Starting phenix.real_space_refine on Tue Mar 12 02:02:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/03_2024/6x6k_22076.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/03_2024/6x6k_22076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/03_2024/6x6k_22076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/03_2024/6x6k_22076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/03_2024/6x6k_22076.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/03_2024/6x6k_22076.pdb" } resolution = 3.1 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= 0.002 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 196 5.16 5 C 39060 2.51 5 N 10332 2.21 5 O 11382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AT ASP 58": "OD1" <-> "OD2" Residue "AT ASP 72": "OD1" <-> "OD2" Residue "AT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT ASP 119": "OD1" <-> "OD2" Residue "AT ASP 172": "OD1" <-> "OD2" Residue "AT ARG 213": "NH1" <-> "NH2" Residue "AX GLU 366": "OE1" <-> "OE2" Residue "AX ARG 394": "NH1" <-> "NH2" Residue "AX ARG 410": "NH1" <-> "NH2" Residue "AX ASP 422": "OD1" <-> "OD2" Residue "AX ASP 452": "OD1" <-> "OD2" Residue "AX ASP 456": "OD1" <-> "OD2" Residue "AX ARG 465": "NH1" <-> "NH2" Residue "AX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX ARG 468": "NH1" <-> "NH2" Residue "AY GLU 1783": "OE1" <-> "OE2" Residue "AY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY ASP 1884": "OD1" <-> "OD2" Residue "BT ASP 58": "OD1" <-> "OD2" Residue "BT ASP 72": "OD1" <-> "OD2" Residue "BT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT ASP 119": "OD1" <-> "OD2" Residue "BT ASP 172": "OD1" <-> "OD2" Residue "BT ARG 213": "NH1" <-> "NH2" Residue "BX GLU 366": "OE1" <-> "OE2" Residue "BX ARG 394": "NH1" <-> "NH2" Residue "BX ARG 410": "NH1" <-> "NH2" Residue "BX ASP 422": "OD1" <-> "OD2" Residue "BX ASP 452": "OD1" <-> "OD2" Residue "BX ASP 456": "OD1" <-> "OD2" Residue "BX ARG 465": "NH1" <-> "NH2" Residue "BX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BX ARG 468": "NH1" <-> "NH2" Residue "BY GLU 1783": "OE1" <-> "OE2" Residue "BY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BY ASP 1884": "OD1" <-> "OD2" Residue "CT ASP 58": "OD1" <-> "OD2" Residue "CT ASP 72": "OD1" <-> "OD2" Residue "CT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT ASP 119": "OD1" <-> "OD2" Residue "CT ASP 172": "OD1" <-> "OD2" Residue "CT ARG 213": "NH1" <-> "NH2" Residue "CX GLU 366": "OE1" <-> "OE2" Residue "CX ARG 394": "NH1" <-> "NH2" Residue "CX ARG 410": "NH1" <-> "NH2" Residue "CX ASP 422": "OD1" <-> "OD2" Residue "CX ASP 452": "OD1" <-> "OD2" Residue "CX ASP 456": "OD1" <-> "OD2" Residue "CX ARG 465": "NH1" <-> "NH2" Residue "CX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CX ARG 468": "NH1" <-> "NH2" Residue "CY GLU 1783": "OE1" <-> "OE2" Residue "CY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY ASP 1884": "OD1" <-> "OD2" Residue "DT ASP 58": "OD1" <-> "OD2" Residue "DT ASP 72": "OD1" <-> "OD2" Residue "DT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DT ASP 119": "OD1" <-> "OD2" Residue "DT ASP 172": "OD1" <-> "OD2" Residue "DT ARG 213": "NH1" <-> "NH2" Residue "DX GLU 366": "OE1" <-> "OE2" Residue "DX ARG 394": "NH1" <-> "NH2" Residue "DX ARG 410": "NH1" <-> "NH2" Residue "DX ASP 422": "OD1" <-> "OD2" Residue "DX ASP 452": "OD1" <-> "OD2" Residue "DX ASP 456": "OD1" <-> "OD2" Residue "DX ARG 465": "NH1" <-> "NH2" Residue "DX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DX ARG 468": "NH1" <-> "NH2" Residue "DY GLU 1783": "OE1" <-> "OE2" Residue "DY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DY ASP 1884": "OD1" <-> "OD2" Residue "ET ASP 58": "OD1" <-> "OD2" Residue "ET ASP 72": "OD1" <-> "OD2" Residue "ET TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ET ASP 119": "OD1" <-> "OD2" Residue "ET ASP 172": "OD1" <-> "OD2" Residue "ET ARG 213": "NH1" <-> "NH2" Residue "EX GLU 366": "OE1" <-> "OE2" Residue "EX ARG 394": "NH1" <-> "NH2" Residue "EX ARG 410": "NH1" <-> "NH2" Residue "EX ASP 422": "OD1" <-> "OD2" Residue "EX ASP 452": "OD1" <-> "OD2" Residue "EX ASP 456": "OD1" <-> "OD2" Residue "EX ARG 465": "NH1" <-> "NH2" Residue "EX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EX ARG 468": "NH1" <-> "NH2" Residue "EY GLU 1783": "OE1" <-> "OE2" Residue "EY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EY ASP 1884": "OD1" <-> "OD2" Residue "FT ASP 58": "OD1" <-> "OD2" Residue "FT ASP 72": "OD1" <-> "OD2" Residue "FT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FT ASP 119": "OD1" <-> "OD2" Residue "FT ASP 172": "OD1" <-> "OD2" Residue "FT ARG 213": "NH1" <-> "NH2" Residue "FX GLU 366": "OE1" <-> "OE2" Residue "FX ARG 394": "NH1" <-> "NH2" Residue "FX ARG 410": "NH1" <-> "NH2" Residue "FX ASP 422": "OD1" <-> "OD2" Residue "FX ASP 452": "OD1" <-> "OD2" Residue "FX ASP 456": "OD1" <-> "OD2" Residue "FX ARG 465": "NH1" <-> "NH2" Residue "FX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FX ARG 468": "NH1" <-> "NH2" Residue "FY GLU 1783": "OE1" <-> "OE2" Residue "FY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FY ASP 1884": "OD1" <-> "OD2" Residue "GT ASP 58": "OD1" <-> "OD2" Residue "GT ASP 72": "OD1" <-> "OD2" Residue "GT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GT ASP 119": "OD1" <-> "OD2" Residue "GT ASP 172": "OD1" <-> "OD2" Residue "GT ARG 213": "NH1" <-> "NH2" Residue "GX GLU 366": "OE1" <-> "OE2" Residue "GX ARG 394": "NH1" <-> "NH2" Residue "GX ARG 410": "NH1" <-> "NH2" Residue "GX ASP 422": "OD1" <-> "OD2" Residue "GX ASP 452": "OD1" <-> "OD2" Residue "GX ASP 456": "OD1" <-> "OD2" Residue "GX ARG 465": "NH1" <-> "NH2" Residue "GX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GX ARG 468": "NH1" <-> "NH2" Residue "GY GLU 1783": "OE1" <-> "OE2" Residue "GY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GY ASP 1884": "OD1" <-> "OD2" Residue "HT ASP 58": "OD1" <-> "OD2" Residue "HT ASP 72": "OD1" <-> "OD2" Residue "HT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HT ASP 119": "OD1" <-> "OD2" Residue "HT ASP 172": "OD1" <-> "OD2" Residue "HT ARG 213": "NH1" <-> "NH2" Residue "HX GLU 366": "OE1" <-> "OE2" Residue "HX ARG 394": "NH1" <-> "NH2" Residue "HX ARG 410": "NH1" <-> "NH2" Residue "HX ASP 422": "OD1" <-> "OD2" Residue "HX ASP 452": "OD1" <-> "OD2" Residue "HX ASP 456": "OD1" <-> "OD2" Residue "HX ARG 465": "NH1" <-> "NH2" Residue "HX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HX ARG 468": "NH1" <-> "NH2" Residue "HY GLU 1783": "OE1" <-> "OE2" Residue "HY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HY ASP 1884": "OD1" <-> "OD2" Residue "IT ASP 58": "OD1" <-> "OD2" Residue "IT ASP 72": "OD1" <-> "OD2" Residue "IT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IT ASP 119": "OD1" <-> "OD2" Residue "IT ASP 172": "OD1" <-> "OD2" Residue "IT ARG 213": "NH1" <-> "NH2" Residue "IX GLU 366": "OE1" <-> "OE2" Residue "IX ARG 394": "NH1" <-> "NH2" Residue "IX ARG 410": "NH1" <-> "NH2" Residue "IX ASP 422": "OD1" <-> "OD2" Residue "IX ASP 452": "OD1" <-> "OD2" Residue "IX ASP 456": "OD1" <-> "OD2" Residue "IX ARG 465": "NH1" <-> "NH2" Residue "IX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IX ARG 468": "NH1" <-> "NH2" Residue "IY GLU 1783": "OE1" <-> "OE2" Residue "IY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IY ASP 1884": "OD1" <-> "OD2" Residue "JT ASP 58": "OD1" <-> "OD2" Residue "JT ASP 72": "OD1" <-> "OD2" Residue "JT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JT ASP 119": "OD1" <-> "OD2" Residue "JT ASP 172": "OD1" <-> "OD2" Residue "JT ARG 213": "NH1" <-> "NH2" Residue "JX GLU 366": "OE1" <-> "OE2" Residue "JX ARG 394": "NH1" <-> "NH2" Residue "JX ARG 410": "NH1" <-> "NH2" Residue "JX ASP 422": "OD1" <-> "OD2" Residue "JX ASP 452": "OD1" <-> "OD2" Residue "JX ASP 456": "OD1" <-> "OD2" Residue "JX ARG 465": "NH1" <-> "NH2" Residue "JX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JX ARG 468": "NH1" <-> "NH2" Residue "JY GLU 1783": "OE1" <-> "OE2" Residue "JY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JY ASP 1884": "OD1" <-> "OD2" Residue "KT ASP 58": "OD1" <-> "OD2" Residue "KT ASP 72": "OD1" <-> "OD2" Residue "KT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KT ASP 119": "OD1" <-> "OD2" Residue "KT ASP 172": "OD1" <-> "OD2" Residue "KT ARG 213": "NH1" <-> "NH2" Residue "KX GLU 366": "OE1" <-> "OE2" Residue "KX ARG 394": "NH1" <-> "NH2" Residue "KX ARG 410": "NH1" <-> "NH2" Residue "KX ASP 422": "OD1" <-> "OD2" Residue "KX ASP 452": "OD1" <-> "OD2" Residue "KX ASP 456": "OD1" <-> "OD2" Residue "KX ARG 465": "NH1" <-> "NH2" Residue "KX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KX ARG 468": "NH1" <-> "NH2" Residue "KY GLU 1783": "OE1" <-> "OE2" Residue "KY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KY ASP 1884": "OD1" <-> "OD2" Residue "LT ASP 58": "OD1" <-> "OD2" Residue "LT ASP 72": "OD1" <-> "OD2" Residue "LT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT ASP 119": "OD1" <-> "OD2" Residue "LT ASP 172": "OD1" <-> "OD2" Residue "LT ARG 213": "NH1" <-> "NH2" Residue "LX GLU 366": "OE1" <-> "OE2" Residue "LX ARG 394": "NH1" <-> "NH2" Residue "LX ARG 410": "NH1" <-> "NH2" Residue "LX ASP 422": "OD1" <-> "OD2" Residue "LX ASP 452": "OD1" <-> "OD2" Residue "LX ASP 456": "OD1" <-> "OD2" Residue "LX ARG 465": "NH1" <-> "NH2" Residue "LX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ARG 468": "NH1" <-> "NH2" Residue "LY GLU 1783": "OE1" <-> "OE2" Residue "LY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LY ASP 1884": "OD1" <-> "OD2" Residue "MT ASP 58": "OD1" <-> "OD2" Residue "MT ASP 72": "OD1" <-> "OD2" Residue "MT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MT ASP 119": "OD1" <-> "OD2" Residue "MT ASP 172": "OD1" <-> "OD2" Residue "MT ARG 213": "NH1" <-> "NH2" Residue "MX GLU 366": "OE1" <-> "OE2" Residue "MX ARG 394": "NH1" <-> "NH2" Residue "MX ARG 410": "NH1" <-> "NH2" Residue "MX ASP 422": "OD1" <-> "OD2" Residue "MX ASP 452": "OD1" <-> "OD2" Residue "MX ASP 456": "OD1" <-> "OD2" Residue "MX ARG 465": "NH1" <-> "NH2" Residue "MX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MX ARG 468": "NH1" <-> "NH2" Residue "MY GLU 1783": "OE1" <-> "OE2" Residue "MY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MY ASP 1884": "OD1" <-> "OD2" Residue "NT ASP 58": "OD1" <-> "OD2" Residue "NT ASP 72": "OD1" <-> "OD2" Residue "NT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NT ASP 119": "OD1" <-> "OD2" Residue "NT ASP 172": "OD1" <-> "OD2" Residue "NT ARG 213": "NH1" <-> "NH2" Residue "NX GLU 366": "OE1" <-> "OE2" Residue "NX ARG 394": "NH1" <-> "NH2" Residue "NX ARG 410": "NH1" <-> "NH2" Residue "NX ASP 422": "OD1" <-> "OD2" Residue "NX ASP 452": "OD1" <-> "OD2" Residue "NX ASP 456": "OD1" <-> "OD2" Residue "NX ARG 465": "NH1" <-> "NH2" Residue "NX TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NX ARG 468": "NH1" <-> "NH2" Residue "NY GLU 1783": "OE1" <-> "OE2" Residue "NY PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NY ASP 1884": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 60970 Number of models: 1 Model: "" Number of chains: 42 Chain: "AT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "AX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "AY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "BT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "BX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "BY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "CT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "CX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "CY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "DT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "DX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "DY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "ET" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "EX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "EY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "FT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "FX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "FY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "GT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "GX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "GY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "HT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "HX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "HY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "IT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "IX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "IY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "JT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "JX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "JY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "KT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "KX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "KY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "LT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "LX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "LY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "MT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "MX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "MY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "NT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "NX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "NY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Time building chain proxies: 23.83, per 1000 atoms: 0.39 Number of scatterers: 60970 At special positions: 0 Unit cell: (231, 231, 141, 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 196 16.00 O 11382 8.00 N 10332 7.00 C 39060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.07 Conformation dependent library (CDL) restraints added in 8.1 seconds 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14392 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 126 sheets defined 33.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.05 Creating SS restraints... Processing helix chain 'AT' and resid 79 through 90 Processing helix chain 'AT' and resid 98 through 113 Processing helix chain 'AT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEAT 195 " --> pdb=" O GLNAT 191 " (cutoff:3.500A) Processing helix chain 'AT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRAT 297 " --> pdb=" O ARGAT 293 " (cutoff:3.500A) Processing helix chain 'AX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSAX 393 " --> pdb=" O HISAX 389 " (cutoff:3.500A) Processing helix chain 'AX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEAX 414 " --> pdb=" O SERAX 411 " (cutoff:3.500A) Processing helix chain 'AX' and resid 460 through 464 Processing helix chain 'AY' and resid 1793 through 1798 Processing helix chain 'AY' and resid 1798 through 1821 Proline residue: AY1815 - end of helix Processing helix chain 'AY' and resid 1850 through 1863 Processing helix chain 'AY' and resid 1897 through 1909 Processing helix chain 'BT' and resid 79 through 90 Processing helix chain 'BT' and resid 98 through 113 Processing helix chain 'BT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEBT 195 " --> pdb=" O GLNBT 191 " (cutoff:3.500A) Processing helix chain 'BT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRBT 297 " --> pdb=" O ARGBT 293 " (cutoff:3.500A) Processing helix chain 'BX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSBX 393 " --> pdb=" O HISBX 389 " (cutoff:3.500A) Processing helix chain 'BX' and resid 411 through 415 removed outlier: 3.551A pdb=" N ILEBX 414 " --> pdb=" O SERBX 411 " (cutoff:3.500A) Processing helix chain 'BX' and resid 460 through 464 Processing helix chain 'BY' and resid 1793 through 1798 Processing helix chain 'BY' and resid 1798 through 1821 Proline residue: BY1815 - end of helix Processing helix chain 'BY' and resid 1850 through 1863 Processing helix chain 'BY' and resid 1897 through 1909 Processing helix chain 'CT' and resid 79 through 90 Processing helix chain 'CT' and resid 98 through 113 Processing helix chain 'CT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILECT 195 " --> pdb=" O GLNCT 191 " (cutoff:3.500A) Processing helix chain 'CT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRCT 297 " --> pdb=" O ARGCT 293 " (cutoff:3.500A) Processing helix chain 'CX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSCX 393 " --> pdb=" O HISCX 389 " (cutoff:3.500A) Processing helix chain 'CX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILECX 414 " --> pdb=" O SERCX 411 " (cutoff:3.500A) Processing helix chain 'CX' and resid 460 through 464 Processing helix chain 'CY' and resid 1793 through 1798 Processing helix chain 'CY' and resid 1798 through 1821 Proline residue: CY1815 - end of helix Processing helix chain 'CY' and resid 1850 through 1863 Processing helix chain 'CY' and resid 1897 through 1909 Processing helix chain 'DT' and resid 79 through 90 Processing helix chain 'DT' and resid 98 through 113 Processing helix chain 'DT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEDT 195 " --> pdb=" O GLNDT 191 " (cutoff:3.500A) Processing helix chain 'DT' and resid 287 through 307 removed outlier: 3.857A pdb=" N TYRDT 297 " --> pdb=" O ARGDT 293 " (cutoff:3.500A) Processing helix chain 'DX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSDX 393 " --> pdb=" O HISDX 389 " (cutoff:3.500A) Processing helix chain 'DX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEDX 414 " --> pdb=" O SERDX 411 " (cutoff:3.500A) Processing helix chain 'DX' and resid 460 through 464 Processing helix chain 'DY' and resid 1793 through 1798 Processing helix chain 'DY' and resid 1798 through 1821 Proline residue: DY1815 - end of helix Processing helix chain 'DY' and resid 1850 through 1863 Processing helix chain 'DY' and resid 1897 through 1909 Processing helix chain 'ET' and resid 79 through 90 Processing helix chain 'ET' and resid 98 through 113 Processing helix chain 'ET' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEET 195 " --> pdb=" O GLNET 191 " (cutoff:3.500A) Processing helix chain 'ET' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRET 297 " --> pdb=" O ARGET 293 " (cutoff:3.500A) Processing helix chain 'EX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSEX 393 " --> pdb=" O HISEX 389 " (cutoff:3.500A) Processing helix chain 'EX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEEX 414 " --> pdb=" O SEREX 411 " (cutoff:3.500A) Processing helix chain 'EX' and resid 460 through 464 Processing helix chain 'EY' and resid 1793 through 1798 Processing helix chain 'EY' and resid 1798 through 1821 Proline residue: EY1815 - end of helix Processing helix chain 'EY' and resid 1850 through 1863 Processing helix chain 'EY' and resid 1897 through 1909 Processing helix chain 'FT' and resid 79 through 90 Processing helix chain 'FT' and resid 98 through 113 Processing helix chain 'FT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEFT 195 " --> pdb=" O GLNFT 191 " (cutoff:3.500A) Processing helix chain 'FT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRFT 297 " --> pdb=" O ARGFT 293 " (cutoff:3.500A) Processing helix chain 'FX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSFX 393 " --> pdb=" O HISFX 389 " (cutoff:3.500A) Processing helix chain 'FX' and resid 411 through 415 removed outlier: 3.551A pdb=" N ILEFX 414 " --> pdb=" O SERFX 411 " (cutoff:3.500A) Processing helix chain 'FX' and resid 460 through 464 Processing helix chain 'FY' and resid 1793 through 1798 Processing helix chain 'FY' and resid 1798 through 1821 Proline residue: FY1815 - end of helix Processing helix chain 'FY' and resid 1850 through 1863 Processing helix chain 'FY' and resid 1897 through 1909 Processing helix chain 'GT' and resid 79 through 90 Processing helix chain 'GT' and resid 98 through 113 Processing helix chain 'GT' and resid 191 through 221 removed outlier: 4.422A pdb=" N ILEGT 195 " --> pdb=" O GLNGT 191 " (cutoff:3.500A) Processing helix chain 'GT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRGT 297 " --> pdb=" O ARGGT 293 " (cutoff:3.500A) Processing helix chain 'GX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSGX 393 " --> pdb=" O HISGX 389 " (cutoff:3.500A) Processing helix chain 'GX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEGX 414 " --> pdb=" O SERGX 411 " (cutoff:3.500A) Processing helix chain 'GX' and resid 460 through 464 Processing helix chain 'GY' and resid 1793 through 1798 Processing helix chain 'GY' and resid 1798 through 1821 Proline residue: GY1815 - end of helix Processing helix chain 'GY' and resid 1850 through 1863 Processing helix chain 'GY' and resid 1897 through 1909 Processing helix chain 'HT' and resid 79 through 90 Processing helix chain 'HT' and resid 98 through 113 Processing helix chain 'HT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEHT 195 " --> pdb=" O GLNHT 191 " (cutoff:3.500A) Processing helix chain 'HT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRHT 297 " --> pdb=" O ARGHT 293 " (cutoff:3.500A) Processing helix chain 'HX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSHX 393 " --> pdb=" O HISHX 389 " (cutoff:3.500A) Processing helix chain 'HX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEHX 414 " --> pdb=" O SERHX 411 " (cutoff:3.500A) Processing helix chain 'HX' and resid 460 through 464 Processing helix chain 'HY' and resid 1793 through 1798 Processing helix chain 'HY' and resid 1798 through 1821 Proline residue: HY1815 - end of helix Processing helix chain 'HY' and resid 1850 through 1863 Processing helix chain 'HY' and