 residue 123 CYS Chi-restraints excluded: chain B3 residue 125 CYS Chi-restraints excluded: chain B3 residue 126 ILE Chi-restraints excluded: chain B3 residue 132 ARG Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 258 MET Chi-restraints excluded: chain B3 residue 283 GLU Chi-restraints excluded: chain B3 residue 340 ASN Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 434 SER Chi-restraints excluded: chain B3 residue 446 ASP Chi-restraints excluded: chain B3 residue 474 THR Chi-restraints excluded: chain B3 residue 484 ASP Chi-restraints excluded: chain b3 residue 39 ASN Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 133 THR Chi-restraints excluded: chain b3 residue 159 THR Chi-restraints excluded: chain b3 residue 186 SER Chi-restraints excluded: chain b3 residue 194 GLN Chi-restraints excluded: chain b3 residue 195 ILE Chi-restraints excluded: chain b3 residue 206 VAL Chi-restraints excluded: chain b3 residue 215 MET Chi-restraints excluded: chain b3 residue 255 MET Chi-restraints excluded: chain b3 residue 337 ASP Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 358 LEU Chi-restraints excluded: chain b3 residue 376 ASN Chi-restraints excluded: chain b3 residue 379 GLN Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 425 VAL Chi-restraints excluded: chain b3 residue 453 MET Chi-restraints excluded: chain b3 residue 456 ASP Chi-restraints excluded: chain b3 residue 478 GLU Chi-restraints excluded: chain b3 residue 489 ILE Chi-restraints excluded: chain f4 residue 12 ILE Chi-restraints excluded: chain f4 residue 25 THR Chi-restraints excluded: chain f4 residue 28 THR Chi-restraints excluded: chain f4 residue 33 GLU Chi-restraints excluded: chain f4 residue 56 VAL Chi-restraints excluded: chain f4 residue 58 VAL Chi-restraints excluded: chain f4 residue 64 SER Chi-restraints excluded: chain f4 residue 67 VAL Chi-restraints excluded: chain f4 residue 69 THR Chi-restraints excluded: chain f4 residue 90 VAL Chi-restraints excluded: chain f4 residue 109 VAL Chi-restraints excluded: chain W4 residue 7 LEU Chi-restraints excluded: chain W4 residue 21 LYS Chi-restraints excluded: chain W4 residue 23 VAL Chi-restraints excluded: chain W4 residue 34 GLU Chi-restraints excluded: chain W4 residue 39 SER Chi-restraints excluded: chain W4 residue 42 ASP Chi-restraints excluded: chain w4 residue 17 LEU Chi-restraints excluded: chain w4 residue 23 VAL Chi-restraints excluded: chain w4 residue 25 THR Chi-restraints excluded: chain w4 residue 38 THR Chi-restraints excluded: chain w4 residue 39 SER Chi-restraints excluded: chain U4 residue 19 LYS Chi-restraints excluded: chain U4 residue 22 THR Chi-restraints excluded: chain U4 residue 27 PHE Chi-restraints excluded: chain U4 residue 42 VAL Chi-restraints excluded: chain U4 residue 52 THR Chi-restraints excluded: chain U4 residue 91 VAL Chi-restraints excluded: chain U4 residue 110 TYR Chi-restraints excluded: chain U4 residue 117 ASP Chi-restraints excluded: chain U4 residue 122 SER Chi-restraints excluded: chain U4 residue 126 LEU Chi-restraints excluded: chain U4 residue 130 ILE Chi-restraints excluded: chain B4 residue 35 LEU Chi-restraints excluded: chain B4 residue 50 LEU Chi-restraints excluded: chain B4 residue 54 THR Chi-restraints excluded: chain B4 residue 82 VAL Chi-restraints excluded: chain B4 residue 125 CYS Chi-restraints excluded: chain B4 residue 131 LYS Chi-restraints excluded: chain B4 residue 151 LEU Chi-restraints excluded: chain B4 residue 173 SER Chi-restraints excluded: chain B4 residue 188 ASN Chi-restraints excluded: chain B4 residue 206 VAL Chi-restraints excluded: chain B4 residue 252 TYR Chi-restraints excluded: chain B4 residue 287 ASP Chi-restraints excluded: chain B4 residue 292 MET Chi-restraints excluded: chain B4 residue 333 LEU Chi-restraints excluded: chain B4 residue 337 ASP Chi-restraints excluded: chain B4 residue 340 ASN Chi-restraints excluded: chain B4 residue 341 LEU Chi-restraints excluded: chain B4 residue 355 GLU Chi-restraints excluded: chain B4 residue 357 SER Chi-restraints excluded: chain B4 residue 358 LEU Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 381 SER Chi-restraints excluded: chain B4 residue 392 SER