resid 1897 through 1909 Processing helix chain 'IT' and resid 79 through 90 Processing helix chain 'IT' and resid 98 through 113 Processing helix chain 'IT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEIT 195 " --> pdb=" O GLNIT 191 " (cutoff:3.500A) Processing helix chain 'IT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRIT 297 " --> pdb=" O ARGIT 293 " (cutoff:3.500A) Processing helix chain 'IX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSIX 393 " --> pdb=" O HISIX 389 " (cutoff:3.500A) Processing helix chain 'IX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEIX 414 " --> pdb=" O SERIX 411 " (cutoff:3.500A) Processing helix chain 'IX' and resid 460 through 464 Processing helix chain 'IY' and resid 1793 through 1798 Processing helix chain 'IY' and resid 1798 through 1821 Proline residue: IY1815 - end of helix Processing helix chain 'IY' and resid 1850 through 1863 Processing helix chain 'IY' and resid 1897 through 1909 Processing helix chain 'JT' and resid 79 through 90 Processing helix chain 'JT' and resid 98 through 113 Processing helix chain 'JT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEJT 195 " --> pdb=" O GLNJT 191 " (cutoff:3.500A) Processing helix chain 'JT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRJT 297 " --> pdb=" O ARGJT 293 " (cutoff:3.500A) Processing helix chain 'JX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSJX 393 " --> pdb=" O HISJX 389 " (cutoff:3.500A) Processing helix chain 'JX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEJX 414 " --> pdb=" O SERJX 411 " (cutoff:3.500A) Processing helix chain 'JX' and resid 460 through 464 Processing helix chain 'JY' and resid 1793 through 1798 Processing helix chain 'JY' and resid 1798 through 1821 Proline residue: JY1815 - end of helix Processing helix chain 'JY' and resid 1850 through 1863 Processing helix chain 'JY' and resid 1897 through 1909 Processing helix chain 'KT' and resid 79 through 90 Processing helix chain 'KT' and resid 98 through 113 Processing helix chain 'KT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEKT 195 " --> pdb=" O GLNKT 191 " (cutoff:3.500A) Processing helix chain 'KT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRKT 297 " --> pdb=" O ARGKT 293 " (cutoff:3.500A) Processing helix chain 'KX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSKX 393 " --> pdb=" O HISKX 389 " (cutoff:3.500A) Processing helix chain 'KX' and resid 411 through 415 removed outlier: 3.551A pdb=" N ILEKX 414 " --> pdb=" O SERKX 411 " (cutoff:3.500A) Processing helix chain 'KX' and resid 460 through 464 Processing helix chain 'KY' and resid 1793 through 1798 Processing helix chain 'KY' and resid 1798 through 1821 Proline residue: KY1815 - end of helix Processing helix chain 'KY' and resid 1850 through 1863 Processing helix chain 'KY' and resid 1897 through 1909 Processing helix chain 'LT' and resid 79 through 90 Processing helix chain 'LT' and resid 98 through 113 Processing helix chain 'LT' and resid 191 through 221 removed outlier: 4.422A pdb=" N ILELT 195 " --> pdb=" O GLNLT 191 " (cutoff:3.500A) Processing helix chain 'LT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRLT 297 " --> pdb=" O ARGLT 293 " (cutoff:3.500A) Processing helix chain 'LX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSLX 393 " --> pdb=" O HISLX 389 " (cutoff:3.500A) Processing helix chain 'LX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILELX 414 " --> pdb=" O SERLX 411 " (cutoff:3.500A) Processing helix chain 'LX' and resid 460 through 464 Processing helix chain 'LY' and resid 1793 through 1798 Processing helix chain 'LY' and resid 1798 through 1821 Proline residue: LY1815 - end of helix Processing helix chain 'LY' and resid 1850 through 1863 Processing helix chain 'LY' and resid 1897 through 1909 Processing helix chain 'MT' and resid 79 through 90 Processing helix chain 'MT' and resid 98 through 113 Processing helix chain 'MT' and resid 191 through 221 removed outlier: 4.424A pdb=" N ILEMT 195 " --> pdb=" O GLNMT 191 " (cutoff:3.500A) Processing helix chain 'MT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRMT 297 " --> pdb=" O ARGMT 293 " (cutoff:3.500A) Processing helix chain 'MX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSMX 393 " --> pdb=" O HISMX 389 " (cutoff:3.500A) Processing helix chain 'MX' and resid 411 through 415 removed outlier: 3.551A pdb=" N ILEMX 414 " --> pdb=" O SERMX 411 " (cutoff:3.500A) Processing helix chain 'MX' and resid 460 through 464 Processing helix chain 'MY' and resid 1793 through 1798 Processing helix chain 'MY' and resid 1798 through 1821 Proline residue: MY1815 - end of helix Processing helix chain 'MY' and resid 1850 through 1863 Processing helix chain 'MY' and resid 1897 through 1909 Processing helix chain 'NT' and resid 79 through 90 Processing helix chain 'NT' and resid 98 through 113 Processing helix chain 'NT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILENT 195 " --> pdb=" O GLNNT 191 " (cutoff:3.500A) Processing helix chain 'NT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRNT 297 " --> pdb=" O ARGNT 293 " (cutoff:3.500A) Processing helix chain 'NX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSNX 393 " --> pdb=" O HISNX 389 " (cutoff:3.500A) Processing helix chain 'NX' and resid 411 through 415 removed outlier: 3.551A pdb=" N ILENX 414 " --> pdb=" O SERNX 411 " (cutoff:3.500A) Processing helix chain 'NX' and resid 460 through 464 Processing helix chain 'NY' and resid 1793 through 1798 Processing helix chain 'NY' and resid 1798 through 1821 Proline residue: NY1815 - end of helix Processing helix chain 'NY' and resid 1850 through 1863 Processing helix chain 'NY' and resid 1897 through 1909 Processing sheet with id=AA1, first strand: chain 'AT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSBX 475 " --> pdb=" O VALBX 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEAT 93 " --> pdb=" O TYRAT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNAT 123 " --> pdb=" O ILEAT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUAT 95 " --> pdb=" O GLNAT 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AX' and resid 448 through 450 removed outlier: 4.986A pdb=" N LYSAX 475 " --> pdb=" O VALAX 442 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AX' and resid 418 through 421 Processing sheet with id=AA5, first strand: chain 'AX' and resid 509 through 513 Processing sheet with id=AA6, first strand: chain 'AY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILENY1757 " --> pdb=" O ALANY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRNY1696 " --> pdb=" O THRNY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSNY1737 " --> pdb=" O ALANY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALANY1762 " --> pdb=" O LYSNY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRNY1739 " --> pdb=" O THRNY1760 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AY' and resid 1691 through 1692 Processing sheet with id=AA8, first strand: chain 'BY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEAY1757 " --> pdb=" O ALAAY1777 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THRAY1696 " --> pdb=" O THRAY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSAY1737 " --> pdb=" O ALAAY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALAAY1762 " --> pdb=" O LYSAY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRAY1739 " --> pdb=" O THRAY1760 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AY' and resid 1706 through 1707 Processing sheet with id=AB1, first strand: chain 'AY' and resid 1722 through 1723 Processing sheet with id=AB2, first strand: chain 'AY' and resid 1754 through 1755 Processing sheet with id=AB3, first strand: chain 'AY' and resid 1891 through 1895 Processing sheet with id=AB4, first strand: chain 'BT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSCX 475 " --> pdb=" O VALCX 442 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'BT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEBT 93 " --> pdb=" O TYRBT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNBT 123 " --> pdb=" O ILEBT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUBT 95 " --> pdb=" O GLNBT 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'BX' and resid 418 through 421 Processing sheet with id=AB7, first strand: chain 'BX' and resid 509 through 513 Processing sheet with id=AB8, first strand: chain 'BY' and resid 1691 through 1692 Processing sheet with id=AB9, first strand: chain 'CY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEBY1757 " --> pdb=" O ALABY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRBY1696 " --> pdb=" O THRBY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSBY1737 " --> pdb=" O ALABY1762 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALABY1762 " --> pdb=" O LYSBY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRBY1739 " --> pdb=" O THRBY1760 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'BY' and resid 1706 through 1707 Processing sheet with id=AC2, first strand: chain 'BY' and resid 1722 through 1723 Processing sheet with id=AC3, first strand: chain 'BY' and resid 1754 through 1755 Processing sheet with id=AC4, first strand: chain 'CT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSDX 475 " --> pdb=" O VALDX 442 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'CT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILECT 93 " --> pdb=" O TYRCT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNCT 123 " --> pdb=" O ILECT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUCT 95 " --> pdb=" O GLNCT 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'CX' and resid 418 through 421 Processing sheet with id=AC7, first strand: chain 'CX' and resid 509 through 513 Processing sheet with id=AC8, first strand: chain 'CY' and resid 1691 through 1692 Processing sheet with id=AC9, first strand: chain 'DY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILECY1757 " --> pdb=" O ALACY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRCY1696 " --> pdb=" O THRCY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSCY1737 " --> pdb=" O ALACY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALACY1762 " --> pdb=" O LYSCY1737 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYRCY1739 " --> pdb=" O THRCY1760 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'CY' and resid 1706 through 1707 Processing sheet with id=AD2, first strand: chain 'CY' and resid 1722 through 1723 Processing sheet with id=AD3, first strand: chain 'CY' and resid 1754 through 1755 Processing sheet with id=AD4, first strand: chain 'DT' and resid 37 through 38 removed outlier: 4.985A pdb=" N LYSEX 475 " --> pdb=" O VALEX 442 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'DT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEDT 93 " --> pdb=" O TYRDT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNDT 123 " --> pdb=" O ILEDT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUDT 95 " --> pdb=" O GLNDT 123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'DX' and resid 418 through 421 Processing sheet with id=AD7, first strand: chain 'DX' and resid 509 through 513 Processing sheet with id=AD8, first strand: chain 'DY' and resid 1691 through 1692 Processing sheet with id=AD9, first strand: chain 'EY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEDY1757 " --> pdb=" O ALADY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRDY1696 " --> pdb=" O THRDY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSDY1737 " --> pdb=" O ALADY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALADY1762 " --> pdb=" O LYSDY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRDY1739 " --> pdb=" O THRDY1760 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'DY' and resid 1706 through 1707 Processing sheet with id=AE2, first strand: chain 'DY' and resid 1722 through 1723 Processing sheet with id=AE3, first strand: chain 'DY' and resid 1754 through 1755 Processing sheet with id=AE4, first strand: chain 'ET' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSFX 475 " --> pdb=" O VALFX 442 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'ET' and resid 61 through 67 removed outlier: 6.433A pdb=" N ILEET 93 " --> pdb=" O TYRET 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNET 123 " --> pdb=" O ILEET 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUET 95 " --> pdb=" O GLNET 123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'EX' and resid 418 through 421 Processing sheet with id=AE7, first strand: chain 'EX' and resid 509 through 513 Processing sheet with id=AE8, first strand: chain 'EY' and resid 1691 through 1692 Processing sheet with id=AE9, first strand: chain 'FY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEEY1757 " --> pdb=" O ALAEY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THREY1696 " --> pdb=" O THREY1881 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYSEY1737 " --> pdb=" O ALAEY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALAEY1762 " --> pdb=" O LYSEY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYREY1739 " --> pdb=" O THREY1760 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'EY' and resid 1706 through 1707 Processing sheet with id=AF2, first strand: chain 'EY' and resid 1722 through 1723 Processing sheet with id=AF3, first strand: chain 'EY' and resid 1754 through 1755 Processing sheet with id=AF4, first strand: chain 'FT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSGX 475 " --> pdb=" O VALGX 442 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'FT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEFT 93 " --> pdb=" O TYRFT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNFT 123 " --> pdb=" O ILEFT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUFT 95 " --> pdb=" O GLNFT 123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'FX' and resid 418 through 421 Processing sheet with id=AF7, first strand: chain 'FX' and resid 509 through 513 Processing sheet with id=AF8, first strand: chain 'FY' and resid 1691 through 1692 Processing sheet with id=AF9, first strand: chain 'GY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILEFY1757 " --> pdb=" O ALAFY1777 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THRFY1696 " --> pdb=" O THRFY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSFY1737 " --> pdb=" O ALAFY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALAFY1762 " --> pdb=" O LYSFY1737 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYRFY1739 " --> pdb=" O THRFY1760 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'FY' and resid 1706 through 1707 Processing sheet with id=AG2, first strand: chain 'FY' and resid 1722 through 1723 Processing sheet with id=AG3, first strand: chain 'FY' and resid 1754 through 1755 Processing sheet with id=AG4, first strand: chain 'GT' and resid 37 through 38 removed outlier: 4.985A pdb=" N LYSHX 475 " --> pdb=" O VALHX 442 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'GT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEGT 93 " --> pdb=" O TYRGT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNGT 123 " --> pdb=" O ILEGT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUGT 95 " --> pdb=" O GLNGT 123 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'GX' and resid 418 through 421 Processing sheet with id=AG7, first strand: chain 'GX' and resid 509 through 513 Processing sheet with id=AG8, first strand: chain 'GY' and resid 1691 through 1692 Processing sheet with id=AG9, first strand: chain 'HY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEGY1757 " --> pdb=" O ALAGY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRGY1696 " --> pdb=" O THRGY1881 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYSGY1737 " --> pdb=" O ALAGY1762 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALAGY1762 " --> pdb=" O LYSGY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRGY1739 " --> pdb=" O THRGY1760 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'GY' and resid 1706 through 1707 Processing sheet with id=AH2, first strand: chain 'GY' and resid 1722 through 1723 Processing sheet with id=AH3, first strand: chain 'GY' and resid 1754 through 1755 Processing sheet with id=AH4, first strand: chain 'HT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSIX 475 " --> pdb=" O VALIX 442 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'HT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEHT 93 " --> pdb=" O TYRHT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNHT 123 " --> pdb=" O ILEHT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUHT 95 " --> pdb=" O GLNHT 123 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'HX' and resid 418 through 421 Processing sheet with id=AH7, first strand: chain 'HX' and resid 509 through 513 Processing sheet with id=AH8, first strand: chain 'HY' and resid 1691 through 1692 Processing sheet with id=AH9, first strand: chain 'IY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILEHY1757 " --> pdb=" O ALAHY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRHY1696 " --> pdb=" O THRHY1881 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYSHY1737 " --> pdb=" O ALAHY1762 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALAHY1762 " --> pdb=" O LYSHY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRHY1739 " --> pdb=" O THRHY1760 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'HY' and resid 1706 through 1707 Processing sheet with id=AI2, first strand: chain 'HY' and resid 1722 through 1723 Processing sheet with id=AI3, first strand: chain 'HY' and resid 1754 through 1755 Processing sheet with id=AI4, first strand: chain 'IT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSJX 475 " --> pdb=" O VALJX 442 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'IT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEIT 93 " --> pdb=" O TYRIT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNIT 123 " --> pdb=" O ILEIT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUIT 95 " --> pdb=" O GLNIT 123 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'IX' and resid 418 through 421 Processing sheet with id=AI7, first strand: chain 'IX' and resid 509 through 513 Processing sheet with id=AI8, first strand: chain 'IY' and resid 1691 through 1692 Processing sheet with id=AI9, first strand: chain 'JY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILEIY1757 " --> pdb=" O ALAIY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRIY1696 " --> pdb=" O THRIY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSIY1737 " --> pdb=" O ALAIY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALAIY1762 " --> pdb=" O LYSIY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRIY1739 " --> pdb=" O THRIY1760 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'IY' and resid 1706 through 1707 Processing sheet with id=AJ2, first strand: chain 'IY' and resid 1722 through 1723 Processing sheet with id=AJ3, first strand: chain 'IY' and resid 1754 through 1755 Processing sheet with id=AJ4, first strand: chain 'JT' and resid 37 through 38 removed outlier: 4.985A pdb=" N LYSKX 475 " --> pdb=" O VALKX 442 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'JT' and resid 61 through 67 removed outlier: 6.431A pdb=" N ILEJT 93 " --> pdb=" O TYRJT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNJT 123 " --> pdb=" O ILEJT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUJT 95 " --> pdb=" O GLNJT 123 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'JX' and resid 418 through 421 Processing sheet with id=AJ7, first strand: chain 'JX' and resid 509 through 513 Processing sheet with id=AJ8, first strand: chain 'JY' and resid 1691 through 1692 Processing sheet with id=AJ9, first strand: chain 'KY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEJY1757 " --> pdb=" O ALAJY1777 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THRJY1696 " --> pdb=" O THRJY1881 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYSJY1737 " --> pdb=" O ALAJY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALAJY1762 " --> pdb=" O LYSJY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRJY1739 " --> pdb=" O THRJY1760 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'JY' and resid 1706 through 1707 Processing sheet with id=AK2, first strand: chain 'JY' and resid 1722 through 1723 Processing sheet with id=AK3, first strand: chain 'JY' and resid 1754 through 1755 Processing sheet with id=AK4, first strand: chain 'KT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSLX 475 " --> pdb=" O VALLX 442 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'KT' and resid 61 through 67 removed outlier: 6.433A pdb=" N ILEKT 93 " --> pdb=" O TYRKT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNKT 123 " --> pdb=" O ILEKT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUKT 95 " --> pdb=" O GLNKT 123 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'KX' and resid 418 through 421 Processing sheet with id=AK7, first strand: chain 'KX' and resid 509 through 513 Processing sheet with id=AK8, first strand: chain 'KY' and resid 1691 through 1692 Processing sheet with id=AK9, first strand: chain 'LY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILEKY1757 " --> pdb=" O ALAKY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRKY1696 " --> pdb=" O THRKY1881 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYSKY1737 " --> pdb=" O ALAKY1762 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALAKY1762 " --> pdb=" O LYSKY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRKY1739 " --> pdb=" O THRKY1760 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'KY' and resid 1706 through 1707 Processing sheet with id=AL2, first strand: chain 'KY' and resid 1722 through 1723 Processing sheet with id=AL3, first strand: chain 'KY' and resid 1754 through 1755 Processing sheet with id=AL4, first strand: chain 'LT' and resid 37 through 38 removed outlier: 4.985A pdb=" N LYSMX 475 " --> pdb=" O VALMX 442 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'LT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILELT 93 " --> pdb=" O TYRLT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNLT 123 " --> pdb=" O ILELT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEULT 95 " --> pdb=" O GLNLT 123 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'LX' and resid 418 through 421 Processing sheet with id=AL7, first strand: chain 'LX' and resid 509 through 513 Processing sheet with id=AL8, first strand: chain 'LY' and resid 1691 through 1692 Processing sheet with id=AL9, first strand: chain 'MY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILELY1757 " --> pdb=" O ALALY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRLY1696 " --> pdb=" O THRLY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSLY1737 " --> pdb=" O ALALY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALALY1762 " --> pdb=" O LYSLY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRLY1739 " --> pdb=" O THRLY1760 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'LY' and resid 1706 through 1707 Processing sheet with id=AM2, first strand: chain 'LY' and resid 1722 through 1723 Processing sheet with id=AM3, first strand: chain 'LY' and resid 1754 through 1755 Processing sheet with id=AM4, first strand: chain 'MT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSNX 475 " --> pdb=" O VALNX 442 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'MT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEMT 93 " --> pdb=" O TYRMT 121 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLNMT 123 " --> pdb=" O ILEMT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUMT 95 " --> pdb=" O GLNMT 123 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'MX' and resid 418 through 421 Processing sheet with id=AM7, first strand: chain 'MX' and resid 509 through 513 Processing sheet with id=AM8, first strand: chain 'MY' and resid 1691 through 1692 Processing sheet with id=AM9, first strand: chain 'NY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILEMY1757 " --> pdb=" O ALAMY1777 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THRMY1696 " --> pdb=" O THRMY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSMY1737 " --> pdb=" O ALAMY1762 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALAMY1762 " --> pdb=" O LYSMY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRMY1739 " --> pdb=" O THRMY1760 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'MY' and resid 1706 through 1707 Processing sheet with id=AN2, first strand: chain 'MY' and resid 1722 through 1723 Processing sheet with id=AN3, first strand: chain 'MY' and resid 1754 through 1755 Processing sheet with id=AN4, first strand: chain 'NT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILENT 93 " --> pdb=" O TYRNT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNNT 123 " --> pdb=" O ILENT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUNT 95 " --> pdb=" O GLNNT 123 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'NX' and resid 418 through 421 Processing sheet with id=AN6, first strand: chain 'NY' and resid 1691 through 1692 Processing sheet with id=AN7, first strand: chain 'NY' and resid 1706 through 1707 Processing sheet with id=AN8, first strand: chain 'NY' and resid 1722 through 1723 Processing sheet with id=AN9, first strand: chain 'NY' and resid 1754 through 1755 3054 hydrogen bonds defined for protein. 8280 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: 26.38 Time building geometry restraints manager: 19.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10583 1.32 - 1.44: 14905 1.44 - 1.56: 36112 1.56 - 1.69: 0 1.69 - 1.81: 392 Bond restraints: 61992 Sorted by residual: bond pdb=" C PHECX 440 " pdb=" N VALCX 441 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.24e-02 6.50e+03 1.49e+01 bond pdb=" C PHEGX 440 " pdb=" N VALGX 441 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.24e-02 6.50e+03 1.49e+01 bond pdb=" C PHENX 440 " pdb=" N VALNX 441 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.24e-02 6.50e+03 1.48e+01 bond pdb=" C PHEMX 440 " pdb=" N VALMX 441 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.24e-02 6.50e+03 1.47e+01 bond pdb=" C PHEHX 440 " pdb=" N VALHX 441 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.24e-02 6.50e+03 1.47e+01 ... (remaining 61987 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.60: 1330 105.60 - 112.68: 32147 112.68 - 119.76: 21549 119.76 - 126.83: 28092 126.83 - 133.91: 476 Bond angle restraints: 83594 Sorted by residual: angle pdb=" N GLNDT 197 " pdb=" CA GLNDT 197 " pdb=" CB GLNDT 197 " ideal model delta sigma weight residual 110.40 119.59 -9.19 1.63e+00 3.76e-01 3.18e+01 angle pdb=" N GLNGT 197 " pdb=" CA GLNGT 197 " pdb=" CB GLNGT 197 " ideal model delta sigma weight residual 110.40 119.58 -9.18 1.63e+00 3.76e-01 3.17e+01 angle pdb=" N GLNNT 197 " pdb=" CA GLNNT 197 " pdb=" CB GLNNT 197 " ideal model delta sigma weight residual 110.40 119.58 -9.18 1.63e+00 3.76e-01 3.17e+01 angle pdb=" N GLNFT 197 " pdb=" CA GLNFT 197 " pdb=" CB GLNFT 197 " ideal model delta sigma weight residual 110.40 119.56 -9.16 1.63e+00 3.76e-01 3.16e+01 angle pdb=" N GLNLT 197 " pdb=" CA GLNLT 197 " pdb=" CB GLNLT 197 " ideal model delta sigma weight residual 110.40 119.55 -9.15 1.63e+00 3.76e-01 3.15e+01 ... (remaining 83589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 33464 15.07 - 30.14: 3705 30.14 - 45.22: 729 45.22 - 60.29: 70 60.29 - 75.36: 140 Dihedral angle restraints: 38108 sinusoidal: 15806 harmonic: 22302 Sorted by residual: dihedral pdb=" CA ILEAX 479 " pdb=" C ILEAX 479 " pdb=" N LYSAX 480 " pdb=" CA LYSAX 480 " ideal model delta harmonic sigma weight residual 180.00 146.08 33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA ILEDX 479 " pdb=" C ILEDX 479 " pdb=" N LYSDX 480 " pdb=" CA LYSDX 480 " ideal model delta harmonic sigma weight residual 180.00 146.12 33.88 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA ILECX 479 " pdb=" C ILECX 479 " pdb=" N LYSCX 480 " pdb=" CA LYSCX 480 " ideal model delta harmonic sigma weight residual 180.00 146.13 33.87 0 5.00e+00 4.00e-02 4.59e+01 ... (remaining 38105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 6428 0.063 - 0.127: 2426 0.127 - 0.190: 546 0.190 - 0.253: 78 0.253 - 0.317: 42 Chirality restraints: 9520 Sorted by residual: chirality pdb=" CB VALIY1786 " pdb=" CA VALIY1786 " pdb=" CG1 VALIY1786 " pdb=" CG2 VALIY1786 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB VALMY1786 " pdb=" CA VALMY1786 " pdb=" CG1 VALMY1786 " pdb=" CG2 VALMY1786 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB VALAY1786 " pdb=" CA VALAY1786 " pdb=" CG1 VALAY1786 " pdb=" CG2 VALAY1786 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 9517 not shown) Planarity restraints: 10598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRBY1739 " -0.013 2.00e-02 2.50e+03 2.15e-02 9.23e+00 pdb=" CG TYRBY1739 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYRBY1739 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYRBY1739 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYRBY1739 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYRBY1739 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYRBY1739 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYRBY1739 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRIY1739 " -0.013 2.00e-02 2.50e+03 2.14e-02 9.18e+00 pdb=" CG TYRIY1739 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYRIY1739 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYRIY1739 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYRIY1739 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYRIY1739 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYRIY1739 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYRIY1739 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRCY1739 " -0.013 2.00e-02 2.50e+03 2.14e-02 9.17e+00 pdb=" CG TYRCY1739 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYRCY1739 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYRCY1739 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYRCY1739 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYRCY1739 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYRCY1739 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYRCY1739 " 0.003 2.00e-02 2.50e+03 ... (remaining 10595 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 8435 2.75 - 3.29: 59590 3.29 - 3.82: 108013 3.82 - 4.36: 129045 4.36 - 4.90: 217400 Nonbonded interactions: 522483 Sorted by model distance: nonbonded pdb=" O PROHX 444 " pdb=" NH1 ARGIX 410 " model vdw 2.210 2.520 nonbonded pdb=" O PROBX 444 " pdb=" NH1 ARGCX 410 " model vdw 2.222 2.520 nonbonded pdb=" OG SERBT 48 " pdb=" O GLYCT 170 " model vdw 2.222 2.440 nonbonded pdb=" OD2 ASPFT 54 " pdb=" OH TYRFX 404 " model vdw 2.263 2.440 nonbonded pdb=" OD2 ASPLT 54 " pdb=" OH TYRLX 404 " model vdw 2.269 2.440 ... (remaining 522478 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 'AT' selection = chain 'BT' selection = chain 'CT' selection = chain 'DT' selection = chain 'ET' selection = chain 'FT' selection = chain 'GT' selection = chain 'HT' selection = chain 'IT' selection = chain 'JT' selection = chain 'KT' selection = chain 'LT' selection = chain 'MT' selection = chain 'NT' } ncs_group { reference = chain 'AX' selection = chain 'BX' selection = chain 'CX' selection = chain 'DX' selection = chain 'EX' selection = chain 'FX' selection = chain 'GX' selection = chain 'HX' selection = chain 'IX' selection = chain 'JX' selection = chain 'KX' selection = chain 'LX' selection = chain 'MX' selection = chain 'NX' } ncs_group { reference = chain 'AY' selection = chain 'BY' selection = chain 'CY' selection = chain 'DY' selection = chain 'EY' selection = chain 'FY' selection = chain 'GY' selection = chain 'HY' selection = chain 'IY' selection = chain 'JY' selection = chain 'KY' selection = chain 'LY' selection = chain 'MY' selection = chain 'NY' } 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 28.330 Check model and map are aligned: 0.680 Set scattering table: 0.450 Process input model: 126.500 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.680 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.011 0.140 61992 Z= 0.696 Angle : 1.233 16.918 83594 Z= 0.650 Chirality : 0.070 0.317 9520 Planarity : 0.007 0.070 10598 Dihedral : 13.772 75.362 23716 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.09), residues: 7406 helix: -1.37 (0.09), residues: 2212 sheet: -1.16 (0.12), residues: 1624 loop : -1.16 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRPNY1723 HIS 0.007 0.002 HISET 169 PHE 0.019 0.003 PHENY1682 TYR 0.051 0.004 TYRBY1739 ARG 0.033 0.002 ARGBX 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2063 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2063 time to evaluate : 5.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AT 64 GLN cc_start: 0.8176 (tt0) cc_final: 0.7538 (mt0) REVERT: AT 194 LYS cc_start: 0.7823 (pttm) cc_final: 0.7573 (tptp) REVERT: AT 197 GLN cc_start: 0.8069 (pm20) cc_final: 0.7850 (tp40) REVERT: AT 201 THR cc_start: 0.8293 (p) cc_final: 0.8010 (p) REVERT: AT 300 ASN cc_start: 0.7020 (m-40) cc_final: 0.6730 (m-40) REVERT: AX 386 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7773 (tp40) REVERT: AX 389 HIS cc_start: 0.7688 (t70) cc_final: 0.7479 (m90) REVERT: AX 405 GLN cc_start: 0.7969 (pt0) cc_final: 0.7244 (pt0) REVERT: AX 459 MET cc_start: 0.8907 (mtp) cc_final: 0.8688 (mtt) REVERT: AY 1715 SER cc_start: 0.8255 (p) cc_final: 0.8029 (p) REVERT: AY 1780 MET cc_start: 0.8451 (mmm) cc_final: 0.8195 (mmt) REVERT: AY 1884 ASP cc_start: 0.7762 (m-30) cc_final: 0.7534 (m-30) REVERT: AY 1907 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7879 (tm-30) REVERT: BT 39 VAL cc_start: 0.9215 (t) cc_final: 0.8996 (t) REVERT: BT 49 GLU cc_start: 0.7392 (mp0) cc_final: 0.7181 (mp0) REVERT: BT 64 GLN cc_start: 0.7931 (tt0) cc_final: 0.7399 (mt0) REVERT: BT 194 LYS cc_start: 0.7933 (pttm) cc_final: 0.7581 (tptp) REVERT: BT 197 GLN cc_start: 0.8081 (pm20) cc_final: 0.7840 (tp-100) REVERT: BT 209 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6847 (tp30) REVERT: BT 210 TYR cc_start: 0.8250 (t80) cc_final: 0.7811 (t80) REVERT: BT 216 ASN cc_start: 0.7559 (m110) cc_final: 0.7158 (m110) REVERT: BX 386 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7987 (tp40) REVERT: BX 389 HIS cc_start: 0.7823 (t-90) cc_final: 0.7580 (m-70) REVERT: BX 405 GLN cc_start: 0.8069 (pt0) cc_final: 0.7580 (pt0) REVERT: BY 1685 LYS cc_start: 0.6911 (mmtm) cc_final: 0.6674 (mmtm) REVERT: BY 1817 ILE cc_start: 0.8746 (mm) cc_final: 0.8419 (mt) REVERT: CT 45 GLU cc_start: 0.7416 (pp20) cc_final: 0.6620 (pp20) REVERT: CT 194 LYS cc_start: 0.8117 (pttm) cc_final: 0.7658 (tptp) REVERT: CT 197 GLN cc_start: 0.8077 (pm20) cc_final: 0.7770 (tp-100) REVERT: CT 201 THR cc_start: 0.8131 (p) cc_final: 0.7887 (p) REVERT: CX 378 ASP cc_start: 0.8085 (m-30) cc_final: 0.7843 (m-30) REVERT: CX 386 GLN cc_start: 0.8376 (tm-30) cc_final: 0.7834 (tp40) REVERT: CX 387 TYR cc_start: 0.8636 (t80) cc_final: 0.8392 (t80) REVERT: CX 389 HIS cc_start: 0.7846 (t70) cc_final: 0.7513 (m90) REVERT: CX 405 GLN cc_start: 0.8044 (pt0) cc_final: 0.7629 (pt0) REVERT: CX 484 LEU cc_start: 0.9156 (tp) cc_final: 0.8937 (tp) REVERT: CY 1685 LYS cc_start: 0.7368 (mmtm) cc_final: 0.7163 (mmtt) REVERT: CY 1817 ILE cc_start: 0.8687 (mm) cc_final: 0.8347 (mt) REVERT: CY 1907 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7939 (tm-30) REVERT: DT 64 GLN cc_start: 0.7971 (tt0) cc_final: 0.7281 (mt0) REVERT: DT 194 LYS cc_start: 0.8097 (pttm) cc_final: 0.7703 (tptp) REVERT: DT 197 GLN cc_start: 0.7972 (pm20) cc_final: 0.7693 (tp-100) REVERT: DT 201 THR cc_start: 0.8416 (p) cc_final: 0.8195 (p) REVERT: DX 386 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7782 (tp40) REVERT: DX 389 HIS cc_start: 0.7862 (t-90) cc_final: 0.7612 (m90) REVERT: DX 405 GLN cc_start: 0.7992 (pt0) cc_final: 0.7792 (pt0) REVERT: DY 1739 TYR cc_start: 0.8929 (m-80) cc_final: 0.8625 (m-80) REVERT: DY 1774 ASN cc_start: 0.8878 (p0) cc_final: 0.8633 (p0) REVERT: DY 1817 ILE cc_start: 0.8653 (mm) cc_final: 0.8347 (mt) REVERT: ET 27 LYS cc_start: 0.7499 (mmtt) cc_final: 0.7244 (mmtm) REVERT: ET 194 LYS cc_start: 0.7809 (pttm) cc_final: 0.7576 (tptp) REVERT: ET 197 GLN cc_start: 0.8004 (pm20) cc_final: 0.7731 (tp40) REVERT: ET 201 THR cc_start: 0.8258 (p) cc_final: 0.7845 (p) REVERT: ET 210 TYR cc_start: 0.8340 (t80) cc_final: 0.8009 (t80) REVERT: ET 215 ASN cc_start: 0.7952 (m-40) cc_final: 0.7575 (m-40) REVERT: ET 290 GLN cc_start: 0.7165 (tp-100) cc_final: 0.6923 (mp10) REVERT: EX 378 ASP cc_start: 0.8037 (m-30) cc_final: 0.7731 (t0) REVERT: EX 386 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8056 (tp40) REVERT: EY 1884 ASP cc_start: 0.7708 (m-30) cc_final: 0.7504 (m-30) REVERT: FT 27 LYS cc_start: 0.7564 (mmtt) cc_final: 0.7335 (mmtm) REVERT: FT 64 GLN cc_start: 0.7935 (tt0) cc_final: 0.7344 (mt0) REVERT: FT 194 LYS cc_start: 0.7746 (pttm) cc_final: 0.7516 (tptp) REVERT: FT 197 GLN cc_start: 0.8209 (pm20) cc_final: 0.7934 (tp40) REVERT: FT 201 THR cc_start: 0.8498 (p) cc_final: 0.8166 (p) REVERT: FT 213 ARG cc_start: 0.6907 (ttp80) cc_final: 0.6670 (ptt180) REVERT: FT 216 ASN cc_start: 0.7616 (m110) cc_final: 0.7225 (m110) REVERT: FX 386 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7768 (tp40) REVERT: FX 405 GLN cc_start: 0.8113 (pt0) cc_final: 0.7892 (pt0) REVERT: FY 1685 LYS cc_start: 0.6991 (mmtm) cc_final: 0.6452 (mmtm) REVERT: FY 1856 ASN cc_start: 0.8249 (t0) cc_final: 0.8029 (t0) REVERT: GT 27 LYS cc_start: 0.7439 (mmtt) cc_final: 0.7235 (mmtt) REVERT: GT 197 GLN cc_start: 0.8098 (pm20) cc_final: 0.7691 (tp40) REVERT: GT 201 THR cc_start: 0.8258 (p) cc_final: 0.7887 (p) REVERT: GT 210 TYR cc_start: 0.8392 (t80) cc_final: 0.7961 (t80) REVERT: GT 216 ASN cc_start: 0.7782 (m110) cc_final: 0.7412 (m-40) REVERT: GX 386 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7857 (tp40) REVERT: GY 1685 LYS cc_start: 0.7133 (mmtm) cc_final: 0.6868 (mmtt) REVERT: GY 1739 TYR cc_start: 0.8957 (m-80) cc_final: 0.8686 (m-80) REVERT: GY 1891 TYR cc_start: 0.8743 (m-80) cc_final: 0.8540 (m-80) REVERT: HT 27 LYS cc_start: 0.7415 (mmtt) cc_final: 0.7183 (mmtm) REVERT: HT 49 GLU cc_start: 0.7278 (mp0) cc_final: 0.7076 (mp0) REVERT: HT 64 GLN cc_start: 0.8185 (tt0) cc_final: 0.7538 (mt0) REVERT: HT 194 LYS cc_start: 0.7841 (pttm) cc_final: 0.7589 (tptp) REVERT: HT 197 GLN cc_start: 0.8086 (pm20) cc_final: 0.7852 (tp40) REVERT: HT 201 THR cc_start: 0.8315 (p) cc_final: 0.8033 (p) REVERT: HT 300 ASN cc_start: 0.7099 (m-40) cc_final: 0.6807 (m-40) REVERT: HX 386 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7780 (tp40) REVERT: HX 405 GLN cc_start: 0.7974 (pt0) cc_final: 0.7259 (pt0) REVERT: HX 459 MET cc_start: 0.8905 (mtp) cc_final: 0.8682 (mtt) REVERT: HY 1715 SER cc_start: 0.8260 (p) cc_final: 0.8034 (p) REVERT: HY 1780 MET cc_start: 0.8460 (mmm) cc_final: 0.8209 (mmt) REVERT: HY 1884 ASP cc_start: 0.7746 (m-30) cc_final: 0.7503 (m-30) REVERT: HY 1907 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7829 (tm-30) REVERT: IT 49 GLU cc_start: 0.7446 (mp0) cc_final: 0.7206 (mp0) REVERT: IT 194 LYS cc_start: 0.7847 (pttm) cc_final: 0.7538 (tptp) REVERT: IT 197 GLN cc_start: 0.8078 (pm20) cc_final: 0.7817 (tp40) REVERT: IT 198 TYR cc_start: 0.8017 (t80) cc_final: 0.7624 (t80) REVERT: IT 209 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6694 (tp30) REVERT: IX 386 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7922 (tp40) REVERT: IX 389 HIS cc_start: 0.7735 (t70) cc_final: 0.7491 (m-70) REVERT: IX 405 GLN cc_start: 0.8108 (pt0) cc_final: 0.7587 (pt0) REVERT: IY 1685 LYS cc_start: 0.6775 (mmtm) cc_final: 0.6535 (mmtm) REVERT: IY 1817 ILE cc_start: 0.8746 (mm) cc_final: 0.8421 (mt) REVERT: JT 45 GLU cc_start: 0.7332 (pp20) cc_final: 0.6439 (pp20) REVERT: JT 64 GLN cc_start: 0.7837 (tt0) cc_final: 0.7478 (mp10) REVERT: JT 194 LYS cc_start: 0.8134 (pttm) cc_final: 0.7733 (tptp) REVERT: JT 197 GLN cc_start: 0.8067 (pm20) cc_final: 0.7812 (tp-100) REVERT: JT 201 THR cc_start: 0.7887 (p) cc_final: 0.7678 (p) REVERT: JT 296 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7190 (tm-30) REVERT: JT 300 ASN cc_start: 0.7047 (m-40) cc_final: 0.6752 (m-40) REVERT: JX 378 ASP cc_start: 0.8146 (m-30) cc_final: 0.7894 (m-30) REVERT: JX 386 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7918 (tp40) REVERT: JX 389 HIS cc_start: 0.7925 (t70) cc_final: 0.7572 (m90) REVERT: JX 405 GLN cc_start: 0.8016 (pt0) cc_final: 0.7515 (pt0) REVERT: JX 484 LEU cc_start: 0.9189 (tp) cc_final: 0.8988 (tp) REVERT: JY 1685 LYS cc_start: 0.7368 (mmtm) cc_final: 0.7166 (mmtt) REVERT: JY 1817 ILE cc_start: 0.8692 (mm) cc_final: 0.8354 (mt) REVERT: KT 64 GLN cc_start: 0.8021 (tt0) cc_final: 0.7276 (mt0) REVERT: KT 194 LYS cc_start: 0.8035 (pttm) cc_final: 0.7692 (tptp) REVERT: KT 197 GLN cc_start: 0.8191 (pm20) cc_final: 0.7852 (tp40) REVERT: KT 210 TYR cc_start: 0.8229 (t80) cc_final: 0.7885 (t80) REVERT: KT 216 ASN cc_start: 0.7696 (m110) cc_final: 0.7314 (m110) REVERT: KX 386 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7959 (tp40) REVERT: KX 389 HIS cc_start: 0.7856 (t-90) cc_final: 0.7631 (m-70) REVERT: KY 1739 TYR cc_start: 0.8924 (m-80) cc_final: 0.8602 (m-80) REVERT: KY 1774 ASN cc_start: 0.8878 (p0) cc_final: 0.8630 (p0) REVERT: KY 1817 ILE cc_start: 0.8648 (mm) cc_final: 0.8348 (mt) REVERT: LT 194 LYS cc_start: 0.7832 (pttm) cc_final: 0.7620 (tptp) REVERT: LT 197 GLN cc_start: 0.8040 (pm20) cc_final: 0.7741 (tp40) REVERT: LT 201 THR cc_start: 0.8296 (p) cc_final: 0.7916 (t) REVERT: LT 210 TYR cc_start: 0.8122 (t80) cc_final: 0.7915 (t80) REVERT: LT 215 ASN cc_start: 0.7967 (m-40) cc_final: 0.7616 (m-40) REVERT: LX 378 ASP cc_start: 0.8057 (m-30) cc_final: 0.7738 (t0) REVERT: LX 386 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8056 (tp40) REVERT: LY 1884 ASP cc_start: 0.7669 (m-30) cc_final: 0.7453 (m-30) REVERT: MT 27 LYS cc_start: 0.7539 (mmtt) cc_final: 0.7310 (mmtm) REVERT: MT 45 GLU cc_start: 0.7388 (pp20) cc_final: 0.7162 (pp20) REVERT: MT 194 LYS cc_start: 0.7712 (pttm) cc_final: 0.7481 (tptp) REVERT: MT 197 GLN cc_start: 0.8174 (pm20) cc_final: 0.7931 (tp40) REVERT: MT 201 THR cc_start: 0.8473 (p) cc_final: 0.8188 (p) REVERT: MX 386 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7774 (tp40) REVERT: MX 405 GLN cc_start: 0.8075 (pt0) cc_final: 0.7813 (pt0) REVERT: MY 1685 LYS cc_start: 0.6986 (mmtm) cc_final: 0.6437 (mmtm) REVERT: MY 1856 ASN cc_start: 0.8254 (t0) cc_final: 0.8034 (t0) REVERT: NT 197 GLN cc_start: 0.8040 (pm20) cc_final: 0.7733 (tp40) REVERT: NT 210 TYR cc_start: 0.8519 (t80) cc_final: 0.7939 (t80) REVERT: NT 216 ASN cc_start: 0.7617 (m110) cc_final: 0.7224 (m-40) REVERT: NX 386 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7864 (tm-30) REVERT: NY 1685 LYS cc_start: 0.7125 (mmtm) cc_final: 0.6859 (mmtt) REVERT: NY 1739 TYR cc_start: 0.8955 (m-80) cc_final: 0.8673 (m-80) outliers start: 0 outliers final: 0 residues processed: 2063 average time/residue: 0.5831 time to fit residues: 2001.9232 Evaluate side-chains 1573 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1573 time to evaluate : 5.