Chi-restraints excluded: chain B4 residue 453 MET Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 132 ARG Chi-restraints excluded: chain b4 residue 144 MET Chi-restraints excluded: chain b4 residue 215 MET Chi-restraints excluded: chain b4 residue 226 LEU Chi-restraints excluded: chain b4 residue 240 VAL Chi-restraints excluded: chain b4 residue 273 ILE Chi-restraints excluded: chain b4 residue 283 GLU Chi-restraints excluded: chain b4 residue 340 ASN Chi-restraints excluded: chain b4 residue 349 ASN Chi-restraints excluded: chain b4 residue 358 LEU Chi-restraints excluded: chain f5 residue 4 PHE Chi-restraints excluded: chain f5 residue 29 ILE Chi-restraints excluded: chain f5 residue 30 THR Chi-restraints excluded: chain f5 residue 42 VAL Chi-restraints excluded: chain f5 residue 56 VAL Chi-restraints excluded: chain f5 residue 69 THR Chi-restraints excluded: chain f5 residue 109 VAL Chi-restraints excluded: chain W5 residue 23 VAL Chi-restraints excluded: chain W5 residue 38 THR Chi-restraints excluded: chain W5 residue 39 SER Chi-restraints excluded: chain W5 residue 51 GLU Chi-restraints excluded: chain w5 residue 23 VAL Chi-restraints excluded: chain w5 residue 39 SER Chi-restraints excluded: chain w5 residue 40 VAL Chi-restraints excluded: chain w5 residue 43 LEU Chi-restraints excluded: chain U5 residue 20 HIS Chi-restraints excluded: chain U5 residue 30 ARG Chi-restraints excluded: chain U5 residue 52 THR Chi-restraints excluded: chain U5 residue 58 SER Chi-restraints excluded: chain U5 residue 67 ILE Chi-restraints excluded: chain U5 residue 75 VAL Chi-restraints excluded: chain U5 residue 110 TYR Chi-restraints excluded: chain U5 residue 117 ASP Chi-restraints excluded: chain U5 residue 122 SER Chi-restraints excluded: chain B5 residue 25 HIS Chi-restraints excluded: chain B5 residue 42 SER Chi-restraints excluded: chain B5 residue 54 THR Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 84 SER Chi-restraints excluded: chain B5 residue 126 ILE Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 202 LEU Chi-restraints excluded: chain B5 residue 206 VAL Chi-restraints excluded: chain B5 residue 252 TYR Chi-restraints excluded: chain B5 residue 269 LEU Chi-restraints excluded: chain B5 residue 284 SER Chi-restraints excluded: chain B5 residue 358 LEU Chi-restraints excluded: chain B5 residue 359 LEU Chi-restraints excluded: chain B5 residue 425 VAL Chi-restraints excluded: chain B5 residue 434 SER Chi-restraints excluded: chain B5 residue 467 LEU Chi-restraints excluded: chain B5 residue 474 THR Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 109 ARG Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 159 THR Chi-restraints excluded: chain b5 residue 186 SER Chi-restraints excluded: chain b5 residue 194 GLN Chi-restraints excluded: chain b5 residue 206 VAL Chi-restraints excluded: chain b5 residue 218 LYS Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 254 VAL Chi-restraints excluded: chain b5 residue 333 LEU Chi-restraints excluded: chain b5 residue 355 GLU Chi-restraints excluded: chain b5 residue 358 LEU Chi-restraints excluded: chain b5 residue 362 ILE Chi-restraints excluded: chain b5 residue 425 VAL Chi-restraints excluded: chain b5 residue 466 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 460 optimal weight: 10.0000 chunk 740 optimal weight: 0.5980 chunk 452 optimal weight: 7.9990 chunk 351 optimal weight: 8.9990 chunk 514 optimal weight: 1.9990 chunk 777 optimal weight: 0.9990 chunk 715 optimal weight: 1.9990 chunk 618 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 477 optimal weight: 7.9990 chunk 379 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 356 GLN ** f2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 53 GLN ** B2 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 342 GLN ** B3 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 342 GLN b3 376 ASN ** W4 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U4 20 HIS ** B4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w5 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 342 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 63648 Z= 0.214 Angle : 0.761 16.082 86070 Z= 0.368 Chirality : 0.043 0.248 9066 Planarity : 0.005 0.122 11430 Dihedral : 5.159 69.092 8847 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.19 % Favored : 91.38 % Rotamer: Outliers : 6.03 % Allowed : 33.97 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.10), residues: 7866 helix: 1.18 (0.09), residues: 3408 sheet: -0.34 (0.16), residues: 1050 loop : -1.49 (0.11), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRPB5 393 HIS 0.006 0.001 HISU4 66 PHE 0.032 0.001 PHEB5 134 TYR 0.031 0.001 TYRU1 51 ARG 0.011 0.000 ARG b 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15732 Ramachandran restraints generated. 