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 0.8980 chunk 551 optimal weight: 0.6980 chunk 306 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 372 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 570 optimal weight: 0.5980 chunk 220 optimal weight: 5.9990 chunk 346 optimal weight: 0.5980 chunk 424 optimal weight: 0.8980 chunk 661 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 204 GLN AY1856 ASN BT 204 GLN BX 373 GLN BX 389 HIS ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BY1726 ASN BY1856 ASN CT 64 GLN CT 204 GLN CX 373 GLN ** CX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN DT 204 GLN DX 373 GLN DX 389 HIS ** DX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 301 GLN EX 373 GLN EX 405 GLN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FT 204 GLN GT 301 GLN GY1856 ASN ** GY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HT 204 GLN HX 373 GLN HY1856 ASN HY1857 GLN IX 373 GLN ** IX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IY1726 ASN IY1856 ASN JT 204 GLN ** JX 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN KT 204 GLN KX 389 HIS ** KX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** KY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 301 GLN LX 373 GLN LX 405 GLN ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MX 373 GLN ** MY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NY1856 ASN ** NY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 61992 Z= 0.200 Angle : 0.622 7.657 83594 Z= 0.330 Chirality : 0.045 0.166 9520 Planarity : 0.005 0.054 10598 Dihedral : 5.614 30.699 8134 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.19 % Allowed : 9.97 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.09), residues: 7406 helix: 0.25 (0.10), residues: 2212 sheet: -1.11 (0.12), residues: 1624 loop : -0.98 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRPEX 466 HIS 0.002 0.001 HISMT 169 PHE 0.011 0.001 PHEDT 84 TYR 0.019 0.001 TYRIT 210 ARG 0.007 0.001 ARGLX 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1937 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1856 time to evaluate : 5.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AT 64 GLN cc_start: 0.8109 (tt0) cc_final: 0.7465 (mt0) REVERT: AT 194 LYS cc_start: 0.7794 (pttm) cc_final: 0.7433 (tptp) REVERT: AT 216 ASN cc_start: 0.7671 (m110) cc_final: 0.7320 (m-40) REVERT: AT 292 GLU cc_start: 0.7985 (tp30) cc_final: 0.7779 (tp30) REVERT: AT 300 ASN cc_start: 0.6884 (m-40) cc_final: 0.6638 (m-40) REVERT: AX 386 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7900 (tp40) REVERT: AX 415 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7853 (mmm) REVERT: AX 450 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8645 (ptm) REVERT: AX 459 MET cc_start: 0.8801 (mtp) cc_final: 0.8580 (mtt) REVERT: AY 1715 SER cc_start: 0.8204 (p) cc_final: 0.7987 (p) REVERT: AY 1780 MET cc_start: 0.8286 (mmm) cc_final: 0.8082 (mmt) REVERT: BT 49 GLU cc_start: 0.7317 (mp0) cc_final: 0.7020 (mp0) REVERT: BT 64 GLN cc_start: 0.7915 (tt0) cc_final: 0.7417 (mt0) REVERT: BT 194 LYS cc_start: 0.7847 (pttm) cc_final: 0.7504 (tptp) REVERT: BT 209 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6598 (tp30) REVERT: BT 216 ASN cc_start: 0.7691 (m110) cc_final: 0.7294 (m110) REVERT: BX 386 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8016 (tp40) REVERT: BX 508 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8365 (mt-10) REVERT: BY 1715 SER cc_start: 0.8319 (p) cc_final: 0.8079 (p) REVERT: CT 45 GLU cc_start: 0.7149 (pp20) cc_final: 0.6939 (pp20) REVERT: CT 49 GLU cc_start: 0.7316 (mp0) cc_final: 0.7095 (mp0) REVERT: CT 64 GLN cc_start: 0.7957 (tt0) cc_final: 0.7386 (mt0) REVERT: CT 194 LYS cc_start: 0.7795 (pttm) cc_final: 0.7393 (tptp) REVERT: CT 214 LYS cc_start: 0.7556 (pptt) cc_final: 0.7169 (pptt) REVERT: CT 216 ASN cc_start: 0.7705 (m110) cc_final: 0.7379 (m110) REVERT: CX 378 ASP cc_start: 0.8012 (m-30) cc_final: 0.7774 (m-30) REVERT: CX 386 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8034 (tp40) REVERT: CX 387 TYR cc_start: 0.8725 (t80) cc_final: 0.8436 (t80) REVERT: CX 389 HIS cc_start: 0.7690 (t70) cc_final: 0.7464 (m90) REVERT: CX 474 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7564 (mm-30) REVERT: CY 1715 SER cc_start: 0.8370 (p) cc_final: 0.8125 (p) REVERT: DT 49 GLU cc_start: 0.7158 (mp0) cc_final: 0.6817 (mp0) REVERT: DT 194 LYS cc_start: 0.7781 (pttm) cc_final: 0.7430 (tptp) REVERT: DT 296 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7261 (tm-30) REVERT: DX 386 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7974 (tp40) REVERT: DY 1739 TYR cc_start: 0.8861 (m-80) cc_final: 0.8603 (m-80) REVERT: DY 1903 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8398 (mt) cc_final: 0.8081 (mt) REVERT: ET 27 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7292 (mmtm) REVERT: ET 64 GLN cc_start: 0.7921 (tt0) cc_final: 0.7402 (mt0) REVERT: ET 194 LYS cc_start: 0.7690 (pttm) cc_final: 0.7153 (tptp) REVERT: ET 209 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6336 (tp30) REVERT: ET 290 GLN cc_start: 0.7255 (tp-100) cc_final: 0.7037 (mp10) REVERT: EX 378 ASP cc_start: 0.7953 (m-30) cc_final: 0.7599 (t0) REVERT: EX 386 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8211 (tp40) REVERT: EX 405 GLN cc_start: 0.7595 (pt0) cc_final: 0.6906 (pt0) REVERT: EX 410 ARG cc_start: 0.7431 (mtm110) cc_final: 0.6981 (mtm110) REVERT: EY 1715 SER cc_start: 0.8373 (p) cc_final: 0.8115 (p) REVERT: FT 27 LYS cc_start: 0.7485 (mmtt) cc_final: 0.7225 (mmtm) REVERT: FT 64 GLN cc_start: 0.7879 (tt0) cc_final: 0.7320 (mt0) REVERT: FT 194 LYS cc_start: 0.7874 (pttm) cc_final: 0.7490 (tptp) REVERT: FT 197 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7873 (tp-100) REVERT: FT 214 LYS cc_start: 0.8021 (ptmt) cc_final: 0.7815 (tppt) REVERT: FT 216 ASN cc_start: 0.7686 (m110) cc_final: 0.7302 (m110) REVERT: FT 296 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7269 (tm-30) REVERT: FX 378 ASP cc_start: 0.8302 (m-30) cc_final: 0.7719 (t0) REVERT: FX 386 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8014 (tp40) REVERT: FX 405 GLN cc_start: 0.7697 (pt0) cc_final: 0.7484 (pt0) REVERT: FX 415 MET cc_start: 0.8422 (mmm) cc_final: 0.8028 (mmm) REVERT: FX 474 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7441 (mm-30) REVERT: FY 1856 ASN cc_start: 0.8257 (t0) cc_final: 0.8026 (t0) REVERT: GT 216 ASN cc_start: 0.7593 (m110) cc_final: 0.7219 (m110) REVERT: GX 386 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7997 (tp40) REVERT: GX 410 ARG cc_start: 0.7389 (mtm110) cc_final: 0.7147 (mtm110) REVERT: GY 1685 LYS cc_start: 0.7126 (mmtm) cc_final: 0.6920 (mmtt) REVERT: HT 49 GLU cc_start: 0.7298 (mp0) cc_final: 0.7027 (mp0) REVERT: HT 64 GLN cc_start: 0.8078 (tt0) cc_final: 0.7454 (mt0) REVERT: HT 193 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7416 (mt-10) REVERT: HT 194 LYS cc_start: 0.7772 (pttm) cc_final: 0.7422 (tptp) REVERT: HT 214 LYS cc_start: 0.8008 (ptmt) cc_final: 0.7730 (tppt) REVERT: HT 216 ASN cc_start: 0.7651 (m110) cc_final: 0.7285 (m-40) REVERT: HT 296 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7334 (tm-30) REVERT: HT 300 ASN cc_start: 0.6833 (m-40) cc_final: 0.6573 (m-40) REVERT: HX 378 ASP cc_start: 0.7963 (m-30) cc_final: 0.7711 (t0) REVERT: HX 386 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7909 (tp40) REVERT: HX 415 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7839 (mmm) REVERT: HX 450 MET cc_start: 0.8942 (ttp) cc_final: 0.8681 (ptm) REVERT: HY 1715 SER cc_start: 0.8215 (p) cc_final: 0.7995 (p) REVERT: IT 49 GLU cc_start: 0.7305 (mp0) cc_final: 0.6991 (mp0) REVERT: IT 64 GLN cc_start: 0.7970 (tt0) cc_final: 0.7418 (mt0) REVERT: IT 194 LYS cc_start: 0.7734 (pttm) cc_final: 0.7395 (tptp) REVERT: IT 198 TYR cc_start: 0.7843 (t80) cc_final: 0.7589 (t80) REVERT: IT 209 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6561 (tp30) REVERT: IT 214 LYS cc_start: 0.7439 (pptt) cc_final: 0.6980 (pptt) REVERT: IX 371 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7398 (tm-30) REVERT: IX 386 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8051 (tp40) REVERT: IX 474 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7472 (mm-30) REVERT: IY 1715 SER cc_start: 0.8303 (p) cc_final: 0.8063 (p) REVERT: IY 1783 GLU cc_start: 0.8901 (pm20) cc_final: 0.8700 (pm20) REVERT: JT 45 GLU cc_start: 0.7138 (pp20) cc_final: 0.6868 (pp20) REVERT: JT 64 GLN cc_start: 0.7740 (tt0) cc_final: 0.7381 (mp10) REVERT: JT 194 LYS cc_start: 0.7881 (pttm) cc_final: 0.7496 (tptp) REVERT: JT 197 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7801 (tp40) REVERT: JT 210 TYR cc_start: 0.8228 (t80) cc_final: 0.7789 (t80) REVERT: JT 216 ASN cc_start: 0.7647 (m110) cc_final: 0.7258 (m110) REVERT: JT 300 ASN cc_start: 0.6717 (m-40) cc_final: 0.6453 (m-40) REVERT: JX 371 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7474 (tm-30) REVERT: JX 378 ASP cc_start: 0.7980 (m-30) cc_final: 0.7690 (t0) REVERT: JX 386 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8026 (tp40) REVERT: JX 389 HIS cc_start: 0.7765 (t70) cc_final: 0.7509 (m90) REVERT: JX 401 TYR cc_start: 0.9036 (m-80) cc_final: 0.8792 (m-80) REVERT: JX 474 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7485 (mm-30) REVERT: JY 1715 SER cc_start: 0.8369 (p) cc_final: 0.8130 (p) REVERT: KT 49 GLU cc_start: 0.7255 (mp0) cc_final: 0.6943 (mp0) REVERT: KT 59 THR cc_start: 0.8617 (m) cc_final: 0.8329 (m) REVERT: KT 73 TYR cc_start: 0.5934 (p90) cc_final: 0.5733 (p90) REVERT: KT 194 LYS cc_start: 0.7817 (pttm) cc_final: 0.7471 (tptp) REVERT: KT 197 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7855 (tp-100) REVERT: KT 209 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7700 (tp30) REVERT: KT 216 ASN cc_start: 0.7666 (m110) cc_final: 0.7357 (m110) REVERT: KT 292 GLU cc_start: 0.8032 (tp30) cc_final: 0.6909 (mt-10) REVERT: KX 371 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7520 (tm-30) REVERT: KX 378 ASP cc_start: 0.8240 (m-30) cc_final: 0.7879 (m-30) REVERT: KX 386 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8129 (tp40) REVERT: KX 389 HIS cc_start: 0.7749 (t70) cc_final: 0.7539 (m-70) REVERT: KY 1739 TYR cc_start: 0.8855 (m-80) cc_final: 0.8555 (m-80) REVERT: KY 1903 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: KY 1904 ILE cc_start: 0.8405 (mt) cc_final: 0.8038 (mt) REVERT: KY 1907 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7471 (tm-30) REVERT: LT 64 GLN cc_start: 0.7891 (tt0) cc_final: 0.7376 (mt0) REVERT: LT 194 LYS cc_start: 0.7650 (pttm) cc_final: 0.7193 (tptp) REVERT: LT 209 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6408 (tp30) REVERT: LT 210 TYR cc_start: 0.8135 (t80) cc_final: 0.7561 (t80) REVERT: LT 216 ASN cc_start: 0.7732 (m110) cc_final: 0.7297 (m110) REVERT: LX 378 ASP cc_start: 0.7967 (m-30) cc_final: 0.7616 (t0) REVERT: LX 386 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8209 (tp40) REVERT: LX 405 GLN cc_start: 0.7590 (pt0) cc_final: 0.6935 (pt0) REVERT: LX 410 ARG cc_start: 0.7418 (mtm110) cc_final: 0.7121 (mtm110) REVERT: LY 1715 SER cc_start: 0.8369 (p) cc_final: 0.8116 (p) REVERT: MT 49 GLU cc_start: 0.7267 (mp0) cc_final: 0.6936 (mp0) REVERT: MT 194 LYS cc_start: 0.7694 (pttm) cc_final: 0.7355 (tptp) REVERT: MT 209 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6430 (tp30) REVERT: MT 216 ASN cc_start: 0.7318 (m110) cc_final: 0.6937 (m110) REVERT: MX 378 ASP cc_start: 0.8286 (m-30) cc_final: 0.7705 (t0) REVERT: MX 386 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8020 (tp40) REVERT: MX 405 GLN cc_start: 0.7883 (pt0) cc_final: 0.7522 (pt0) REVERT: MX 415 MET cc_start: 0.8405 (mmm) cc_final: 0.7859 (mmm) REVERT: MX 450 MET cc_start: 0.8902 (ttp) cc_final: 0.8587 (ptm) REVERT: MX 474 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7443 (mm-30) REVERT: MY 1856 ASN cc_start: 0.8264 (t0) cc_final: 0.8034 (t0) REVERT: NT 64 GLN cc_start: 0.7869 (tt0) cc_final: 0.7350 (mt0) REVERT: NT 209 GLU cc_start: 0.8233 (mm-30) cc_final: 0.8029 (pt0) REVERT: NT 216 ASN cc_start: 0.7687 (m110) cc_final: 0.7349 (m-40) REVERT: NX 386 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8000 (tp40) REVERT: NX 410 ARG cc_start: 0.7343 (mtm110) cc_final: 0.7136 (mtm110) REVERT: NY 1685 LYS cc_start: 0.7128 (mmtm) cc_final: 0.6916 (mmtt) outliers start: 81 outliers final: 41 residues processed: 1886 average time/residue: 0.5764 time to fit residues: 1814.4269 Evaluate side-chains 1674 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1625 time to evaluate : 5.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AX residue 450 MET Chi-restraints excluded: chain AY residue 1713 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 204 GLN Chi-restraints excluded: chain CX residue 377 LEU Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 424 THR Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 30 LYS Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain EX residue 460 THR Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1752 MET Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 197 GLN Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HX residue 415 MET Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 197 GLN Chi-restraints excluded: chain JX residue 424 THR Chi-restraints excluded: chain KT residue 30 LYS Chi-restraints excluded: chain KT residue 197 GLN Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1903 GLU Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LX residue 460 THR Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain NT residue 136 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.5980 chunk 205 optimal weight: 4.9990 chunk 550 optimal weight: 6.9990 chunk 450 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 662 optimal weight: 3.9990 chunk 715 optimal weight: 0.7980 chunk 589 optimal weight: 9.9990 chunk 656 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 531 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 169 HIS AT 301 GLN AY1743 GLN AY1856 ASN AY1907 GLN BT 169 HIS ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN BY1726 ASN BY1856 ASN CT 197 GLN CT 204 GLN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN ** DY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 169 HIS ET 301 GLN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EY1856 ASN ** EY1857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FT 169 HIS ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 196 ASN GX 373 GLN GY1694 GLN ** GY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GY1857 GLN ** GY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HT 169 HIS ** HT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1694 GLN HY1743 GLN HY1856 ASN HY1857 GLN HY1907 GLN IT 169 HIS IX 413 HIS IX 443 GLN IY1726 ASN ** IY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 204 GLN JT 208 GLN ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN KX 413 HIS ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 301 GLN LY1856 ASN ** LY1857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 31 GLN ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 169 HIS MY1694 GLN ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 196 ASN NT 301 GLN NY1694 GLN ** NY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NY1857 GLN ** NY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 61992 Z= 0.271 Angle : 0.598 12.381 83594 Z= 0.320 Chirality : 0.046 0.170 9520 Planarity : 0.004 0.047 10598 Dihedral : 5.248 29.382 8134 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.15 % Allowed : 12.33 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.10), residues: 7406 helix: 0.92 (0.11), residues: 2212 sheet: -1.07 (0.12), residues: 1666 loop : -0.84 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPJX 466 HIS 0.002 0.000 HISLT 169 PHE 0.010 0.001 PHEMY1682 TYR 0.025 0.001 TYRMT 36 ARG 0.007 0.000 ARGHX 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1954 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1740 time to evaluate : 5.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AT 64 GLN cc_start: 0.8138 (tt0) cc_final: 0.7478 (mt0) REVERT: AT 194 LYS cc_start: 0.7844 (pttm) cc_final: 0.7191 (tptp) REVERT: AT 213 ARG cc_start: 0.5899 (ptt180) cc_final: 0.5574 (ptt180) REVERT: AT 216 ASN cc_start: 0.7641 (m110) cc_final: 0.7365 (m110) REVERT: AT 301 GLN cc_start: 0.7382 (tp40) cc_final: 0.7135 (tp-100) REVERT: AX 386 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7975 (tp40) REVERT: AX 405 GLN cc_start: 0.7894 (pt0) cc_final: 0.7385 (pt0) REVERT: AX 415 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7960 (mmm) REVERT: AX 450 MET cc_start: 0.9019 (ttp) cc_final: 0.8817 (ptm) REVERT: AX 459 MET cc_start: 0.8834 (mtp) cc_final: 0.8587 (mtt) REVERT: BT 49 GLU cc_start: 0.7434 (mp0) cc_final: 0.7126 (mp0) REVERT: BT 64 GLN cc_start: 0.7991 (tt0) cc_final: 0.7462 (mt0) REVERT: BT 194 LYS cc_start: 0.7981 (pttm) cc_final: 0.7386 (tptp) REVERT: BT 209 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6658 (tp30) REVERT: BT 216 ASN cc_start: 0.7652 (m110) cc_final: 0.7230 (m110) REVERT: BX 386 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8088 (tp40) REVERT: BY 1715 SER cc_start: 0.8333 (p) cc_final: 0.8096 (p) REVERT: CT 194 LYS cc_start: 0.7969 (pttm) cc_final: 0.7405 (tptp) REVERT: CT 204 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: CT 209 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7660 (tp30) REVERT: CT 210 TYR cc_start: 0.8113 (t80) cc_final: 0.7735 (t80) REVERT: CT 214 LYS cc_start: 0.7550 (pptt) cc_final: 0.7189 (pptt) REVERT: CT 216 ASN cc_start: 0.7734 (m110) cc_final: 0.7415 (m110) REVERT: CX 378 ASP cc_start: 0.8018 (m-30) cc_final: 0.7715 (m-30) REVERT: CX 386 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8093 (tp40) REVERT: CX 387 TYR cc_start: 0.8722 (t80) cc_final: 0.8370 (t80) REVERT: CX 389 HIS cc_start: 0.7737 (t70) cc_final: 0.7513 (m90) REVERT: CX 409 LYS cc_start: 0.7669 (ttpt) cc_final: 0.7407 (ttmt) REVERT: CX 410 ARG cc_start: 0.7358 (mtm110) cc_final: 0.6954 (mtm110) REVERT: CY 1715 SER cc_start: 0.8479 (p) cc_final: 0.8268 (p) REVERT: CY 1724 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.9058 (p0) REVERT: CY 1873 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: DT 59 THR cc_start: 0.8662 (m) cc_final: 0.8364 (m) REVERT: DT 194 LYS cc_start: 0.7943 (pttm) cc_final: 0.7266 (tptp) REVERT: DT 208 GLN cc_start: 0.7548 (tp40) cc_final: 0.7346 (tp40) REVERT: DT 296 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7323 (tm-30) REVERT: DX 374 LYS cc_start: 0.7917 (ptmm) cc_final: 0.7426 (ptpp) REVERT: DX 386 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8047 (tp40) REVERT: DY 1739 TYR cc_start: 0.8975 (m-80) cc_final: 0.8751 (m-80) REVERT: DY 1772 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8135 (pp) REVERT: DY 1873 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: DY 1903 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8349 (mt) cc_final: 0.8051 (mt) REVERT: ET 27 LYS cc_start: 0.7502 (mmtt) cc_final: 0.7288 (mmtm) REVERT: ET 59 THR cc_start: 0.8738 (m) cc_final: 0.8439 (m) REVERT: ET 64 GLN cc_start: 0.7987 (tt0) cc_final: 0.7453 (mt0) REVERT: ET 194 LYS cc_start: 0.7787 (pttm) cc_final: 0.7245 (tptp) REVERT: ET 209 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6225 (tp30) REVERT: ET 292 GLU cc_start: 0.8056 (tp30) cc_final: 0.7851 (tp30) REVERT: EX 378 ASP cc_start: 0.8092 (m-30) cc_final: 0.7687 (t0) REVERT: EX 386 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8215 (tp40) REVERT: EX 405 GLN cc_start: 0.7413 (pt0) cc_final: 0.7040 (pt0) REVERT: EX 415 MET cc_start: 0.8205 (mmm) cc_final: 0.7978 (mmm) REVERT: FT 27 LYS cc_start: 0.7552 (mmtt) cc_final: 0.7267 (mmtm) REVERT: FT 194 LYS cc_start: 0.7885 (pttm) cc_final: 0.7545 (tptp) REVERT: FT 197 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8077 (tp-100) REVERT: FT 213 ARG cc_start: 0.6380 (ttp-170) cc_final: 0.6157 (ptt180) REVERT: FT 214 LYS cc_start: 0.8111 (ptmt) cc_final: 0.7874 (tppt) REVERT: FT 216 ASN cc_start: 0.7797 (m110) cc_final: 0.7444 (m110) REVERT: FX 378 ASP cc_start: 0.8301 (m-30) cc_final: 0.7691 (t0) REVERT: FX 386 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8065 (tp40) REVERT: FX 405 GLN cc_start: 0.7860 (pt0) cc_final: 0.7389 (pt0) REVERT: FX 415 MET cc_start: 0.8476 (mmm) cc_final: 0.7944 (mmm) REVERT: FX 450 MET cc_start: 0.9001 (ttp) cc_final: 0.8722 (ptm) REVERT: GT 59 THR cc_start: 0.8707 (m) cc_final: 0.8422 (m) REVERT: GT 216 ASN cc_start: 0.7636 (m110) cc_final: 0.7230 (m110) REVERT: GT 292 GLU cc_start: 0.8101 (tp30) cc_final: 0.7154 (mt-10) REVERT: GX 374 LYS cc_start: 0.7809 (ptmm) cc_final: 0.7483 (ptpp) REVERT: GX 386 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8099 (tp40) REVERT: GX 410 ARG cc_start: 0.7431 (mtm110) cc_final: 0.7182 (mtm110) REVERT: GY 1685 LYS cc_start: 0.6984 (mmtm) cc_final: 0.6777 (mmtt) REVERT: HT 49 GLU cc_start: 0.7459 (mp0) cc_final: 0.7147 (mp0) REVERT: HT 64 GLN cc_start: 0.8151 (tt0) cc_final: 0.7500 (mt0) REVERT: HT 194 LYS cc_start: 0.7891 (pttm) cc_final: 0.7237 (tptp) REVERT: HT 214 LYS cc_start: 0.7943 (ptmt) cc_final: 0.7643 (tppt) REVERT: HT 216 ASN cc_start: 0.7674 (m110) cc_final: 0.7352 (m-40) REVERT: HT 296 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7297 (tm-30) REVERT: HT 300 ASN cc_start: 0.6694 (m-40) cc_final: 0.6424 (m-40) REVERT: HX 374 LYS cc_start: 0.8014 (ptmm) cc_final: 