7866 Oldfield, 0 Emsley, 7866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1768 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 1382 time to evaluate : 5.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 34 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: W 49 GLU cc_start: 0.9333 (tm-30) cc_final: 0.9114 (tm-30) REVERT: w 51 GLU cc_start: 0.9402 (pt0) cc_final: 0.8948 (pt0) REVERT: U 4 MET cc_start: 0.4880 (mmp) cc_final: 0.4536 (mmp) REVERT: U 62 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8517 (tm-30) REVERT: U 134 MET cc_start: 0.8357 (mtm) cc_final: 0.8121 (mtm) REVERT: B 140 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: B 144 MET cc_start: 0.9233 (tpt) cc_final: 0.8960 (tpt) REVERT: B 366 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9322 (mm) REVERT: B 453 MET cc_start: 0.8243 (ppp) cc_final: 0.7916 (ppp) REVERT: B 463 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8607 (mm-30) REVERT: b 252 TYR cc_start: 0.9260 (OUTLIER) cc_final: 0.8250 (t80) REVERT: b 359 LEU cc_start: 0.9783 (OUTLIER) cc_final: 0.9470 (mm) REVERT: b 469 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8921 (mm-30) REVERT: w1 31 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7519 (mtm-85) REVERT: w1 49 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8973 (pm20) REVERT: U1 19 LYS cc_start: 0.9329 (ttpp) cc_final: 0.9096 (ttpp) REVERT: B1 241 GLU cc_start: 0.8290 (pp20) cc_final: 0.7716 (pp20) REVERT: B1 252 TYR cc_start: 0.9505 (OUTLIER) cc_final: 0.8292 (t80) REVERT: B1 256 GLU cc_start: 0.9071 (pm20) cc_final: 0.8839 (pm20) REVERT: B1 302 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7950 (mm-30) REVERT: B1 366 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9398 (mm) REVERT: B1 380 MET cc_start: 0.8632 (mmm) cc_final: 0.8388 (mmm) REVERT: B1 386 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8621 (mmm-85) REVERT: B1 453 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7940 (ppp) REVERT: B1 463 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8863 (mm-30) REVERT: b1 439 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8496 (mtt180) REVERT: f2 86 GLU cc_start: 0.9190 (tp30) cc_final: 0.8852 (tm-30) REVERT: W2 44 LYS cc_start: 0.9762 (mtpp) cc_final: 0.9560 (mtmm) REVERT: w2 16 ASP cc_start: 0.9261 (t70) cc_final: 0.8961 (t70) REVERT: w2 51 GLU cc_start: 0.9198 (pt0) cc_final: 0.8905 (pt0) REVERT: U2 62 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8263 (tm-30) REVERT: B2 187 ARG cc_start: 0.9236 (ttm110) cc_final: 0.8781 (ttm110) REVERT: B2 265 GLN cc_start: 0.8886 (mm110) cc_final: 0.8646 (mm-40) REVERT: B2 346 ASP cc_start: 0.8890 (t0) cc_final: 0.8656 (t0) REVERT: B2 463 GLU cc_start: 0.9473 (OUTLIER) cc_final: 0.8904 (mm-30) REVERT: b2 137 MET cc_start: 0.9585 (mmm) cc_final: 0.9316 (mmm) REVERT: b2 356 GLN cc_start: 0.9322 (mm-40) cc_final: 0.8978 (mm-40) REVERT: b2 453 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8358 (ppp) REVERT: b2 460 GLU cc_start: 0.8924 (tp30) cc_final: 0.8635 (tp30) REVERT: b2 479 CYS cc_start: 0.9323 (m) cc_final: 0.8839 (p) REVERT: f3 16 ASP cc_start: 0.8877 (t0) cc_final: 0.8600 (t0) REVERT: f3 17 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8586 (mm-30) REVERT: f3 77 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8454 (ttt180) REVERT: w3 27 GLN cc_start: 0.9293 (tt0) cc_final: 0.8680 (tt0) REVERT: w3 31 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7644 (mtm-85) REVERT: U3 50 GLU cc_start: 0.7870 (mp0) cc_final: 0.7309 (mp0) REVERT: U3 62 GLN cc_start: 0.8570 (pp30) cc_final: 0.7725 (pm20) REVERT: U3 64 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8572 (tt0) REVERT: U3 105 MET cc_start: 0.9180 (tpp) cc_final: 0.8972 (tpp) REVERT: U3 120 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9437 (mm) REVERT: B3 140 GLU cc_start: 0.9176 (tp30) cc_final: 0.8856 (tt0) REVERT: B3 463 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8685 (mm-30) REVERT: b3 252 TYR cc_start: 0.9311 (OUTLIER) cc_final: 0.8354 (t80) REVERT: b3 339 LEU cc_start: 0.9463 (tp) cc_final: 0.9098 (tp) REVERT: b3 379 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: b3 453 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7656 (ppp) REVERT: b3 498 MET cc_start: 0.9212 (tmm) cc_final: 0.8965 (tmm) REVERT: W4 21 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8715 (mmmm) REVERT: W4 45 LYS cc_start: 0.9599 (mtpp) cc_final: 0.9328 (mtmm) REVERT: U4 27 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.7076 (m-10) REVERT: U4 114 ARG cc_start: 0.8566 (ptp-110) cc_final: 0.8187 (ptp-110) REVERT: B4 35 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9118 (pp) REVERT: B4 252 TYR cc_start: 0.9495 (OUTLIER) cc_final: 0.8431 (t80) REVERT: B4 366 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9191 (mm) REVERT: B4 393 TRP cc_start: 0.9178 (t60) cc_final: 0.8908 (t60) REVERT: b4 359 LEU cc_start: 0.9772 (mm) cc_final: 0.9545 (mm) REVERT: b4 399 ARG cc_start: 0.9344 (mmm-85) cc_final: 0.8805 (tpp80) REVERT: b4 469 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8897 (mm-30) REVERT: b4 472 LEU cc_start: 0.9428 (mt) cc_final: 0.9221 (tt) REVERT: w5 51 GLU cc_start: 0.9213 (pt0) cc_final: 0.8975 (pt0) REVERT: U5 62 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8579 (tm-30) REVERT: B5 112 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9206 (mm-30) REVERT: B5 150 GLU cc_start: 0.8563 (pt0) cc_final: 0.8308 (pt0) REVERT: B5 197 ASP cc_start: 0.9534 (p0) cc_final: 0.9245 (p0) REVERT: B5 241 GLU cc_start: 0.8409 (pp20) cc_final: 0.8024 (pp20) REVERT: B5 463 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8498 (mm-30) REVERT: b5 109 ARG cc_start: 0.9459 (OUTLIER) cc_final: 0.9059 (ptp-110) REVERT: b5 137 MET cc_start: 0.9607 (mmm) cc_final: 0.9402 (mmm) REVERT: b5 194 GLN cc_start: 0.9490 (OUTLIER) cc_final: 0.9102 (tp40) REVERT: b5 252 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.8410 (t80) REVERT: b5 466 MET cc_start: 0.9488 (OUTLIER) cc_final: 0.8545 (ppp) outliers start: 386 outliers final: 334 residues processed: 1612 average time/residue: 0.5742 time to fit residues: 1564.5151 Evaluate side-chains 1710 residues out of total 6426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1346 time to evaluate : 5.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 4 PHE Chi-restraints excluded: chain f residue 6 ASN Chi-restraints excluded: chain f residue 12 ILE Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 34 GLN Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 109 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain w residue 23 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 33 VAL Chi-restraints excluded: chain w residue 42 ASP Chi-restraints excluded: chain w residue 52 VAL Chi-restraints excluded: chain w residue 56 MET Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain U residue 110 TYR Chi-restraints excluded: chain U residue 117 ASP Chi-restraints excluded: chain U residue 122 SER Chi-restraints excluded: chain U residue 123 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain b residue 25 HIS Chi-restraints excluded: chain b residue 39 ASN Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain b residue 226 LEU Chi-restraints excluded: chain b residue 252 TYR Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 337 ASP Chi-restraints excluded: chain b residue 339 LEU Chi-restraints excluded: chain b residue 358 LEU Chi-restraints excluded: chain b residue 359 LEU Chi-restraints excluded: chain b residue 456 ASP Chi-restraints excluded: chain b residue 466 MET Chi-restraints excluded: chain b residue 474 THR Chi-restraints excluded: chain f1 residue 4 PHE Chi-restraints excluded: chain f1 residue 25 THR Chi-restraints excluded: chain f1 residue 29 ILE Chi-restraints