0.7570 (ptpp) REVERT: HX 378 ASP cc_start: 0.8066 (m-30) cc_final: 0.7776 (t0) REVERT: HX 386 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7935 (tp40) REVERT: HX 405 GLN cc_start: 0.7864 (pt0) cc_final: 0.7297 (pt0) REVERT: HX 415 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7949 (mmm) REVERT: IT 64 GLN cc_start: 0.8011 (tt0) cc_final: 0.7435 (mt0) REVERT: IT 192 LEU cc_start: 0.7118 (mm) cc_final: 0.6677 (tp) REVERT: IT 194 LYS cc_start: 0.7906 (pttm) cc_final: 0.7289 (tptp) REVERT: IT 209 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6505 (tp30) REVERT: IT 292 GLU cc_start: 0.7999 (tp30) cc_final: 0.7587 (tp30) REVERT: IX 386 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7897 (tp40) REVERT: IY 1715 SER cc_start: 0.8329 (p) cc_final: 0.8083 (p) REVERT: JT 64 GLN cc_start: 0.7865 (tt0) cc_final: 0.7428 (mp10) REVERT: JT 194 LYS cc_start: 0.7966 (pttm) cc_final: 0.7568 (tptp) REVERT: JT 216 ASN cc_start: 0.7774 (m110) cc_final: 0.7493 (m110) REVERT: JT 296 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7171 (tm-30) REVERT: JX 371 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7302 (tm-30) REVERT: JX 378 ASP cc_start: 0.7979 (m-30) cc_final: 0.7588 (t0) REVERT: JX 386 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8138 (tp40) REVERT: JX 401 TYR cc_start: 0.9028 (m-80) cc_final: 0.8748 (m-80) REVERT: JY 1715 SER cc_start: 0.8488 (p) cc_final: 0.8267 (p) REVERT: JY 1724 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.9064 (p0) REVERT: JY 1861 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8553 (tm-30) REVERT: KT 59 THR cc_start: 0.8599 (m) cc_final: 0.8292 (m) REVERT: KT 194 LYS cc_start: 0.7815 (pttm) cc_final: 0.7393 (tptp) REVERT: KT 197 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8184 (tp-100) REVERT: KT 209 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7686 (tp30) REVERT: KT 216 ASN cc_start: 0.7610 (m110) cc_final: 0.7338 (m110) REVERT: KT 292 GLU cc_start: 0.7996 (tp30) cc_final: 0.6859 (mt-10) REVERT: KX 371 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7443 (tm-30) REVERT: KX 378 ASP cc_start: 0.8330 (m-30) cc_final: 0.7833 (t0) REVERT: KX 386 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8152 (tp40) REVERT: KY 1739 TYR cc_start: 0.8975 (m-80) cc_final: 0.8696 (m-80) REVERT: KY 1772 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8128 (pp) REVERT: KY 1903 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: KY 1904 ILE cc_start: 0.8371 (mt) cc_final: 0.8075 (mt) REVERT: LT 64 GLN cc_start: 0.7964 (tt0) cc_final: 0.7442 (mt0) REVERT: LT 194 LYS cc_start: 0.7757 (pttm) cc_final: 0.6989 (tptp) REVERT: LT 209 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6297 (tp30) REVERT: LT 216 ASN cc_start: 0.7704 (m110) cc_final: 0.7332 (m110) REVERT: LT 292 GLU cc_start: 0.8052 (tp30) cc_final: 0.7833 (tp30) REVERT: LX 378 ASP cc_start: 0.8095 (m-30) cc_final: 0.7688 (t0) REVERT: LX 386 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8226 (tp40) REVERT: LX 405 GLN cc_start: 0.7376 (pt0) cc_final: 0.6967 (pt0) REVERT: MT 49 GLU cc_start: 0.7323 (mp0) cc_final: 0.7108 (mp0) REVERT: MT 194 LYS cc_start: 0.7968 (pttm) cc_final: 0.7354 (tptp) REVERT: MT 209 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6365 (tp30) REVERT: MT 216 ASN cc_start: 0.7400 (m110) cc_final: 0.7124 (m110) REVERT: MX 378 ASP cc_start: 0.8302 (m-30) cc_final: 0.7646 (t0) REVERT: MX 386 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8042 (tp40) REVERT: MX 405 GLN cc_start: 0.7893 (pt0) cc_final: 0.7457 (pt0) REVERT: MX 415 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7953 (mmm) REVERT: MX 450 MET cc_start: 0.9011 (ttp) cc_final: 0.8744 (ptm) REVERT: NT 59 THR cc_start: 0.8697 (m) cc_final: 0.8429 (m) REVERT: NT 64 GLN cc_start: 0.7918 (tt0) cc_final: 0.7414 (mt0) REVERT: NT 216 ASN cc_start: 0.7626 (m110) cc_final: 0.7265 (m-40) REVERT: NT 292 GLU cc_start: 0.8244 (tp30) cc_final: 0.7899 (tp30) REVERT: NX 386 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8129 (tp40) REVERT: NY 1685 LYS cc_start: 0.6987 (mmtm) cc_final: 0.6777 (mmtt) REVERT: NY 1907 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7454 (tm-30) outliers start: 214 outliers final: 122 residues processed: 1872 average time/residue: 0.5707 time to fit residues: 1796.3490 Evaluate side-chains 1728 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1592 time to evaluate : 5.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 35 VAL Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AY residue 1713 ILE Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain AY residue 1873 GLU Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BY residue 1724 ASN Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 82 LEU Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CT residue 204 GLN Chi-restraints excluded: chain CX residue 383 LEU Chi-restraints excluded: chain CX residue 424 THR Chi-restraints excluded: chain CY residue 1724 ASN Chi-restraints excluded: chain CY residue 1873 GLU Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 30 LYS Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 383 LEU Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1724 ASN Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1873 GLU Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain ET residue 201 THR Chi-restraints excluded: chain EX residue 383 LEU Chi-restraints excluded: chain EX residue 424 THR Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1752 MET Chi-restraints excluded: chain EY residue 1873 GLU Chi-restraints excluded: chain FT residue 80 VAL Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FT residue 197 GLN Chi-restraints excluded: chain FT residue 201 THR Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GT residue 201 THR Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1751 ILE Chi-restraints excluded: chain GY residue 1873 GLU Chi-restraints excluded: chain HT residue 35 VAL Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 383 LEU Chi-restraints excluded: chain HX residue 415 MET Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain HY residue 1873 GLU Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 377 LEU Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IY residue 1724 ASN Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 204 GLN Chi-restraints excluded: chain JX residue 377 LEU Chi-restraints excluded: chain JX residue 424 THR Chi-restraints excluded: chain JX residue 460 THR Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1724 ASN Chi-restraints excluded: chain KT residue 35 VAL Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KT residue 197 GLN Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1724 ASN Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1809 SER Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1903 GLU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LT residue 201 THR Chi-restraints excluded: chain LX residue 383 LEU Chi-restraints excluded: chain LX residue 424 THR Chi-restraints excluded: chain LX residue 459 MET Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1752 MET Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MT residue 201 THR Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain NT residue 35 VAL Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NT residue 201 THR Chi-restraints excluded: chain NY residue 1751 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 1.9990 chunk 497 optimal weight: 1.9990 chunk 343 optimal weight: 0.0970 chunk 73 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 444 optimal weight: 4.9990 chunk 664 optimal weight: 0.3980 chunk 703 optimal weight: 0.8980 chunk 347 optimal weight: 4.9990 chunk 629 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1694 GLN AY1743 GLN AY1857 GLN ** AY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 301 GLN ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BY1694 GLN CT 204 GLN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN DX 413 HIS ** DY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 301 GLN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EY1694 GLN EY1907 GLN ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FY1694 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN HY1857 GLN ** HY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 443 GLN IY1694 GLN JT 204 GLN JY1694 GLN ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN ** JY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KX 373 GLN ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 301 GLN LY1694 GLN ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 61992 Z= 0.223 Angle : 0.588 10.431 83594 Z= 0.309 Chirality : 0.045 0.163 9520 Planarity : 0.004 0.045 10598 Dihedral : 5.053 28.246 8134 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.89 % Allowed : 14.40 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 7406 helix: 1.28 (0.11), residues: 2212 sheet: -0.88 (0.12), residues: 1624 loop : -0.83 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPCX 466 HIS 0.002 0.000 HISCT 169 PHE 0.009 0.001 PHEHY1682 TYR 0.020 0.001 TYRIT 210 ARG 0.009 0.000 ARGHX 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1914 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1718 time to evaluate : 5.693 Fit side-chains REVERT: AT 64 GLN cc_start: 0.8145 (tt0) cc_final: 0.7484 (mt0) REVERT: AT 194 LYS cc_start: 0.7880 (pttm) cc_final: 0.7329 (tptp) REVERT: AT 292 GLU cc_start: 0.7975 (tp30) cc_final: 0.6961 (mt-10) REVERT: AT 301 GLN cc_start: 0.7503 (tp40) cc_final: 0.7213 (tp-100) REVERT: AX 386 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7971 (tp40) REVERT: AX 405 GLN cc_start: 0.7949 (pt0) cc_final: 0.7482 (pt0) REVERT: AX 415 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7912 (mmm) REVERT: AX 459 MET cc_start: 0.8815 (mtp) cc_final: 0.8594 (mtt) REVERT: AX 472 ILE cc_start: 0.8652 (mm) cc_final: 0.8408 (mm) REVERT: BT 64 GLN cc_start: 0.8003 (tt0) cc_final: 0.7438 (mt0) REVERT: BT 194 LYS cc_start: 0.7953 (pttm) cc_final: 0.7468 (tptp) REVERT: BT 209 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6620 (tp30) REVERT: BT 216 ASN cc_start: 0.7773 (m110) cc_final: 0.7390 (m110) REVERT: BX 386 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8253 (tp40) REVERT: BY 1715 SER cc_start: 0.8263 (p) cc_final: 0.8020 (p) REVERT: CT 209 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7669 (tp30) REVERT: CT 210 TYR cc_start: 0.8186 (t80) cc_final: 0.7665 (t80) REVERT: CT 214 LYS cc_start: 0.7662 (pptt) cc_final: 0.7304 (pptt) REVERT: CT 216 ASN cc_start: 0.7675 (m110) cc_final: 0.7381 (m110) REVERT: CT 292 GLU cc_start: 0.8177 (tp30) cc_final: 0.7085 (mt-10) REVERT: CX 386 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8098 (tp40) REVERT: CX 387 TYR cc_start: 0.8672 (t80) cc_final: 0.8288 (t80) REVERT: CY 1715 SER cc_start: 0.8452 (p) cc_final: 0.8242 (p) REVERT: CY 1873 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7979 (pm20) REVERT: DT 59 THR cc_start: 0.8574 (m) cc_final: 0.8274 (m) REVERT: DT 192 LEU cc_start: 0.6898 (mm) cc_final: 0.6656 (mm) REVERT: DT 193 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7588 (mt-10) REVERT: DT 194 LYS cc_start: 0.7961 (pttm) cc_final: 0.7555 (tptp) REVERT: DT 208 GLN cc_start: 0.7600 (tp40) cc_final: 0.7355 (tp40) REVERT: DT 214 LYS cc_start: 0.6955 (pptt) cc_final: 0.6526 (pptt) REVERT: DT 296 GLU cc_start: 0.7652 (tm-30) cc_final: 0.6830 (tm-30) REVERT: DT 300 ASN cc_start: 0.6989 (m-40) cc_final: 0.6303 (m-40) REVERT: DX 374 LYS cc_start: 0.7895 (ptmm) cc_final: 0.7468 (ptpp) REVERT: DX 378 ASP cc_start: 0.8252 (m-30) cc_final: 0.7741 (t0) REVERT: DX 386 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8091 (tp40) REVERT: DY 1739 TYR cc_start: 0.8979 (m-80) cc_final: 0.8699 (m-80) REVERT: DY 1772 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8044 (pp) REVERT: DY 1873 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: DY 1903 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8309 (mt) cc_final: 0.7997 (mt) REVERT: ET 27 LYS cc_start: 0.7481 (mmtt) cc_final: 0.7244 (mmtm) REVERT: ET 59 THR cc_start: 0.8736 (m) cc_final: 0.8457 (m) REVERT: ET 64 GLN cc_start: 0.8013 (tt0) cc_final: 0.7438 (mt0) REVERT: ET 194 LYS cc_start: 0.7760 (pttm) cc_final: 0.7359 (tptp) REVERT: ET 210 TYR cc_start: 0.8118 (t80) cc_final: 0.7414 (t80) REVERT: ET 296 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7195 (tm-30) REVERT: ET 300 ASN cc_start: 0.6788 (m-40) cc_final: 0.6369 (m110) REVERT: EX 378 ASP cc_start: 0.8132 (m-30) cc_final: 0.7700 (t0) REVERT: EY 1685 LYS cc_start: 0.7545 (mmtt) cc_final: 0.7308 (mmtt) REVERT: FT 27 LYS cc_start: 0.7534 (mmtt) cc_final: 0.7318 (mmtm) REVERT: FT 194 LYS cc_start: 0.7833 (pttm) cc_final: 0.7565 (tptp) REVERT: FT 197 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8115 (tp-100) REVERT: FT 213 ARG cc_start: 0.6415 (ttp-170) cc_final: 0.6097 (ptt180) REVERT: FT 214 LYS cc_start: 0.8119 (ptmt) cc_final: 0.7906 (tppt) REVERT: FT 216 ASN cc_start: 0.7933 (m110) cc_final: 0.7644 (m110) REVERT: FT 296 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7167 (tm-30) REVERT: FT 300 ASN cc_start: 0.6579 (m-40) cc_final: 0.6256 (m-40) REVERT: FX 378 ASP cc_start: 0.8268 (m-30) cc_final: 0.7668 (t0) REVERT: FX 386 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8074 (tp40) REVERT: FX 405 GLN cc_start: 0.7854 (pt0) cc_final: 0.7258 (pt0) REVERT: FX 415 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7888 (mmm) REVERT: GT 216 ASN cc_start: 0.7736 (m110) cc_final: 0.7463 (m110) REVERT: GT 292 GLU cc_start: 0.8144 (tp30) cc_final: 0.7171 (mt-10) REVERT: GX 374 LYS cc_start: 0.7794 (ptmm) cc_final: 0.7431 (ptpp) REVERT: GY 1685 LYS cc_start: 0.7063 (mmtm) cc_final: 0.6852 (mmtt) REVERT: HT 27 LYS cc_start: 0.7202 (mmtt) cc_final: 0.7001 (mmtm) REVERT: HT 49 GLU cc_start: 0.7391 (mp0) cc_final: 0.7075 (mp0) REVERT: HT 64 GLN cc_start: 0.8102 (tt0) cc_final: 0.7467 (mt0) REVERT: HT 194 LYS cc_start: 0.7849 (pttm) cc_final: 0.7358 (tptp) REVERT: HT 214 LYS cc_start: 0.7848 (ptmt) cc_final: 0.7581 (tppt) REVERT: HT 216 ASN cc_start: 0.7627 (m110) cc_final: 0.7387 (m-40) REVERT: HT 292 GLU cc_start: 0.7959 (tp30) cc_final: 0.6928 (mt-10) REVERT: HT 296 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7206 (tm-30) REVERT: HT 300 ASN cc_start: 0.6748 (m-40) cc_final: 0.6421 (m-40) REVERT: HX 374 LYS cc_start: 0.8021 (ptmm) cc_final: 0.7561 (ptpp) REVERT: HX 378 ASP cc_start: 0.8194 (m-30) cc_final: 0.7892 (t0) REVERT: HX 386 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7925 (tp40) REVERT: HX 405 GLN cc_start: 0.7953 (pt0) cc_final: 0.7494 (pt0) REVERT: HX 415 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7931 (mmm) REVERT: IT 49 GLU cc_start: 0.7351 (mp0) cc_final: 0.7092 (mp0) REVERT: IT 194 LYS cc_start: 0.7955 (pttm) cc_final: 0.7437 (tptp) REVERT: IT 209 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6541 (tp30) REVERT: IX 386 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8209 (tp40) REVERT: IY 1715 SER cc_start: 0.8245 (p) cc_final: 0.8004 (p) REVERT: JT 194 LYS cc_start: 0.8010 (pttm) cc_final: 0.7494 (tptp) REVERT: JT 216 ASN cc_start: 0.7747 (m110) cc_final: 0.7487 (m110) REVERT: JT 296 GLU cc_start: 0.7623 (tm-30) cc_final: 0.6977 (tm-30) REVERT: JT 300 ASN cc_start: 0.6361 (m-40) cc_final: 0.5794 (m-40) REVERT: JX 371 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7186 (tm-30) REVERT: JX 378 ASP cc_start: 0.8067 (m-30) cc_final: 0.7596 (t0) REVERT: JX 386 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8087 (tp40) REVERT: JX 401 TYR cc_start: 0.9040 (m-80) cc_final: 0.8718 (m-80) REVERT: JX 410 ARG cc_start: 0.7485 (mtm110) cc_final: 0.6857 (mtm110) REVERT: JY 1715 SER cc_start: 0.8456 (p) cc_final: 0.8244 (p) REVERT: KT 59 THR cc_start: 0.8574 (m) cc_final: 0.8291 (m) REVERT: KT 194 LYS cc_start: 0.7801 (pttm) cc_final: 0.7397 (tptp) REVERT: KT 197 GLN cc_start: 0.8405 (pm20) cc_final: 0.8160 (tp-100) REVERT: KT 209 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7676 (tp30) REVERT: KT 216 ASN cc_start: 0.7724 (m110) cc_final: 0.7382 (m110) REVERT: KT 292 GLU cc_start: 0.8024 (tp30) cc_final: 0.6979 (mt-10) REVERT: KX 371 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7395 (tm-30) REVERT: KX 378 ASP cc_start: 0.8321 (m-30) cc_final: 0.7727 (t0) REVERT: KX 386 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8152 (tp40) REVERT: KY 1739 TYR cc_start: 0.8970 (m-80) cc_final: 0.8711 (m-80) REVERT: KY 1772 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8100 (pp) REVERT: KY 1873 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: KY 1903 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: KY 1904 ILE cc_start: 0.8317 (mt) cc_final: 0.8000 (mt) REVERT: LT 64 GLN cc_start: 0.7964 (tt0) cc_final: 0.7454 (mt0) REVERT: LT 194 LYS cc_start: 0.7719 (pttm) cc_final: 0.7288 (tptp) REVERT: LT 209 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6185 (tp30) REVERT: LT 216 ASN cc_start: 0.7723 (m110) cc_final: 0.7391 (m110) REVERT: LT 296 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7271 (tm-30) REVERT: LT 300 ASN cc_start: 0.6725 (m-40) cc_final: 0.6353 (m-40) REVERT: LX 378 ASP cc_start: 0.8137 (m-30) cc_final: 0.7699 (t0) REVERT: LY 1685 LYS cc_start: 0.7549 (mmtt) cc_final: 0.7320 (mmtt) REVERT: MT 49 GLU cc_start: 0.7330 (mp0) cc_final: 0.7091 (mp0) REVERT: MT 194 LYS cc_start: 0.7811 (pttm) cc_final: 0.7436 (tptp) REVERT: MT 209 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6283 (tp30) REVERT: MT 216 ASN cc_start: 0.7468 (m110) cc_final: 0.7206 (m110) REVERT: MT 297 TYR cc_start: 0.7733 (t80) cc_final: 0.7476 (t80) REVERT: MX 378 ASP cc_start: 0.8245 (m-30) cc_final: 0.7667 (t0) REVERT: MX 386 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8079 (tp40) REVERT: MX 415 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8178 (mmm) REVERT: NT 64 GLN cc_start: 0.7909 (tt0) cc_final: 0.7412 (mt0) REVERT: NT 216 ASN cc_start: 0.7683 (m110) cc_final: 0.7372 (m-40) REVERT: NT 296 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7235 (tm-30) REVERT: NT 300 ASN cc_start: 0.6705 (m-40) cc_final: 0.6432 (m-40) REVERT: NY 1685 LYS cc_start: 0.7064 (mmtm) cc_final: 0.6851 (mmtt) outliers start: 196 outliers final: 108 residues processed: 1837 average time/residue: 0.5716 time to fit residues: 1761.7124 Evaluate side-chains 1696 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1576 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 35 VAL Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AY residue 1713 ILE Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain AY residue 1873 GLU Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 459 MET Chi-restraints excluded: chain BY residue 1724 ASN Chi-restraints excluded: chain BY residue 1725 MET Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CT residue 204 GLN Chi-restraints excluded: chain CX residue 424 THR Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain CY residue 1873 GLU Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1724 ASN Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1873 GLU Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1724 ASN Chi-restraints excluded: chain EY residue 1752 MET Chi-restraints excluded: chain FT residue 80 VAL Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FT residue 197 GLN Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GY residue 1751 ILE Chi-restraints excluded: chain GY residue 1873 GLU Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 383 LEU Chi-restraints excluded: chain HX residue 415 MET Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1724 ASN Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain HY residue 1873 GLU Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IY residue 1724 ASN Chi-restraints excluded: chain IY residue 1725 MET Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 204 GLN Chi-restraints excluded: chain JX residue 424 THR Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain KT residue 35 VAL Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KY residue 1724 ASN Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1809 SER Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1903 GLU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1724 ASN Chi-restraints excluded: chain LY residue 1752 MET Chi-restraints excluded: chain LY residue 1813 THR Chi-restraints excluded: chain LY residue 1894 LYS Chi-restraints excluded: chain MT residue 80 VAL Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1751 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 3.9990 chunk 399 optimal weight: 3.9990 chunk 10 optimal weight: 0.0060 chunk 523 optimal weight: 0.0970 chunk 290 optimal weight: 6.9990 chunk 600 optimal weight: 5.9990 chunk 486 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 359 optimal weight: 0.9980 chunk 631 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 197 GLN AY1743 GLN ** AY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN ** BY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 204 GLN CX 413 HIS CY1694 GLN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN ** DT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 301 GLN DX 443 GLN ** EX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 443 GLN ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GX 386 GLN ** GX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HX 373 GLN HY1743 GLN IX 443 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IY1907 GLN JT 64 GLN JT 197 GLN JT 