excluded: chain f1 residue 30 THR Chi-restraints excluded: chain f1 residue 56 VAL Chi-restraints excluded: chain f1 residue 109 VAL Chi-restraints excluded: chain W1 residue 23 VAL Chi-restraints excluded: chain W1 residue 39 SER Chi-restraints excluded: chain W1 residue 52 VAL Chi-restraints excluded: chain w1 residue 23 VAL Chi-restraints excluded: chain w1 residue 25 THR Chi-restraints excluded: chain w1 residue 31 ARG Chi-restraints excluded: chain w1 residue 33 VAL Chi-restraints excluded: chain w1 residue 38 THR Chi-restraints excluded: chain w1 residue 39 SER Chi-restraints excluded: chain w1 residue 49 GLU Chi-restraints excluded: chain w1 residue 53 GLN Chi-restraints excluded: chain U1 residue 44 VAL Chi-restraints excluded: chain U1 residue 110 TYR Chi-restraints excluded: chain U1 residue 117 ASP Chi-restraints excluded: chain U1 residue 126 LEU Chi-restraints excluded: chain B1 residue 25 HIS Chi-restraints excluded: chain B1 residue 54 THR Chi-restraints excluded: chain B1 residue 76 LEU Chi-restraints excluded: chain B1 residue 125 CYS Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 182 ASN Chi-restraints excluded: chain B1 residue 252 TYR Chi-restraints excluded: chain B1 residue 269 LEU Chi-restraints excluded: chain B1 residue 302 GLU Chi-restraints excluded: chain B1 residue 325 LEU Chi-restraints excluded: chain B1 residue 333 LEU Chi-restraints excluded: chain B1 residue 337 ASP Chi-restraints excluded: chain B1 residue 355 GLU Chi-restraints excluded: chain B1 residue 359 LEU Chi-restraints excluded: chain B1 residue 366 LEU Chi-restraints excluded: chain B1 residue 386 ARG Chi-restraints excluded: chain B1 residue 392 SER Chi-restraints excluded: chain B1 residue 453 MET Chi-restraints excluded: chain B1 residue 461 VAL Chi-restraints excluded: chain B1 residue 468 ILE Chi-restraints excluded: chain B1 residue 474 THR Chi-restraints excluded: chain b1 residue 31 PHE Chi-restraints excluded: chain b1 residue 39 ASN Chi-restraints excluded: chain b1 residue 45 VAL Chi-restraints excluded: chain b1 residue 50 LEU Chi-restraints excluded: chain b1 residue 144 MET Chi-restraints excluded: chain b1 residue 159 THR Chi-restraints excluded: chain b1 residue 185 ASP Chi-restraints excluded: chain b1 residue 186 SER Chi-restraints excluded: chain b1 residue 226 LEU Chi-restraints excluded: chain b1 residue 356 GLN Chi-restraints excluded: chain b1 residue 358 LEU Chi-restraints excluded: chain b1 residue 413 LEU Chi-restraints excluded: chain b1 residue 425 VAL Chi-restraints excluded: chain b1 residue 439 ARG Chi-restraints excluded: chain b1 residue 463 GLU Chi-restraints excluded: chain b1 residue 474 THR Chi-restraints excluded: chain b1 residue 478 GLU Chi-restraints excluded: chain f2 residue 7 LEU Chi-restraints excluded: chain f2 residue 56 VAL Chi-restraints excluded: chain f2 residue 67 VAL Chi-restraints excluded: chain f2 residue 109 VAL Chi-restraints excluded: chain W2 residue 23 VAL Chi-restraints excluded: chain W2 residue 34 GLU Chi-restraints excluded: chain W2 residue 39 SER Chi-restraints excluded: chain W2 residue 47 ILE Chi-restraints excluded: chain W2 residue 50 LEU Chi-restraints excluded: chain W2 residue 51 GLU Chi-restraints excluded: chain w2 residue 23 VAL Chi-restraints excluded: chain w2 residue 39 SER Chi-restraints excluded: chain w2 residue 52 VAL Chi-restraints excluded: chain U2 residue 9 LEU Chi-restraints excluded: chain U2 residue 33 VAL Chi-restraints excluded: chain U2 residue 42 VAL Chi-restraints excluded: chain U2 residue 52 THR Chi-restraints excluded: chain U2 residue 106 VAL Chi-restraints excluded: chain U2 residue 110 TYR Chi-restraints excluded: chain U2 residue 114 ARG Chi-restraints excluded: chain U2 residue 122 SER Chi-restraints excluded: chain U2 residue 123 SER Chi-restraints excluded: chain B2 residue 25 HIS Chi-restraints excluded: chain B2 residue 35 LEU Chi-restraints excluded: chain B2 residue 43 GLU Chi-restraints excluded: chain B2 residue 63 LEU Chi-restraints excluded: chain B2 residue 82 VAL Chi-restraints excluded: chain B2 residue 133 THR Chi-restraints excluded: chain B2 residue 182 ASN Chi-restraints excluded: chain B2 residue 206 