204 GLN ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN LX 386 GLN ** LX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 31 GLN ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 208 GLN ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NX 386 GLN NX 413 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 61992 Z= 0.262 Angle : 0.594 13.875 83594 Z= 0.314 Chirality : 0.045 0.175 9520 Planarity : 0.004 0.043 10598 Dihedral : 4.997 27.880 8134 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.24 % Allowed : 15.26 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.10), residues: 7406 helix: 1.31 (0.11), residues: 2296 sheet: -1.01 (0.12), residues: 1666 loop : -0.81 (0.10), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPJX 466 HIS 0.001 0.000 HISCT 169 PHE 0.010 0.001 PHEAY1682 TYR 0.017 0.001 TYRJX 492 ARG 0.006 0.000 ARGEX 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1855 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1635 time to evaluate : 5.760 Fit side-chains revert: symmetry clash REVERT: AT 64 GLN cc_start: 0.8122 (tt0) cc_final: 0.7436 (mt0) REVERT: AT 194 LYS cc_start: 0.7890 (pttm) cc_final: 0.7324 (tptp) REVERT: AT 292 GLU cc_start: 0.7970 (tp30) cc_final: 0.6996 (mt-10) REVERT: AT 296 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7042 (tm-30) REVERT: AT 300 ASN cc_start: 0.6574 (m-40) cc_final: 0.6138 (m-40) REVERT: AT 301 GLN cc_start: 0.7514 (tp40) cc_final: 0.7202 (tp-100) REVERT: AX 374 LYS cc_start: 0.8119 (ptmm) cc_final: 0.7585 (ptpp) REVERT: AX 386 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7986 (tp40) REVERT: AX 405 GLN cc_start: 0.7998 (pt0) cc_final: 0.7549 (pt0) REVERT: AX 415 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7943 (mmm) REVERT: AX 459 MET cc_start: 0.8822 (mtp) cc_final: 0.8578 (mtt) REVERT: AX 474 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7574 (mm-30) REVERT: BT 64 GLN cc_start: 0.8037 (tt0) cc_final: 0.7454 (mt0) REVERT: BT 67 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9065 (mt) REVERT: BT 194 LYS cc_start: 0.8003 (pttm) cc_final: 0.7482 (tptp) REVERT: BT 209 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6638 (tp30) REVERT: BT 216 ASN cc_start: 0.7789 (m110) cc_final: 0.7398 (m110) REVERT: BT 296 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7084 (tm-30) REVERT: BT 300 ASN cc_start: 0.6737 (m-40) cc_final: 0.6337 (m-40) REVERT: BY 1715 SER cc_start: 0.8328 (p) cc_final: 0.8066 (p) REVERT: BY 1863 MET cc_start: 0.8577 (tpt) cc_final: 0.8366 (tpt) REVERT: CT 209 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7692 (tp30) REVERT: CT 216 ASN cc_start: 0.7681 (m110) cc_final: 0.7274 (m110) REVERT: CT 292 GLU cc_start: 0.8128 (tp30) cc_final: 0.7105 (mt-10) REVERT: CX 378 ASP cc_start: 0.8095 (m-30) cc_final: 0.7858 (m-30) REVERT: CX 386 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8111 (tp40) REVERT: CX 401 TYR cc_start: 0.9029 (m-80) cc_final: 0.8785 (m-80) REVERT: DT 59 THR cc_start: 0.8579 (m) cc_final: 0.8280 (m) REVERT: DT 194 LYS cc_start: 0.8022 (pttm) cc_final: 0.7554 (tptp) REVERT: DT 214 LYS cc_start: 0.7203 (pptt) cc_final: 0.6762 (pptt) REVERT: DT 296 GLU cc_start: 0.7671 (tm-30) cc_final: 0.6821 (tm-30) REVERT: DT 300 ASN cc_start: 0.6934 (m-40) cc_final: 0.6229 (m-40) REVERT: DT 301 GLN cc_start: 0.7347 (tp40) cc_final: 0.7124 (tp-100) REVERT: DX 374 LYS cc_start: 0.7933 (ptmm) cc_final: 0.7473 (ptpp) REVERT: DX 378 ASP cc_start: 0.8318 (m-30) cc_final: 0.7815 (t0) REVERT: DX 386 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8133 (tp40) REVERT: DY 1739 TYR cc_start: 0.9019 (m-80) cc_final: 0.8767 (m-80) REVERT: DY 1772 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8071 (pp) REVERT: DY 1873 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: DY 1903 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8318 (mt) cc_final: 0.8007 (mt) REVERT: ET 27 LYS cc_start: 0.7497 (mmtt) cc_final: 0.7291 (mmtm) REVERT: ET 59 THR cc_start: 0.8726 (m) cc_final: 0.8436 (m) REVERT: ET 194 LYS cc_start: 0.7775 (pttm) cc_final: 0.7355 (tptp) REVERT: ET 210 TYR cc_start: 0.8178 (t80) cc_final: 0.7536 (t80) REVERT: EX 378 ASP cc_start: 0.8172 (m-30) cc_final: 0.7654 (t0) REVERT: EX 386 GLN cc_start: 0.8408 (tp40) cc_final: 0.8176 (tp40) REVERT: EX 405 GLN cc_start: 0.7882 (pt0) cc_final: 0.7142 (pt0) REVERT: EX 415 MET cc_start: 0.8383 (mmm) cc_final: 0.7994 (mmm) REVERT: FT 27 LYS cc_start: 0.7527 (mmtt) cc_final: 0.7307 (mmtm) REVERT: FT 194 LYS cc_start: 0.7835 (pttm) cc_final: 0.7575 (tptp) REVERT: FT 197 GLN cc_start: 0.8422 (pm20) cc_final: 0.8128 (tp-100) REVERT: FT 214 LYS cc_start: 0.8118 (ptmt) cc_final: 0.7897 (tppt) REVERT: FT 216 ASN cc_start: 0.7939 (m110) cc_final: 0.7644 (m110) REVERT: FT 292 GLU cc_start: 0.7903 (tp30) cc_final: 0.6943 (mt-10) REVERT: FT 296 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7112 (tm-30) REVERT: FT 300 ASN cc_start: 0.6633 (m-40) cc_final: 0.6338 (m-40) REVERT: FX 378 ASP cc_start: 0.8254 (m-30) cc_final: 0.7652 (t0) REVERT: FX 386 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8127 (tp40) REVERT: FY 1685 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7488 (mmtt) REVERT: GT 216 ASN cc_start: 0.7763 (m110) cc_final: 0.7510 (m110) REVERT: GX 374 LYS cc_start: 0.7823 (ptmm) cc_final: 0.7454 (ptpp) REVERT: GY 1685 LYS cc_start: 0.7094 (mmtm) cc_final: 0.6811 (mmtt) REVERT: HT 49 GLU cc_start: 0.7442 (mp0) cc_final: 0.7115 (mp0) REVERT: HT 64 GLN cc_start: 0.8134 (tt0) cc_final: 0.7463 (mt0) REVERT: HT 194 LYS cc_start: 0.7876 (pttm) cc_final: 0.7384 (tptp) REVERT: HT 214 LYS cc_start: 0.7875 (ptmt) cc_final: 0.7654 (tppt) REVERT: HT 216 ASN cc_start: 0.7608 (m110) cc_final: 0.7379 (m-40) REVERT: HT 292 GLU cc_start: 0.7934 (tp30) cc_final: 0.7000 (mt-10) REVERT: HT 296 GLU cc_start: 0.7598 (tm-30) cc_final: 0.6821 (tm-30) REVERT: HT 300 ASN cc_start: 0.6721 (m-40) cc_final: 0.6318 (m-40) REVERT: HX 374 LYS cc_start: 0.8035 (ptmm) cc_final: 0.7526 (ptpp) REVERT: HX 386 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7966 (tp40) REVERT: HX 405 GLN cc_start: 0.8041 (pt0) cc_final: 0.7614 (pt0) REVERT: HX 415 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7941 (mmm) REVERT: HX 474 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7587 (mm-30) REVERT: IT 49 GLU cc_start: 0.7424 (mp0) cc_final: 0.7122 (mp0) REVERT: IT 64 GLN cc_start: 0.8016 (tt0) cc_final: 0.7462 (mt0) REVERT: IT 67 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9064 (mt) REVERT: IT 209 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6484 (tp30) REVERT: IT 296 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7000 (tm-30) REVERT: IT 300 ASN cc_start: 0.6699 (m-40) cc_final: 0.6307 (m-40) REVERT: IX 386 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8286 (tp40) REVERT: IY 1715 SER cc_start: 0.8335 (p) cc_final: 0.8062 (p) REVERT: IY 1863 MET cc_start: 0.8570 (tpt) cc_final: 0.8355 (tpt) REVERT: IY 1907 GLN cc_start: 0.7836 (tt0) cc_final: 0.7412 (tt0) REVERT: JT 216 ASN cc_start: 0.7741 (m110) cc_final: 0.7469 (m110) REVERT: JT 296 GLU cc_start: 0.7552 (tm-30) cc_final: 0.6882 (tm-30) REVERT: JT 300 ASN cc_start: 0.6284 (m-40) cc_final: 0.5716 (m-40) REVERT: JX 371 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7221 (tm-30) REVERT: JX 378 ASP cc_start: 0.8102 (m-30) cc_final: 0.7608 (m-30) REVERT: JX 386 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8174 (tp40) REVERT: JX 401 TYR cc_start: 0.9017 (m-80) cc_final: 0.8725 (m-80) REVERT: JX 410 ARG cc_start: 0.7492 (mtm110) cc_final: 0.6790 (mtm110) REVERT: KT 59 THR cc_start: 0.8568 (m) cc_final: 0.8272 (m) REVERT: KT 194 LYS cc_start: 0.7798 (pttm) cc_final: 0.7427 (tptp) REVERT: KT 209 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7715 (tp30) REVERT: KT 216 ASN cc_start: 0.7724 (m110) cc_final: 0.7385 (m110) REVERT: KT 292 GLU cc_start: 0.7983 (tp30) cc_final: 0.7027 (mt-10) REVERT: KT 296 GLU cc_start: 0.7641 (tm-30) cc_final: 0.6979 (tm-30) REVERT: KT 300 ASN cc_start: 0.6861 (m-40) cc_final: 0.6478 (m-40) REVERT: KX 371 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7401 (tm-30) REVERT: KX 378 ASP cc_start: 0.8299 (m-30) cc_final: 0.7703 (t0) REVERT: KX 386 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8153 (tp40) REVERT: KY 1739 TYR cc_start: 0.9037 (m-80) cc_final: 0.8800 (m-80) REVERT: KY 1772 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8077 (pp) REVERT: KY 1873 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: KY 1903 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: KY 1904 ILE cc_start: 0.8339 (mt) cc_final: 0.8017 (mt) REVERT: LT 64 GLN cc_start: 0.7998 (tt0) cc_final: 0.7452 (mt0) REVERT: LT 194 LYS cc_start: 0.7730 (pttm) cc_final: 0.7302 (tptp) REVERT: LT 216 ASN cc_start: 0.7670 (m110) cc_final: 0.7347 (m110) REVERT: LT 292 GLU cc_start: 0.7868 (tp30) cc_final: 0.6985 (mt-10) REVERT: LT 296 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7304 (tm-30) REVERT: LX 378 ASP cc_start: 0.8206 (m-30) cc_final: 0.7694 (t0) REVERT: MT 49 GLU cc_start: 0.7357 (mp0) cc_final: 0.7142 (mp0) REVERT: MT 194 LYS cc_start: 0.7856 (pttm) cc_final: 0.7434 (tptp) REVERT: MT 209 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6330 (tp30) REVERT: MT 216 ASN cc_start: 0.7567 (m110) cc_final: 0.7308 (m110) REVERT: MT 296 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7211 (tm-30) REVERT: MT 300 ASN cc_start: 0.6425 (m-40) cc_final: 0.5987 (m110) REVERT: MX 378 ASP cc_start: 0.8218 (m-30) cc_final: 0.7615 (t0) REVERT: MX 386 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8057 (tp40) REVERT: MY 1685 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7475 (mmtt) REVERT: NT 209 GLU cc_start: 0.7304 (pp20) cc_final: 0.6311 (tm-30) REVERT: NT 216 ASN cc_start: 0.7705 (m110) cc_final: 0.7399 (m-40) REVERT: NT 296 GLU cc_start: 0.7610 (tm-30) cc_final: 0.6959 (tm-30) REVERT: NT 300 ASN cc_start: 0.6608 (m-40) cc_final: 0.6256 (m-40) REVERT: NX 374 LYS cc_start: 0.7797 (ptmm) cc_final: 0.7440 (ptpp) REVERT: NY 1685 LYS cc_start: 0.7095 (mmtm) cc_final: 0.6810 (mmtt) outliers start: 220 outliers final: 144 residues processed: 1763 average time/residue: 0.5794 time to fit residues: 1720.8628 Evaluate side-chains 1715 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1561 time to evaluate : 5.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 67 LEU Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AY residue 1713 ILE Chi-restraints excluded: chain AY residue 1724 ASN Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain AY residue 1873 GLU Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BX residue 459 MET Chi-restraints excluded: chain BY residue 1724 ASN Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1813 THR Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 65 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 82 LEU Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CX residue 383 LEU Chi-restraints excluded: chain CX residue 424 THR Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 383 LEU Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DX residue 460 THR Chi-restraints excluded: chain DY residue 1724 ASN Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1873 GLU Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain ET residue 201 THR Chi-restraints excluded: chain EX residue 383 LEU Chi-restraints excluded: chain EX residue 424 THR Chi-restraints excluded: chain EX residue 459 MET Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1724 ASN Chi-restraints excluded: chain EY residue 1752 MET Chi-restraints excluded: chain FT residue 80 VAL Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FT residue 201 THR Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 471 GLU Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1751 ILE Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain FY residue 1873 GLU Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 93 ILE Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1751 ILE Chi-restraints excluded: chain GY residue 1873 GLU Chi-restraints excluded: chain HT residue 67 LEU Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 383 LEU Chi-restraints excluded: chain HX residue 415 MET Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1724 ASN Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain HY residue 1873 GLU Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IY residue 1724 ASN Chi-restraints excluded: chain IY residue 1725 MET Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1813 THR Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 204 GLN Chi-restraints excluded: chain JX residue 424 THR Chi-restraints excluded: chain KT residue 35 VAL Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 377 LEU Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1724 ASN Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1809 SER Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1903 GLU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LT residue 201 THR Chi-restraints excluded: chain LX residue 383 LEU Chi-restraints excluded: chain LX residue 386 GLN Chi-restraints excluded: chain LX residue 424 THR Chi-restraints excluded: chain LX residue 459 MET Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1724 ASN Chi-restraints excluded: chain LY residue 1752 MET Chi-restraints excluded: chain LY residue 1813 THR Chi-restraints excluded: chain LY residue 1894 LYS Chi-restraints excluded: chain MT residue 80 VAL Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MT residue 201 THR Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 471 GLU Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1751 ILE Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain MY residue 1873 GLU Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1751 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 4.9990 chunk 633 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 413 optimal weight: 3.9990 chunk 173 optimal weight: 9.9990 chunk 704 optimal weight: 2.9990 chunk 584 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 369 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1743 GLN ** BT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN BY1907 GLN CT 204 GLN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN DX 443 GLN ** ET 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 197 GLN EX 386 GLN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 443 GLN EY1856 ASN ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 41 ASN GX 413 HIS ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HT 301 GLN ** HX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN ** HY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 443 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 64 GLN ** JX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN LT 197 GLN ** LX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 64 GLN NT 196 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 61992 Z= 0.425 Angle : 0.668 13.033 83594 Z= 0.351 Chirality : 0.048 0.194 9520 Planarity : 0.004 0.052 10598 Dihedral : 5.191 28.001 8134 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.73 % Allowed : 15.63 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.10), residues: 7406 helix: 1.11 (0.11), residues: 2324 sheet: -1.06 (0.12), residues: 1666 loop : -0.82 (0.10), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRPCX 466 HIS 0.005 0.001 HISLX 389 PHE 0.014 0.002 PHEHY1759 TYR 0.021 0.002 TYRIT 210 ARG 0.012 0.001 ARGAX 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1834 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1581 time to evaluate : 5.778 Fit side-chains revert: symmetry clash REVERT: AT 64 GLN cc_start: 0.8186 (tt0) cc_final: 0.7493 (mt0) REVERT: AT 194 LYS cc_start: 0.7936 (pttm) cc_final: 0.7425 (tptp) REVERT: AT 296 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6855 (tm-30) REVERT: AT 300 ASN cc_start: 0.6493 (m-40) cc_final: 0.6028 (m-40) REVERT: AT 301 GLN cc_start: 0.7498 (tp40) cc_final: 0.7173 (tp-100) REVERT: AX 374 LYS cc_start: 0.8121 (ptmm) cc_final: 0.7608 (ptpp) REVERT: AX 386 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7982 (tp40) REVERT: AX 405 GLN cc_start: 0.8081 (pt0) cc_final: 0.7746 (pt0) REVERT: AX 415 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8162 (mmm) REVERT: BT 49 GLU cc_start: 0.7437 (mp0) cc_final: 0.7229 (mp0) REVERT: BT 64 GLN cc_start: 0.8110 (tt0) cc_final: 0.7551 (mt0) REVERT: BT 67 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9115 (mt) REVERT: BT 194 LYS cc_start: 0.8020 (pttm) cc_final: 0.7571 (tptp) REVERT: BT 209 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6639 (tp30) REVERT: BT 216 ASN cc_start: 0.7645 (m110) cc_final: 0.7208 (m110) REVERT: BT 292 GLU cc_start: 0.8076 (tp30) cc_final: 0.6962 (mt-10) REVERT: BT 296 GLU cc_start: 0.7578 (tm-30) cc_final: 0.6935 (tm-30) REVERT: BT 300 ASN cc_start: 0.6734 (m-40) cc_final: 0.6254 (m-40) REVERT: BX 410 ARG cc_start: 0.7361 (mtm110) cc_final: 0.7103 (mtm110) REVERT: CT 209 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7653 (tp30) REVERT: CT 210 TYR cc_start: 0.8092 (t80) cc_final: 0.7707 (t80) REVERT: CT 216 ASN cc_start: 0.7801 (m110) cc_final: 0.7517 (m110) REVERT: CX 378 ASP cc_start: 0.8232 (m-30) cc_final: 0.7971 (m-30) REVERT: CX 386 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8194 (tp40) REVERT: CX 401 TYR cc_start: 0.9038 (m-80) cc_final: 0.8799 (m-80) REVERT: CX 474 GLU cc_start: 0.8143 (tp30) cc_final: 0.7635 (mp0) REVERT: CX 506 TYR cc_start: 0.9171 (p90) cc_final: 0.8886 (p90) REVERT: DT 59 THR cc_start: 0.8642 (m) cc_final: 0.8317 (m) REVERT: DT 194 LYS cc_start: 0.8099 (pttm) cc_final: 0.7592 (tptp) REVERT: DT 208 GLN cc_start: 0.7605 (tp-100) cc_final: 0.7380 (tp40) REVERT: DT 296 GLU cc_start: 0.7685 (tm-30) cc_final: 0.6819 (tm-30) REVERT: DT 297 TYR cc_start: 0.7866 (t80) cc_final: 0.7579 (t80) REVERT: DT 300 ASN cc_start: 0.6873 (m-40) cc_final: 0.6177 (m-40) REVERT: DT 301 GLN cc_start: 0.7346 (tp40) cc_final: 0.7086 (tp-100) REVERT: DX 374 LYS cc_start: 0.7960 (ptmm) cc_final: 0.7502 (ptpp) REVERT: DX 378 ASP cc_start: 0.8332 (m-30) cc_final: 0.7737 (t0) REVERT: DX 386 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8164 (tp40) REVERT: DY 1739 TYR cc_start: 0.9074 (m-80) cc_final: 0.8770 (m-80) REVERT: DY 1772 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8214 (pp) REVERT: DY 1903 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8455 (mt) cc_final: 0.8079 (mt) REVERT: ET 59 THR cc_start: 0.8738 (m) cc_final: 0.8408 (m) REVERT: ET 64 GLN cc_start: 0.8068 (tt0) cc_final: 0.7487 (mt0) REVERT: ET 194 LYS cc_start: 0.8003 (pttm) cc_final: 0.7567 (tptp) REVERT: EX 368 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.6296 (mm) REVERT: EY 1903 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7999 (tm-30) REVERT: FT 194 LYS cc_start: 0.7962 (pttm) cc_final: 0.7586 (tptp) REVERT: FT 214 LYS cc_start: 0.8143 (ptmt) cc_final: 0.7896 (tppt) REVERT: FT 216 ASN cc_start: 0.7900 (m110) cc_final: 0.7605 (m110) REVERT: FT 296 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7293 (tm-30) REVERT: FX 378 ASP cc_start: 0.8249 (m-30) cc_final: 0.7639 (t0) REVERT: FX 386 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8188 (tp40) REVERT: GT 209 GLU cc_start: 0.7425 (pp20) cc_final: 0.6361 (tm-30) REVERT: GT 216 ASN cc_start: 0.7647 (m110) cc_final: 0.7278 (m110) REVERT: GX 374 LYS cc_start: 0.7873 (ptmm) cc_final: 0.7482 (ptpp) REVERT: GX 459 MET cc_start: 0.8802 (mtp) cc_final: 0.8509 (mtp) REVERT: GX 471 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6791 (mt-10) REVERT: GY 1685 LYS cc_start: 0.7035 (mmtm) cc_final: 0.6708 (mmtt) REVERT: GY 1739 TYR cc_start: 0.9111 (m-80) cc_final: 0.8822 (m-80) REVERT: HT 49 GLU cc_start: 0.7518 (mp0) cc_final: 0.7172 (mp0) REVERT: HT 64 GLN cc_start: 0.8170 (tt0) cc_final: 0.7577 (mt0) REVERT: HT 194 LYS cc_start: 0.7949 (pttm) cc_final: 0.7492 (tptp) REVERT: HT 216 ASN cc_start: 0.7581 (m110) cc_final: 0.7345 (m-40) REVERT: HT 296 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6721 (tm-30) REVERT: HT 300 ASN cc_start: 0.6589 (m-40) cc_final: 0.6179 (m-40) REVERT: HT 301 GLN cc_start: 0.7432 (tp40) cc_final: 0.7209 (tp-100) REVERT: HX 374 LYS cc_start: 0.8051 (ptmm) cc_final: 0.7559 (ptpp) REVERT: HX 386 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7945 (tp40) REVERT: HX 474 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7730 (mm-30) REVERT: IT 64 GLN cc_start: 0.8086 (tt0) cc_final: 0.7496 (mt0) REVERT: IT 67 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9107 (mt) REVERT: IT 209 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6613 (tp30) REVERT: IT 216 ASN cc_start: 0.7650 (m110) cc_final: 0.7219 (m110) REVERT: IT 296 GLU cc_start: 0.7621 (tm-30) cc_final: 0.6980 (tm-30) REVERT: IT 300 ASN cc_start: 0.6767 (m-40) cc_final: 0.6301 (m-40) REVERT: IX 371 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7238 (tm-30) REVERT: JT 204 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: JT 210 TYR cc_start: 0.8193 (t80) cc_final: 0.7752 (t80) REVERT: JT 216 ASN cc_start: 0.7824 (m110) cc_final: 0.7535 (m110) REVERT: JT 296 GLU cc_start: 0.7559 (tm-30) cc_final: 0.6798 (tm-30) REVERT: JT 300 ASN cc_start: 0.6242 (m-40) cc_final: 0.5641 (m-40) REVERT: JX 369 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7725 (mtt180) REVERT: JX 371 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7059 (tm-30) REVERT: JX 378 ASP cc_start: 0.8205 (m-30) cc_final: 0.7770 (m-30) REVERT: JX 386 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8139 (tp40) REVERT: JX 401 TYR cc_start: 0.9056 (m-80) cc_final: 0.8726 (m-80) REVERT: JX 474 GLU cc_start: 0.8211 (tp30) cc_final: 0.7997 (tp30) REVERT: KT 59 THR cc_start: 0.8671 (m) cc_final: 0.8373 (m) REVERT: KT 194 LYS cc_start: 0.8101 (pttm) cc_final: 0.7522 (tptp) REVERT: KT 209 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7660 (tp30) REVERT: KT 216 ASN cc_start: 0.7727 (m110) cc_final: 0.7379 (m110) REVERT: KT 292 GLU cc_start: 0.8102 (tp30) cc_final: 0.7020 (mt-10) REVERT: KT 296 GLU cc_start: 0.7633 (tm-30) cc_final: 0.6881 (tm-30) REVERT: KT 300 ASN cc_start: 0.6889 (m-40) cc_final: 0.6421 (m-40) REVERT: KX 371 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7371 (tm-30) REVERT: KX 378 ASP cc_start: 0.8340 (m-30) cc_final: 0.7831 (t0) REVERT: KX 386 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8135 (tp40) REVERT: KX 474 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7811 (tp30) REVERT: KY 1739 TYR cc_start: 0.9070 (m-80) cc_final: 0.8770 (m-80) REVERT: KY 1772 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8212 (pp) REVERT: KY 1873 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8087 (pm20) REVERT: KY 1903 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: KY 1904 ILE cc_start: 0.8456 (mt) cc_final: 0.8057 (mt) REVERT: LT 64 GLN cc_start: 0.8058 (tt0) cc_final: 0.7490 (mt0) REVERT: LT 194 LYS cc_start: 0.7973 (pttm) cc_final: 0.7549 (tptp) REVERT: LT 216 ASN cc_start: 0.7766 (m110) cc_final: 0.7353 (m110) REVERT: LT 292 GLU cc_start: 0.7771 (tp30) cc_final: 0.6884 (mt-10) REVERT: LT 296 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7335 (tm-30) REVERT: LX 368 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.6363 (mm) REVERT: MT 194 LYS cc_start: 0.7874 (pttm) cc_final: 0.7492 (tptp) REVERT: MT 208 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7391 (tp40) REVERT: MT 209 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6268 (tp30) REVERT: MT 216 ASN cc_start: 0.7600 (m110) cc_final: 0.7349 (m110) REVERT: MT 296 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7065 (tm-30) REVERT: MT 300 ASN cc_start: 0.6427 (m-40) cc_final: 0.6038 (m110) REVERT: MX 378 ASP cc_start: 0.8241 (m-30) cc_final: 0.7605 (t0) REVERT: MX 386 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8174 (tp40) REVERT: MY 1685 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7324 (mmtm) REVERT: NT 216 ASN cc_start: 0.7685 (m110) cc_final: 0.7263 (m110) REVERT: NT 296 GLU cc_start: 0.7568 (tm-30) cc_final: 0.6821 (tm-30) REVERT: NT 300 ASN cc_start: 0.6565 (m-40) cc_final: 0.5967 (m-40) REVERT: NX 374 LYS cc_start: 0.7860 (ptmm) cc_final: 0.7505 (ptpp) REVERT: NX 459 MET cc_start: 0.8805 (mtp) cc_final: 0.8507 (mtp) REVERT: NX 471 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6824 (mt-10) REVERT: NY 1685 LYS cc_start: 0.7039 (mmtm) cc_final: 0.6707 (mmtt) outliers start: 253 outliers final: 162 residues processed: 1734 average time/residue: 0.5824 time to fit residues: 1694.7647 Evaluate side-chains 1680 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1507 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AT residue 209 GLU Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AX residue 424 THR Chi-restraints excluded: chain AY residue 1711 THR Chi-restraints excluded: chain AY residue 1713 ILE Chi-restraints excluded: chain AY residue 1724 ASN Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1873 GLU Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 385 THR Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BY residue 1694 GLN Chi-restraints excluded: chain BY residue 1724 ASN Chi-restraints excluded: chain BY residue 1725 MET Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1813 THR Chi-restraints excluded: chain BY residue 1879 ILE Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 65 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 82 LEU Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CX residue 383 LEU Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 424 THR Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain CY residue 1711 THR Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 52 LEU Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 383 LEU Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1711 THR Chi-restraints excluded: chain DY residue 1724 ASN Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1880 LEU Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 368 ILE Chi-restraints excluded: chain EX residue 383 LEU Chi-restraints excluded: chain EX residue 411 SER Chi-restraints excluded: chain EX residue 424 THR Chi-restraints excluded: chain EX residue 460 THR Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1711 THR Chi-restraints excluded: chain EY residue 1724 ASN Chi-restraints excluded: chain EY residue 1752 MET Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FT residue 201 THR Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 471 GLU Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1711 THR Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1751 ILE Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain FY residue 1873 GLU Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 93 ILE Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1711 THR Chi-restraints excluded: chain GY residue 1751 ILE Chi-restraints excluded: chain GY residue 1873 GLU Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 383 LEU Chi-restraints excluded: chain HX residue 385 THR Chi-restraints excluded: chain HX residue 424 THR Chi-restraints excluded: chain HY residue 1711 THR Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1724 ASN Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1873 GLU Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 508 GLU Chi-restraints excluded: chain IX residue 509 LEU Chi-restraints excluded: chain IY residue 1694 GLN Chi-restraints excluded: chain IY residue 1724 ASN Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1813 THR Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 52 LEU Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 204 GLN Chi-restraints excluded: chain JX residue 411 SER Chi-restraints excluded: chain JX residue 424 THR Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1694 GLN Chi-restraints excluded: chain JY residue 1711 THR Chi-restraints excluded: chain KT residue 52 LEU Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 385 THR Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 460 THR Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1711 THR Chi-restraints excluded: chain KY residue 1724 ASN Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1809 SER Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1880 LEU Chi-restraints excluded: chain KY residue 1903 GLU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 368 ILE Chi-restraints excluded: chain LX residue 383 LEU Chi-restraints excluded: chain LX residue 424 THR Chi-restraints excluded: chain LX residue 460 THR Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1694 GLN Chi-restraints excluded: chain LY residue 1711 THR Chi-restraints excluded: chain LY residue 1724 ASN Chi-restraints excluded: chain LY residue 1813 THR Chi-restraints excluded: chain LY residue 1894 LYS Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MT residue 201 THR Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 471 GLU Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1711 THR Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1751 ILE Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain MY residue 1873 GLU Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1711 THR Chi-restraints excluded: chain NY residue 1751 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 401 optimal weight: 0.7980 chunk 514 optimal weight: 7.9990 chunk 398 optimal weight: 0.6980 chunk 592 optimal weight: 4.9990 chunk 393 optimal weight: 0.7980 chunk 701 optimal weight: 0.6980 chunk 439 optimal weight: 0.6980 chunk 427 optimal weight: 0.1980 chunk 323 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 197 GLN AY1743 GLN ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN DX 443 GLN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 443 GLN ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FX 413 HIS FX 443 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN HY1864 ASN IT 169 HIS IX 443 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JT 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN LY1856 ASN ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 53 ASN MT 169 HIS MX 413 HIS MX 443 GLN ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 64 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 61992 Z= 0.181 Angle : 0.585 14.704 83594 Z= 0.308 Chirality : 0.045 0.196 9520 Planarity : 0.004 0.043 10598 Dihedral : 4.903 26.751 8134 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.68 % Allowed : 17.08 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.10), residues: 7406 helix: 1.36 (0.11), residues: 2324 sheet: -1.10 (0.12), residues: 1666 loop : -0.71 (0.11), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPIY1723 HIS 0.002 0.000 HISGT 89 PHE 0.009 0.001 PHEJX 420 TYR 0.016 0.001 TYRNT 210 ARG 0.005 0.000 ARGKX 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1866 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1684 time to evaluate : 5.753 Fit side-chains revert: symmetry clash REVERT: AT 64 GLN cc_start: 0.8173 (tt0) cc_final: 0.7453 (mt0) REVERT: AT 194 LYS cc_start: 0.7908 (pttm) cc_final: 0.7346 (tptp) REVERT: AT 216 ASN cc_start: 0.7622 (m110) cc_final: 0.7421 (m110) REVERT: AT 292 GLU cc_start: 0.8077 (tp30) cc_final: 0.7162 (mt-10) REVERT: AT 300 ASN cc_start: 0.6400 (m-40) cc_final: 0.6156 (m-40) REVERT: AT 301 GLN cc_start: 0.7439 (tp40) cc_final: 0.7014 (mm110) REVERT: AX 386 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8020 (tp40) REVERT: AX 415 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8016 (mmm) REVERT: AX 474 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7522 (mm-30) REVERT: BT 64 GLN cc_start: 0.8040 (tt0) cc_final: 0.7426 (mt0) REVERT: BT 67 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9046 (mt) REVERT: BT 194 LYS cc_start: 0.8041 (pttm) cc_final: 0.7589 (tptp) REVERT: BT 209 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6569 (tp30) REVERT: BT 210 TYR cc_start: 0.8079 (t80) cc_final: 0.7634 (t80) REVERT: BT 216 ASN cc_start: 0.7733 (m110) cc_final: 0.7364 (m110) REVERT: BT 292 GLU cc_start: 0.8008 (tp30) cc_final: 0.6978 (mt-10) REVERT: BT 296 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7046 (tm-30) REVERT: BT 300 ASN cc_start: 0.6782 (m-40) cc_final: 0.6340 (m-40) REVERT: BX 384 GLU cc_start: 0.8205 (tt0) cc_final: 0.7785 (tt0) REVERT: BX 410 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6794 (mtm110) REVERT: BY 1715 SER cc_start: 0.8216 (p) cc_final: 0.7967 (p) REVERT: BY 1903 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7881 (tm-30) REVERT: CT 209 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7643 (tp30) REVERT: CT 210 TYR cc_start: 0.8161 (t80) cc_final: 0.7855 (t80) REVERT: CT 216 ASN cc_start: 0.7673 (m110) cc_final: 0.7262 (m110) REVERT: CT 292 GLU cc_start: 0.8081 (tp30) cc_final: 0.7053 (mt-10) REVERT: CT 300 ASN cc_start: 0.6344 (m-40) cc_final: 0.6129 (m-40) REVERT: CX 401 TYR cc_start: 0.8945 (m-80) cc_final: 0.8743 (m-80) REVERT: CY 1800 PHE cc_start: 0.8705 (m-10) cc_final: 0.8455 (m-80) REVERT: DT 59 THR cc_start: 0.8572 (m) cc_final: 0.8274 (m) REVERT: DT 194 LYS cc_start: 0.8110 (pttm) cc_final: 0.7425 (tptp) REVERT: DT 208 GLN cc_start: 0.7548 (tp-100) cc_final: 0.7320 (tp40) REVERT: DT 292 GLU cc_start: 0.8102 (tp30) cc_final: 0.6925 (mt-10) REVERT: DT 296 GLU cc_start: 0.7691 (tm-30) cc_final: 0.6775 (tm-30) REVERT: DT 300 ASN cc_start: 0.6801 (m-40) cc_final: 0.6118 (m-40) REVERT: DT 301 GLN cc_start: 0.7361 (tp40) cc_final: 0.7077 (tp-100) REVERT: DX 374 LYS cc_start: 0.7948 (ptmm) cc_final: 0.7469 (ptpp) REVERT: DX 387 TYR cc_start: 0.8602 (t80) cc_final: 0.8020 (t80) REVERT: DX 410 ARG cc_start: 0.7487 (mtm110) cc_final: 0.7164 (mtm110) REVERT: DY 1739 TYR cc_start: 0.9028 (m-80) cc_final: 0.8774 (m-80) REVERT: DY 1772 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8024 (pp) REVERT: DY 1903 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8281 (mt) cc_final: 0.7981 (mt) REVERT: ET 59 THR cc_start: 0.8712 (m) cc_final: 0.8412 (m) REVERT: ET 64 GLN cc_start: 0.8031 (tt0) cc_final: 0.7441 (mt0) REVERT: ET 194 LYS cc_start: 0.7857 (pttm) cc_final: 0.7452 (tptp) REVERT: ET 210 TYR cc_start: 0.8207 (t80) cc_final: 0.7956 (t80) REVERT: ET 300 ASN cc_start: 0.6494 (m-40) cc_final: 0.6205 (m110) REVERT: ET 301 GLN cc_start: 0.7302 (tp40) cc_final: 0.6882 (mm110) REVERT: FT 194 LYS cc_start: 0.7880 (pttm) cc_final: 0.7446 (tptp) REVERT: FT 213 ARG cc_start: 0.6473 (ttp-170) cc_final: 0.6159 (ttp-170) REVERT: FT 214 LYS cc_start: 0.8102 (ptmt) cc_final: 0.7897 (tppt) REVERT: FT 216 ASN cc_start: 0.7893 (m110) cc_final: 0.7612 (m110) REVERT: FT 292 GLU cc_start: 0.7768 (tp30) cc_final: 0.6915 (mt-10) REVERT: FT 296 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7206 (tm-30) REVERT: FT 300 ASN cc_start: 0.6695 (m-40) cc_final: 0.6212 (m110) REVERT: FX 378 ASP cc_start: 0.8209 (m-30) cc_final: 0.7603 (t0) REVERT: FX 472 ILE cc_start: 0.8851 (mm) cc_final: 0.8648 (mm) REVERT: GT 216 ASN cc_start: 0.7736 (m110) cc_final: 0.7496 (m-40) REVERT: GT 292 GLU cc_start: 0.7642 (tp30) cc_final: 0.6872 (mt-10) REVERT: GT 300 ASN cc_start: 0.6521 (m-40) cc_final: 0.6285 (m-40) REVERT: GX 374 LYS cc_start: 0.7823 (ptmm) cc_final: 0.7457 (ptpp) REVERT: GX 459 MET cc_start: 0.8731 (mtp) cc_final: 0.8410 (mtp) REVERT: GY 1685 LYS cc_start: 0.6950 (mmtm) cc_final: 0.6620 (mmtt) REVERT: HT 49 GLU cc_start: 0.7498 (mp0) cc_final: 0.7134 (mp0) REVERT: HT 64 GLN cc_start: 0.8164 (tt0) cc_final: 0.7466 (mt0) REVERT: HT 194 LYS cc_start: 0.7882 (pttm) cc_final: 0.7394 (tptp) REVERT: HT 201 THR cc_start: 0.8383 (p) cc_final: 0.7991 (t) REVERT: HT 292 GLU cc_start: 0.7757 (tp30) cc_final: 0.6842 (mt-10) REVERT: HT 296 GLU cc_start: 0.7731 (tm-30) cc_final: 0.6855 (tm-30) REVERT: HT 300 ASN cc_start: 0.6741 (m-40) cc_final: 0.6381 (m-40) REVERT: HX 374 LYS cc_start: 0.8024 (ptmm) cc_final: 0.7529 (ptpp) REVERT: HX 386 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7966 (tp40) REVERT: HX 415 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7969 (mmm) REVERT: IT 64 GLN cc_start: 0.8031 (tt0) cc_final: 0.7390 (mt0) REVERT: IT 67 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9039 (mt) REVERT: IT 209 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6559 (tp30) REVERT: IT 210 TYR cc_start: 0.8215 (t80) cc_final: 0.7955 (t80) REVERT: IT 216 ASN cc_start: 0.7759 (m110) cc_final: 0.7385 (m110) REVERT: IT 296 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6969 (tm-30) REVERT: IT 300 ASN cc_start: 0.6843 (m-40) cc_final: 0.6365 (m-40) REVERT: IX 371 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7213 (tm-30) REVERT: IX 384 GLU cc_start: 0.8255 (tt0) cc_final: 0.7816 (tt0) REVERT: IY 1715 SER cc_start: 0.8220 (p) cc_final: 0.7961 (p) REVERT: IY 1907 GLN cc_start: 0.7752 (tt0) cc_final: 0.7322 (tt0) REVERT: JT 210 TYR cc_start: 0.8122 (t80) cc_final: 0.7637 (t80) REVERT: JT 216 ASN cc_start: 0.7756 (m110) cc_final: 0.7476 (m110) REVERT: JT 296 GLU cc_start: 0.7651 (tm-30) cc_final: 0.6909 (tm-30) REVERT: JT 300 ASN cc_start: 0.6032 (m-40) cc_final: 0.5605 (m-40) REVERT: JX 369 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7847 (mtt180) REVERT: JX 371 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7164 (tm-30) REVERT: JX 378 ASP cc_start: 0.8151 (m-30) cc_final: 0.7696 (m-30) REVERT: JX 401 TYR cc_start: 0.8997 (m-80) cc_final: 0.8710 (m-80) REVERT: JX 484 LEU cc_start: 0.9213 (tp) cc_final: 0.9011 (tp) REVERT: JY 1715 SER cc_start: 0.8411 (p) cc_final: 0.8211 (p) REVERT: JY 1800 PHE cc_start: 0.8714 (m-10) cc_final: 0.8504 (m-10) REVERT: KT 59 THR cc_start: 0.8599 (m) cc_final: 0.8307 (m) REVERT: KT 194 LYS cc_start: 0.8041 (pttm) cc_final: 0.7532 (tptp) REVERT: KT 201 THR cc_start: 0.8403 (p) cc_final: 0.8048 (t) REVERT: KT 209 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7755 (tp30) REVERT: KT 216 ASN cc_start: 0.7744 (m110) cc_final: 0.7436 (m110) REVERT: KT 292 GLU cc_start: 0.8041 (tp30) cc_final: 0.6970 (mt-10) REVERT: KT 296 GLU cc_start: 0.7678 (tm-30) cc_final: 0.6997 (tm-30) REVERT: KT 300 ASN cc_start: 0.6875 (m-40) cc_final: 0.6484 (m-40) REVERT: KX 369 ARG cc_start: 0.6921 (mtt-85) cc_final: 0.6707 (ptp-170) REVERT: KX 371 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7399 (tm-30) REVERT: KX 378 ASP cc_start: 0.8282 (m-30) cc_final: 0.7756 (t0) REVERT: KX 386 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8182 (tp40) REVERT: KX 509 LEU cc_start: 0.9024 (mt) cc_final: 0.8728 (mt) REVERT: KY 1739 TYR cc_start: 0.9021 (m-80) cc_final: 0.8711 (m-80) REVERT: KY 1772 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8057 (pp) REVERT: KY 1904 ILE cc_start: 0.8180 (mt) cc_final: 0.7844 (mt) REVERT: LT 64 GLN cc_start: 0.8015 (tt0) cc_final: 0.7426 (mt0) REVERT: LT 194 LYS cc_start: 0.7841 (pttm) cc_final: 0.7463 (tptp) REVERT: LT 210 TYR cc_start: 0.8165 (t80) cc_final: 0.7904 (t80) REVERT: LT 216 ASN cc_start: 0.7759 (m110) cc_final: 0.7401 (m110) REVERT: LT 292 GLU cc_start: 0.7748 (tp30) cc_final: 0.6916 (mt-10) REVERT: LT 300 ASN cc_start: 0.6696 (m-40) cc_final: 0.6254 (m110) REVERT: LX 386 GLN cc_start: 0.8500 (tp40) cc_final: 0.8187 (tp40) REVERT: LX 387 TYR cc_start: 0.8349 (t80) cc_final: 0.7792 (t80) REVERT: MT 194 LYS cc_start: 0.7835 (pttm) cc_final: 0.7381 (tptp) REVERT: MT 216 ASN cc_start: 0.7662 (m110) cc_final: 0.7439 (m110) REVERT: MT 296 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6788 (tm-30) REVERT: MT 300 ASN cc_start: 0.6581 (m-40) cc_final: 0.6247 (m-40) REVERT: MX 378 ASP cc_start: 0.8247 (m-30) cc_final: 0.7609 (t0) REVERT: MY 1685 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7294 (mmtm) REVERT: NT 209 GLU cc_start: 0.7267 (pp20) cc_final: 0.6247 (tm-30) REVERT: NT 216 ASN cc_start: 0.7690 (m110) cc_final: 0.7385 (m-40) REVERT: NT 296 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7038 (tm-30) REVERT: NT 300 ASN cc_start: 0.6527 (m-40) cc_final: 0.6041 (m-40) REVERT: NX 459 MET cc_start: 0.8730 (mtp) cc_final: 0.8407 (mtp) REVERT: NY 1685 LYS cc_start: 0.6948 (mmtm) cc_final: 0.6618 (mmtt) outliers start: 182 outliers final: 115 residues processed: 1776 average time/residue: 0.5856 time to fit residues: 1747.9639 Evaluate side-chains 1699 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1577 time to evaluate : 5.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AY residue 1724 ASN Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain AY residue 1873 GLU Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 385 THR Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BY residue 1694 GLN Chi-restraints excluded: chain BY residue 1724 ASN Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1813 THR Chi-restraints excluded: chain BY residue 1879 ILE Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 52 LEU Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1724 ASN Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 385 THR Chi-restraints excluded: chain EX residue 460 THR Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1724 ASN Chi-restraints excluded: chain FT residue 52 LEU Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 460 THR Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain FY residue 1873 GLU Chi-restraints excluded: chain FY residue 1879 ILE Chi-restraints excluded: chain GT residue 67 LEU Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GT residue 297 TYR Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1873 GLU Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 415 MET Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1724 ASN Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 377 LEU Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 508 GLU Chi-restraints excluded: chain IY residue 1694 GLN Chi-restraints excluded: chain IY residue 1724 ASN Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1813 THR Chi-restraints excluded: chain IY residue 1879 ILE Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 377 LEU Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 449 SER Chi-restraints excluded: chain KX residue 460 THR Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1724 ASN Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1809 SER Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1880 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 388 VAL Chi-restraints excluded: chain LX residue 460 THR Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1724 ASN Chi-restraints excluded: chain LY residue 1894 LYS Chi-restraints excluded: chain MT residue 52 LEU Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 460 THR Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain MY residue 1873 GLU Chi-restraints excluded: chain MY residue 1879 ILE Chi-restraints excluded: chain NT residue 67 LEU Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 9.9990 chunk 280 optimal weight: 0.0980 chunk 419 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 446 optimal weight: 5.9990 chunk 478 optimal weight: 2.9990 chunk 346 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 551 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 196 ASN ** AY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1743 GLN ** BT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BY1907 GLN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN ** DT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 443 GLN ** DX 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ET 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EY1856 ASN ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 169 HIS HY1743 GLN ** HY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 196 ASN JT 204 GLN ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN ** LT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN MT 31 GLN ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 64 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 61992 Z= 0.261 Angle : 0.619 14.638 83594 Z= 0.323 Chirality : 0.046 0.198 9520 Planarity : 0.004 0.042 10598 Dihedral : 4.918 27.313 8134 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.74 % Allowed : 17.67 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.10), residues: 7406 helix: 1.34 (0.11), residues: 2324 sheet: -1.07 (0.12), residues: 1666 loop : -0.69 (0.11), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPJX 466 HIS 0.002 0.000 HISCT 169 PHE 0.011 0.001 PHEAY1682 TYR 0.020 0.001 TYRMT 73 ARG 0.010 0.000 ARGBX 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1762 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1576 time to evaluate : 5.