VAL Chi-restraints excluded: chain B2 residue 215 MET Chi-restraints excluded: chain B2 residue 252 TYR Chi-restraints excluded: chain B2 residue 341 LEU Chi-restraints excluded: chain B2 residue 349 ASN Chi-restraints excluded: chain B2 residue 358 LEU Chi-restraints excluded: chain B2 residue 359 LEU Chi-restraints excluded: chain B2 residue 366 LEU Chi-restraints excluded: chain B2 residue 425 VAL Chi-restraints excluded: chain B2 residue 455 ILE Chi-restraints excluded: chain B2 residue 463 GLU Chi-restraints excluded: chain B2 residue 467 LEU Chi-restraints excluded: chain B2 residue 474 THR Chi-restraints excluded: chain b2 residue 39 ASN Chi-restraints excluded: chain b2 residue 49 LEU Chi-restraints excluded: chain b2 residue 109 ARG Chi-restraints excluded: chain b2 residue 132 ARG Chi-restraints excluded: chain b2 residue 171 MET Chi-restraints excluded: chain b2 residue 202 LEU Chi-restraints excluded: chain b2 residue 226 LEU Chi-restraints excluded: chain b2 residue 240 VAL Chi-restraints excluded: chain b2 residue 269 LEU Chi-restraints excluded: chain b2 residue 283 GLU Chi-restraints excluded: chain b2 residue 340 ASN Chi-restraints excluded: chain b2 residue 358 LEU Chi-restraints excluded: chain b2 residue 425 VAL Chi-restraints excluded: chain b2 residue 453 MET Chi-restraints excluded: chain b2 residue 466 MET Chi-restraints excluded: chain b2 residue 474 THR Chi-restraints excluded: chain f3 residue 4 PHE Chi-restraints excluded: chain f3 residue 25 THR Chi-restraints excluded: chain f3 residue 56 VAL Chi-restraints excluded: chain f3 residue 69 THR Chi-restraints excluded: chain f3 residue 77 ARG Chi-restraints excluded: chain f3 residue 109 VAL Chi-restraints excluded: chain W3 residue 23 VAL Chi-restraints excluded: chain W3 residue 26 VAL Chi-restraints excluded: chain W3 residue 39 SER Chi-restraints excluded: chain w3 residue 23 VAL Chi-restraints excluded: chain w3 residue 25 THR Chi-restraints excluded: chain w3 residue 31 ARG Chi-restraints excluded: chain w3 residue 33 VAL Chi-restraints excluded: chain w3 residue 39 SER Chi-restraints excluded: chain U3 residue 9 LEU Chi-restraints excluded: chain U3 residue 17 LEU Chi-restraints excluded: chain U3 residue 52 THR Chi-restraints excluded: chain U3 residue 74 GLN Chi-restraints excluded: chain U3 residue 102 ILE Chi-restraints excluded: chain U3 residue 110 TYR Chi-restraints excluded: chain U3 residue 120 LEU Chi-restraints excluded: chain B3 residue 25 HIS Chi-restraints excluded: chain B3 residue 37 SER Chi-restraints excluded: chain B3 residue 50 LEU Chi-restraints excluded: chain B3 residue 74 ILE Chi-restraints excluded: chain B3 residue 84 SER Chi-restraints excluded: chain B3 residue 121 ASP Chi-restraints excluded: chain B3 residue 123 CYS Chi-restraints excluded: chain B3 residue 125 CYS Chi-restraints excluded: chain B3 residue 126 ILE Chi-restraints excluded: chain B3 residue 132 ARG Chi-restraints excluded: chain B3 residue 182 ASN Chi-restraints excluded: chain B3 residue 206 VAL Chi-restraints excluded: chain B3 residue 258 MET Chi-restraints excluded: chain B3 residue 273 ILE Chi-restraints excluded: chain B3 residue 283 GLU Chi-restraints excluded: chain B3 residue 340 ASN Chi-restraints excluded: chain B3 residue 358 LEU Chi-restraints excluded: chain B3 residue 392 SER Chi-restraints excluded: chain B3 residue 425 VAL Chi-restraints excluded: chain B3 residue 434 SER Chi-restraints excluded: chain B3 residue 446 ASP Chi-restraints excluded: chain B3 residue 474 THR Chi-restraints excluded: chain b3 residue 39 ASN Chi-restraints excluded: chain b3 residue 43 GLU Chi-restraints excluded: chain b3 residue 133 THR Chi-restraints excluded: chain b3 residue 159 THR Chi-restraints excluded: chain b3 residue 166 ARG Chi-restraints excluded: chain b3 residue 186 SER Chi-restraints excluded: chain b3 residue 194 GLN Chi-restraints excluded: chain b3 residue 195 ILE Chi-restraints excluded: chain b3 residue 215 MET Chi-restraints excluded: chain b3 residue 252 TYR Chi-restraints excluded: chain b3 residue 255 MET Chi-restraints excluded: chain b3 residue 337 ASP Chi-restraints excluded: chain b3 residue 340 ASN Chi-restraints excluded: chain b3 residue 358 LEU Chi-restraints excluded: chain b3 residue 376 ASN Chi-restraints excluded: chain b3 residue 379 GLN Chi-restraints excluded: chain b3 residue 392 SER Chi-restraints excluded: chain b3 residue 425 VAL Chi-restraints excluded: chain b3 residue 453 MET Chi-restraints excluded: chain b3 residue 456 ASP Chi-restraints excluded: chain b3 residue 478 GLU Chi-restraints excluded: chain b3 residue 489 ILE Chi-restraints excluded: chain f4 residue 12 ILE Chi-restraints excluded: chain f4 residue 25 THR Chi-restraints excluded: chain f4 residue 28 THR Chi-restraints excluded: chain f4 residue 33 GLU Chi-restraints excluded: chain f4 residue 56 VAL Chi-restraints excluded: chain f4 residue 58 VAL Chi-restraints excluded: chain f4 residue 64 SER Chi-restraints excluded: chain f4 residue 69 THR Chi-restraints excluded: chain f4 residue 90 VAL Chi-restraints excluded: chain f4 residue 109 VAL Chi-restraints excluded: chain W4 residue 7 LEU Chi-restraints excluded: chain W4 residue 21 LYS Chi-restraints excluded: chain W4 residue 23 VAL Chi-restraints excluded: chain W4 residue 34 GLU Chi-restraints excluded: chain W4 residue 39 SER Chi-restraints excluded: chain w4 residue 17 LEU Chi-restraints excluded: chain w4 residue 23 VAL Chi-restraints excluded: chain w4 residue 25 THR Chi-restraints excluded: chain w4 residue 38 THR Chi-restraints excluded: chain w4 residue 39 SER Chi-restraints excluded: chain U4 residue 20 HIS Chi-restraints excluded: chain U4 residue 22 THR Chi-restraints excluded: chain U4 residue 27 PHE Chi-restraints excluded: chain U4 residue 42 VAL Chi-restraints excluded: chain U4 residue 52 THR Chi-restraints excluded: chain U4 residue 91 VAL Chi-restraints excluded: chain U4 residue 110 TYR Chi-restraints excluded: chain U4 residue 117 ASP Chi-restraints excluded: chain U4 residue 122 SER Chi-restraints excluded: chain U4 residue 126 LEU Chi-restraints excluded: chain U4 residue 130 ILE Chi-restraints excluded: chain B4 residue 35 LEU Chi-restraints excluded: chain B4 residue 50 LEU Chi-restraints excluded: chain B4 residue 54 THR Chi-restraints excluded: chain B4 residue 82 VAL Chi-restraints excluded: chain B4 residue 125 CYS Chi-restraints excluded: chain B4 residue 151 LEU Chi-restraints excluded: chain B4 residue 173 SER Chi-restraints excluded: chain B4 residue 188 ASN Chi-restraints excluded: chain B4 residue 206 VAL Chi-restraints excluded: chain B4 residue 252 TYR Chi-restraints excluded: chain B4 residue 287 ASP Chi-restraints excluded: chain B4 residue 292 MET Chi-restraints excluded: chain B4 residue 333 LEU Chi-restraints excluded: chain B4 residue 337 ASP Chi-restraints excluded: chain B4 residue 340 ASN Chi-restraints excluded: chain B4 residue 341 LEU Chi-restraints excluded: chain B4 residue 355 GLU Chi-restraints excluded: chain B4 residue 357 SER Chi-restraints excluded: chain B4 residue 358 LEU Chi-restraints excluded: chain B4 residue 366 LEU Chi-restraints excluded: chain B4 residue 381 SER Chi-restraints excluded: chain B4 residue 392 SER Chi-restraints excluded: chain B4 residue 453 MET Chi-restraints excluded: chain b4 residue 45 VAL Chi-restraints excluded: chain b4 residue 132 ARG Chi-restraints excluded: chain b4 residue 144 MET Chi-restraints excluded: chain b4 residue 157 TRP Chi-restraints excluded: chain b4 residue 215 MET Chi-restraints excluded: chain b4 residue 226 LEU Chi-restraints excluded: chain b4 residue 240 VAL Chi-restraints excluded: chain b4 residue 273 ILE Chi-restraints excluded: chain b4 residue 340 ASN Chi-restraints excluded: chain b4 residue 349 ASN Chi-restraints excluded: chain b4 residue 358 LEU Chi-restraints excluded: chain b4 residue 413 LEU Chi-restraints excluded: chain f5 residue 4 PHE Chi-restraints excluded: chain f5 residue 29 ILE Chi-restraints excluded: chain f5 residue 42 VAL Chi-restraints excluded: chain f5 residue 56 VAL Chi-restraints excluded: chain f5 residue 69 THR Chi-restraints excluded: chain f5 residue 109 VAL Chi-restraints excluded: chain W5 residue 23 VAL Chi-restraints excluded: chain W5 residue 39 SER Chi-restraints excluded: chain W5 residue 51 GLU Chi-restraints excluded: chain w5 residue 23 VAL Chi-restraints excluded: chain w5 residue 39 SER Chi-restraints excluded: chain w5 residue 40 VAL Chi-restraints excluded: chain w5 residue 43 LEU Chi-restraints excluded: chain w5 residue 68 VAL Chi-restraints excluded: chain U5 residue 20 HIS Chi-restraints excluded: chain U5 residue 30 ARG Chi-restraints excluded: chain U5 residue 52 THR Chi-restraints excluded: chain U5 residue 58 SER Chi-restraints excluded: chain U5 residue 67 ILE Chi-restraints excluded: chain U5 residue 75 VAL Chi-restraints excluded: chain U5 residue 110 TYR Chi-restraints excluded: chain U5 residue 117 ASP Chi-restraints excluded: chain U5 residue 122 SER Chi-restraints excluded: chain B5 residue 25 HIS Chi-restraints excluded: chain B5 residue 42 SER Chi-restraints excluded: chain B5 residue 54 THR Chi-restraints excluded: chain B5 residue 63 LEU Chi-restraints excluded: chain B5 residue 126 ILE Chi-restraints excluded: chain B5 residue 182 ASN Chi-restraints excluded: chain B5 residue 202 LEU Chi-restraints excluded: chain B5 residue 206 VAL Chi-restraints excluded: chain B5 residue 252 TYR Chi-restraints excluded: chain B5 residue 269 LEU Chi-restraints excluded: chain B5 residue 284 SER Chi-restraints excluded: chain B5 residue 337 ASP Chi-restraints excluded: chain B5 residue 340 ASN Chi-restraints excluded: chain B5 residue 358 LEU Chi-restraints excluded: chain B5 residue 359 LEU Chi-restraints excluded: chain B5 residue 425 VAL Chi-restraints excluded: chain B5 residue 434 SER Chi-restraints excluded: chain B5 residue 455 ILE Chi-restraints excluded: chain B5 residue 467 LEU Chi-restraints excluded: chain B5 residue 489 ILE Chi-restraints excluded: chain b5 residue 43 GLU Chi-restraints excluded: chain b5 residue 109 ARG Chi-restraints excluded: chain b5 residue 126 ILE Chi-restraints excluded: chain b5 residue 159 THR Chi-restraints excluded: chain b5 residue 186 SER Chi-restraints excluded: chain b5 residue 194 GLN Chi-restraints excluded: chain b5 residue 202 LEU Chi-restraints excluded: chain b5 residue 206 VAL Chi-restraints excluded: chain b5 residue 218 LYS Chi-restraints excluded: chain b5 residue 252 TYR Chi-restraints excluded: chain b5 residue 333 LEU Chi-restraints excluded: chain b5 residue 355 GLU Chi-restraints excluded: chain b5 residue 358 LEU Chi-restraints excluded: chain b5 residue 362 ILE Chi-restraints excluded: chain b5 residue 392 SER Chi-restraints excluded: chain b5 residue 425 VAL Chi-restraints excluded: chain b5 residue 466 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 491 optimal weight: 0.3980 chunk 659 optimal weight: 30.0000 chunk 189 optimal weight: 3.9990 chunk 570 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 619 optimal weight: 20.0000 chunk 259 optimal weight: 0.1980 chunk 636 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 356 GLN ** f2 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w2 53 GLN ** B2 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 342 GLN w3 4 GLN ** B3 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 34 GLN b3 342 GLN b3 376 ASN ** W4 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b4 342 GLN ** B5 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5 342 GLN b5 372 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.074045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.060196 restraints weight = 196255.725| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 4.46 r_work: 0.2689 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 63648 Z= 0.258 Angle : 0.848 59.199 86070 Z= 0.446 Chirality : 0.045 1.063 9066 Planarity : 0.006 0.220 11430 Dihedral : 5.166 69.064 8847 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.15 % Favored : 91.39 % Rotamer: Outliers : 5.98 % Allowed : 34.16 % Favored : 59.86 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.10), residues: 7866 helix: 1.17 (0.09), residues: 3408 sheet: -0.35 (0.16), residues: 1050 loop : -1.48 (0.11), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRPb5 393 HIS 0.377 0.002 HISU4 20 PHE 0.029 0.001 PHEB5 134 TYR 0.024 0.001 TYRU1 51 ARG 0.014 0.000 ARGw4 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20613.76 seconds wall clock time: 357 minutes 55.45 seconds (21475.45 seconds total)