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AT 64 GLN cc_start: 0.8186 (tt0) cc_final: 0.7466 (mt0) REVERT: AT 194 LYS cc_start: 0.7846 (pttm) cc_final: 0.7251 (tptp) REVERT: AT 201 THR cc_start: 0.8384 (p) cc_final: 0.8003 (t) REVERT: AT 292 GLU cc_start: 0.8047 (tp30) cc_final: 0.7103 (mt-10) REVERT: AT 296 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7305 (tm-30) REVERT: AX 386 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8099 (tp40) REVERT: BT 64 GLN cc_start: 0.8056 (tt0) cc_final: 0.7435 (mt0) REVERT: BT 67 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9082 (mt) REVERT: BT 168 LEU cc_start: 0.8148 (pp) cc_final: 0.7890 (pp) REVERT: BT 196 ASN cc_start: 0.7353 (m-40) cc_final: 0.7070 (m110) REVERT: BT 209 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6585 (tp30) REVERT: BT 210 TYR cc_start: 0.8067 (t80) cc_final: 0.7664 (t80) REVERT: BT 216 ASN cc_start: 0.7795 (m110) cc_final: 0.7412 (m110) REVERT: BT 296 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7022 (tm-30) REVERT: BT 300 ASN cc_start: 0.6776 (m-40) cc_final: 0.6303 (m-40) REVERT: BX 369 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7378 (mtt-85) REVERT: BX 384 GLU cc_start: 0.8224 (tt0) cc_final: 0.7837 (tt0) REVERT: BX 410 ARG cc_start: 0.7375 (mtm110) cc_final: 0.7000 (mtm110) REVERT: BY 1715 SER cc_start: 0.8264 (p) cc_final: 0.8003 (p) REVERT: CT 208 GLN cc_start: 0.7773 (tp-100) cc_final: 0.7532 (tp40) REVERT: CT 209 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7667 (tp30) REVERT: CT 216 ASN cc_start: 0.7677 (m110) cc_final: 0.7271 (m110) REVERT: CT 292 GLU cc_start: 0.8087 (tp30) cc_final: 0.7053 (mt-10) REVERT: CT 300 ASN cc_start: 0.6402 (m-40) cc_final: 0.6175 (m-40) REVERT: CX 369 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7580 (mtt180) REVERT: CX 374 LYS cc_start: 0.7700 (ptmm) cc_final: 0.7233 (ptpp) REVERT: DT 59 THR cc_start: 0.8564 (m) cc_final: 0.8256 (m) REVERT: DT 194 LYS cc_start: 0.8186 (pttm) cc_final: 0.7601 (tptp) REVERT: DT 208 GLN cc_start: 0.7561 (tp-100) cc_final: 0.7322 (tp40) REVERT: DT 296 GLU cc_start: 0.7683 (tm-30) cc_final: 0.6782 (tm-30) REVERT: DT 297 TYR cc_start: 0.7686 (t80) cc_final: 0.7390 (t80) REVERT: DT 300 ASN cc_start: 0.6726 (m-40) cc_final: 0.6072 (m-40) REVERT: DT 301 GLN cc_start: 0.7401 (tp40) cc_final: 0.7102 (tp-100) REVERT: DX 374 LYS cc_start: 0.7925 (ptmm) cc_final: 0.7405 (ptpp) REVERT: DX 410 ARG cc_start: 0.7432 (mtm110) cc_final: 0.7094 (mtm110) REVERT: DY 1739 TYR cc_start: 0.9044 (m-80) cc_final: 0.8735 (m-80) REVERT: DY 1772 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8044 (pp) REVERT: DY 1903 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8203 (mt) cc_final: 0.7868 (mt) REVERT: ET 59 THR cc_start: 0.8697 (m) cc_final: 0.8382 (m) REVERT: ET 64 GLN cc_start: 0.8039 (tt0) cc_final: 0.7458 (mt0) REVERT: ET 194 LYS cc_start: 0.7875 (pttm) cc_final: 0.7447 (tptp) REVERT: ET 201 THR cc_start: 0.8149 (p) cc_final: 0.7752 (t) REVERT: ET 210 TYR cc_start: 0.8220 (t80) cc_final: 0.7899 (t80) REVERT: ET 292 GLU cc_start: 0.7704 (tp30) cc_final: 0.6822 (mt-10) REVERT: ET 296 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7324 (tm-30) REVERT: ET 300 ASN cc_start: 0.6628 (m-40) cc_final: 0.6356 (m110) REVERT: EY 1739 TYR cc_start: 0.9036 (m-80) cc_final: 0.8600 (m-80) REVERT: FT 194 LYS cc_start: 0.7931 (pttm) cc_final: 0.7544 (tptp) REVERT: FT 213 ARG cc_start: 0.6496 (ttp-170) cc_final: 0.6179 (ttp-170) REVERT: FT 216 ASN cc_start: 0.7893 (m110) cc_final: 0.7605 (m110) REVERT: FT 292 GLU cc_start: 0.7727 (tp30) cc_final: 0.6896 (mt-10) REVERT: FT 296 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7087 (tm-30) REVERT: FT 300 ASN cc_start: 0.6737 (m-40) cc_final: 0.6222 (m110) REVERT: FX 378 ASP cc_start: 0.8219 (m-30) cc_final: 0.7610 (t0) REVERT: FX 474 GLU cc_start: 0.7866 (tp30) cc_final: 0.7380 (mp0) REVERT: FY 1907 GLN cc_start: 0.7935 (tt0) cc_final: 0.7592 (tt0) REVERT: GT 209 GLU cc_start: 0.7429 (pp20) cc_final: 0.6306 (tm-30) REVERT: GT 215 ASN cc_start: 0.7486 (m-40) cc_final: 0.7203 (p0) REVERT: GT 216 ASN cc_start: 0.7748 (m110) cc_final: 0.7265 (m110) REVERT: GT 292 GLU cc_start: 0.7681 (tp30) cc_final: 0.6897 (mt-10) REVERT: GT 296 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7318 (tm-30) REVERT: GT 300 ASN cc_start: 0.6530 (m-40) cc_final: 0.6166 (m110) REVERT: GT 301 GLN cc_start: 0.7157 (tp40) cc_final: 0.6631 (mm110) REVERT: GX 369 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7375 (mtt180) REVERT: GX 374 LYS cc_start: 0.7820 (ptmm) cc_final: 0.7422 (ptpp) REVERT: GX 459 MET cc_start: 0.8755 (mtp) cc_final: 0.8392 (mtp) REVERT: GX 471 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6747 (mt-10) REVERT: GY 1685 LYS cc_start: 0.6976 (mmtm) cc_final: 0.6641 (mmtt) REVERT: HT 49 GLU cc_start: 0.7529 (mp0) cc_final: 0.7203 (mp0) REVERT: HT 64 GLN cc_start: 0.8186 (tt0) cc_final: 0.7546 (mt0) REVERT: HT 194 LYS cc_start: 0.7885 (pttm) cc_final: 0.7408 (tptp) REVERT: HT 201 THR cc_start: 0.8243 (p) cc_final: 0.7849 (t) REVERT: HT 292 GLU cc_start: 0.7805 (tp30) cc_final: 0.6874 (mt-10) REVERT: HT 296 GLU cc_start: 0.7646 (tm-30) cc_final: 0.6756 (tm-30) REVERT: HT 300 ASN cc_start: 0.6619 (m-40) cc_final: 0.6177 (m-40) REVERT: HT 301 GLN cc_start: 0.7335 (tp40) cc_final: 0.6806 (mm110) REVERT: HX 374 LYS cc_start: 0.8029 (ptmm) cc_final: 0.7525 (ptpp) REVERT: HX 386 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7983 (tp40) REVERT: IT 64 GLN cc_start: 0.8052 (tt0) cc_final: 0.7403 (mt0) REVERT: IT 67 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9067 (mt) REVERT: IT 209 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6512 (tp30) REVERT: IT 210 TYR cc_start: 0.8219 (t80) cc_final: 0.7892 (t80) REVERT: IT 216 ASN cc_start: 0.7778 (m110) cc_final: 0.7420 (m110) REVERT: IT 292 GLU cc_start: 0.7988 (tp30) cc_final: 0.6977 (mt-10) REVERT: IT 296 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7014 (tm-30) REVERT: IT 300 ASN cc_start: 0.6844 (m-40) cc_final: 0.6354 (m-40) REVERT: IX 371 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7257 (tm-30) REVERT: IX 384 GLU cc_start: 0.8284 (tt0) cc_final: 0.7867 (tt0) REVERT: IY 1715 SER cc_start: 0.8213 (p) cc_final: 0.7956 (p) REVERT: IY 1907 GLN cc_start: 0.7859 (tt0) cc_final: 0.7452 (tt0) REVERT: JT 210 TYR cc_start: 0.8177 (t80) cc_final: 0.7730 (t80) REVERT: JT 216 ASN cc_start: 0.7751 (m110) cc_final: 0.7468 (m110) REVERT: JT 292 GLU cc_start: 0.8029 (tp30) cc_final: 0.7000 (mt-10) REVERT: JT 296 GLU cc_start: 0.7648 (tm-30) cc_final: 0.6860 (tm-30) REVERT: JT 300 ASN cc_start: 0.6126 (m-40) cc_final: 0.5583 (m-40) REVERT: JX 369 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7824 (mtt180) REVERT: JX 371 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7128 (tm-30) REVERT: JX 386 GLN cc_start: 0.8464 (tp40) cc_final: 0.8245 (tp40) REVERT: JX 484 LEU cc_start: 0.9204 (tp) cc_final: 0.8991 (tp) REVERT: KT 59 THR cc_start: 0.8580 (m) cc_final: 0.8291 (m) REVERT: KT 194 LYS cc_start: 0.8062 (pttm) cc_final: 0.7542 (tptp) REVERT: KT 209 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7732 (tp30) REVERT: KT 216 ASN cc_start: 0.7786 (m110) cc_final: 0.7464 (m110) REVERT: KT 292 GLU cc_start: 0.8002 (tp30) cc_final: 0.6917 (mt-10) REVERT: KT 296 GLU cc_start: 0.7653 (tm-30) cc_final: 0.6956 (tm-30) REVERT: KT 300 ASN cc_start: 0.6825 (m-40) cc_final: 0.6442 (m-40) REVERT: KX 371 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7331 (tm-30) REVERT: KX 386 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8134 (tp40) REVERT: KX 509 LEU cc_start: 0.9123 (mt) cc_final: 0.8775 (mt) REVERT: KY 1739 TYR cc_start: 0.9038 (m-80) cc_final: 0.8725 (m-80) REVERT: KY 1772 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8089 (pp) REVERT: KY 1904 ILE cc_start: 0.8060 (mt) cc_final: 0.7831 (mt) REVERT: LT 64 GLN cc_start: 0.8028 (tt0) cc_final: 0.7436 (mt0) REVERT: LT 194 LYS cc_start: 0.7850 (pttm) cc_final: 0.7457 (tptp) REVERT: LT 201 THR cc_start: 0.8172 (p) cc_final: 0.7775 (t) REVERT: LT 210 TYR cc_start: 0.8277 (t80) cc_final: 0.7982 (t80) REVERT: LT 216 ASN cc_start: 0.7742 (m110) cc_final: 0.7334 (m110) REVERT: LT 292 GLU cc_start: 0.7737 (tp30) cc_final: 0.6921 (mt-10) REVERT: LX 386 GLN cc_start: 0.8558 (tp40) cc_final: 0.8240 (tp40) REVERT: LX 387 TYR cc_start: 0.8383 (t80) cc_final: 0.7868 (t80) REVERT: LY 1739 TYR cc_start: 0.9035 (m-80) cc_final: 0.8593 (m-80) REVERT: MT 194 LYS cc_start: 0.7863 (pttm) cc_final: 0.7441 (tptp) REVERT: MT 216 ASN cc_start: 0.7657 (m110) cc_final: 0.7427 (m110) REVERT: MT 296 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6706 (tm-30) REVERT: MT 300 ASN cc_start: 0.6829 (m-40) cc_final: 0.6432 (m-40) REVERT: MX 378 ASP cc_start: 0.8253 (m-30) cc_final: 0.7618 (t0) REVERT: MY 1685 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7290 (mmtm) REVERT: NT 209 GLU cc_start: 0.7380 (pp20) cc_final: 0.6399 (tm-30) REVERT: NT 216 ASN cc_start: 0.7712 (m110) cc_final: 0.7387 (m110) REVERT: NT 296 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7008 (tm-30) REVERT: NT 300 ASN cc_start: 0.6515 (m-40) cc_final: 0.5898 (m-40) REVERT: NX 374 LYS cc_start: 0.7804 (ptmm) cc_final: 0.7465 (ptpp) REVERT: NX 459 MET cc_start: 0.8754 (mtp) cc_final: 0.8395 (mtp) REVERT: NX 471 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6831 (mt-10) REVERT: NY 1685 LYS cc_start: 0.6974 (mmtm) cc_final: 0.6636 (mmtt) REVERT: NY 1699 GLU cc_start: 0.7752 (tt0) cc_final: 0.7454 (tt0) outliers start: 186 outliers final: 136 residues processed: 1691 average time/residue: 0.5934 time to fit residues: 1690.7501 Evaluate side-chains 1674 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1533 time to evaluate : 5.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 67 LEU Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AY residue 1724 ASN Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain AY residue 1873 GLU Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BX residue 508 GLU Chi-restraints excluded: chain BY residue 1711 THR Chi-restraints excluded: chain BY residue 1724 ASN Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1813 THR Chi-restraints excluded: chain BY residue 1879 ILE Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 65 VAL Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain CY residue 1711 THR Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 52 LEU Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1724 ASN Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1880 LEU Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 388 VAL Chi-restraints excluded: chain EX residue 460 THR Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1711 THR Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1724 ASN Chi-restraints excluded: chain EY residue 1813 THR Chi-restraints excluded: chain FT residue 52 LEU Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FT residue 201 THR Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1711 THR Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain FY residue 1813 THR Chi-restraints excluded: chain FY residue 1873 GLU Chi-restraints excluded: chain FY residue 1879 ILE Chi-restraints excluded: chain GT residue 67 LEU Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1711 THR Chi-restraints excluded: chain GY residue 1751 ILE Chi-restraints excluded: chain GY residue 1873 GLU Chi-restraints excluded: chain HT residue 67 LEU Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 424 THR Chi-restraints excluded: chain HY residue 1724 ASN Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 508 GLU Chi-restraints excluded: chain IY residue 1711 THR Chi-restraints excluded: chain IY residue 1724 ASN Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1813 THR Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 196 ASN Chi-restraints excluded: chain JT residue 204 GLN Chi-restraints excluded: chain JX residue 424 THR Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1711 THR Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 377 LEU Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 418 GLU Chi-restraints excluded: chain KX residue 449 SER Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1724 ASN Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1809 SER Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1880 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 460 THR Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1711 THR Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1724 ASN Chi-restraints excluded: chain MT residue 52 LEU Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1711 THR Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain MY residue 1813 THR Chi-restraints excluded: chain MY residue 1873 GLU Chi-restraints excluded: chain MY residue 1879 ILE Chi-restraints excluded: chain NT residue 67 LEU Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1711 THR Chi-restraints excluded: chain NY residue 1751 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 6.9990 chunk 672 optimal weight: 4.9990 chunk 613 optimal weight: 7.9990 chunk 653 optimal weight: 4.9990 chunk 393 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 513 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 590 optimal weight: 6.9990 chunk 618 optimal weight: 10.0000 chunk 651 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 300 ASN AY1726 ASN AY1743 GLN ** BT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN BY1907 GLN CT 197 GLN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN ** DT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 443 GLN ** ET 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 443 GLN ** EY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FX 443 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GX 443 GLN ** GY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN ** IT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 443 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 196 ASN JT 204 GLN ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN ** LT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 300 ASN ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN MT 31 GLN ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MX 443 GLN ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 41 ASN ** NT 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NX 373 GLN NY1856 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 61992 Z= 0.456 Angle : 0.711 14.218 83594 Z= 0.371 Chirality : 0.050 0.211 9520 Planarity : 0.005 0.058 10598 Dihedral : 5.213 27.311 8134 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.02 % Allowed : 18.09 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 7406 helix: 1.19 (0.11), residues: 2324 sheet: -1.07 (0.12), residues: 1666 loop : -0.82 (0.10), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPNY1723 HIS 0.003 0.001 HISNT 169 PHE 0.016 0.002 PHEHY1759 TYR 0.022 0.002 TYRIY1870 ARG 0.009 0.001 ARGIX 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1720 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1515 time to evaluate : 5.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AT 194 LYS cc_start: 0.7928 (pttm) cc_final: 0.7345 (tptp) REVERT: AT 292 GLU cc_start: 0.7959 (tp30) cc_final: 0.7054 (mt-10) REVERT: AX 369 ARG cc_start: 0.7710 (mmm160) cc_final: 0.7269 (mtt180) REVERT: AX 415 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7742 (mmm) REVERT: AX 474 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7758 (mm-30) REVERT: BT 64 GLN cc_start: 0.8051 (tt0) cc_final: 0.7511 (mt0) REVERT: BT 67 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9106 (mt) REVERT: BT 209 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6564 (tp30) REVERT: BT 216 ASN cc_start: 0.7657 (m110) cc_final: 0.7205 (m110) REVERT: BT 296 GLU cc_start: 0.7726 (tm-30) cc_final: 0.6999 (tm-30) REVERT: BT 300 ASN cc_start: 0.6683 (m-40) cc_final: 0.6210 (m-40) REVERT: BX 369 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7476 (mtt-85) REVERT: BX 410 ARG cc_start: 0.7388 (mtm110) cc_final: 0.7178 (mtm110) REVERT: BX 450 MET cc_start: 0.9055 (ttp) cc_final: 0.8817 (ptm) REVERT: BY 1907 GLN cc_start: 0.7724 (tt0) cc_final: 0.7498 (tt0) REVERT: CT 209 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7709 (tp30) REVERT: CT 216 ASN cc_start: 0.7757 (m110) cc_final: 0.7473 (m110) REVERT: CT 292 GLU cc_start: 0.8117 (tp30) cc_final: 0.7054 (mt-10) REVERT: CT 296 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7390 (tm-30) REVERT: CT 300 ASN cc_start: 0.6386 (m-40) cc_final: 0.6110 (m110) REVERT: CX 369 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7534 (mtt180) REVERT: CX 374 LYS cc_start: 0.7702 (ptmm) cc_final: 0.7299 (ptpp) REVERT: DT 59 THR cc_start: 0.8621 (m) cc_final: 0.8304 (m) REVERT: DT 194 LYS cc_start: 0.8273 (pttm) cc_final: 0.7770 (tptp) REVERT: DT 296 GLU cc_start: 0.7683 (tm-30) cc_final: 0.6797 (tm-30) REVERT: DT 297 TYR cc_start: 0.7794 (t80) cc_final: 0.7542 (t80) REVERT: DT 300 ASN cc_start: 0.6917 (m-40) cc_final: 0.6126 (m-40) REVERT: DX 374 LYS cc_start: 0.7980 (ptmm) cc_final: 0.7454 (ptpp) REVERT: DY 1739 TYR cc_start: 0.9095 (m-80) cc_final: 0.8778 (m-80) REVERT: DY 1772 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8235 (pp) REVERT: DY 1903 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8462 (mt) cc_final: 0.8092 (mt) REVERT: ET 59 THR cc_start: 0.8721 (m) cc_final: 0.8395 (m) REVERT: ET 64 GLN cc_start: 0.8064 (tt0) cc_final: 0.7484 (mt0) REVERT: ET 194 LYS cc_start: 0.7991 (pttm) cc_final: 0.7623 (tptp) REVERT: ET 210 TYR cc_start: 0.8209 (t80) cc_final: 0.7877 (t80) REVERT: ET 292 GLU cc_start: 0.7678 (tp30) cc_final: 0.6829 (mt-10) REVERT: ET 296 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7282 (tm-30) REVERT: ET 300 ASN cc_start: 0.6665 (m-40) cc_final: 0.6349 (m110) REVERT: EY 1739 TYR cc_start: 0.9094 (m-80) cc_final: 0.8632 (m-80) REVERT: FT 194 LYS cc_start: 0.7950 (pttm) cc_final: 0.7601 (tptp) REVERT: FT 216 ASN cc_start: 0.7879 (m110) cc_final: 0.7585 (m110) REVERT: FT 292 GLU cc_start: 0.7671 (tp30) cc_final: 0.6857 (mt-10) REVERT: FX 386 GLN cc_start: 0.8553 (tp40) cc_final: 0.8288 (tp40) REVERT: GT 216 ASN cc_start: 0.7560 (m110) cc_final: 0.7124 (m110) REVERT: GX 369 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7441 (mtt180) REVERT: GX 374 LYS cc_start: 0.7856 (ptmm) cc_final: 0.7464 (ptpp) REVERT: GX 459 MET cc_start: 0.8811 (mtp) cc_final: 0.8480 (mtp) REVERT: GY 1685 LYS cc_start: 0.7055 (mmtm) cc_final: 0.6705 (mmtt) REVERT: HT 49 GLU cc_start: 0.7485 (mp0) cc_final: 0.7192 (mp0) REVERT: HT 194 LYS cc_start: 0.7948 (pttm) cc_final: 0.7481 (tptp) REVERT: HT 292 GLU cc_start: 0.7815 (tp30) cc_final: 0.6881 (mt-10) REVERT: HT 296 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6663 (tm-30) REVERT: HT 300 ASN cc_start: 0.6602 (m-40) cc_final: 0.6036 (m-40) REVERT: HX 369 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7372 (mtt-85) REVERT: HX 374 LYS cc_start: 0.8064 (ptmm) cc_final: 0.7551 (ptpp) REVERT: IT 64 GLN cc_start: 0.8072 (tt0) cc_final: 0.7506 (mt0) REVERT: IT 67 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9094 (mt) REVERT: IT 209 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6553 (tp30) REVERT: IT 216 ASN cc_start: 0.7629 (m110) cc_final: 0.7204 (m110) REVERT: IX 384 GLU cc_start: 0.8298 (tt0) cc_final: 0.7894 (tt0) REVERT: IX 410 ARG cc_start: 0.7360 (mtm110) cc_final: 0.7074 (mtm110) REVERT: JT 210 TYR cc_start: 0.8199 (t80) cc_final: 0.7825 (t80) REVERT: JT 216 ASN cc_start: 0.7814 (m110) cc_final: 0.7505 (m110) REVERT: JT 296 GLU cc_start: 0.7664 (tm-30) cc_final: 0.6883 (tm-30) REVERT: JT 300 ASN cc_start: 0.6384 (m-40) cc_final: 0.5764 (m-40) REVERT: JX 369 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7817 (mtt180) REVERT: JX 371 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7022 (tm-30) REVERT: JX 386 GLN cc_start: 0.8507 (tp40) cc_final: 0.8238 (tp40) REVERT: JX 401 TYR cc_start: 0.9067 (m-80) cc_final: 0.8752 (m-80) REVERT: KT 59 THR cc_start: 0.8694 (m) cc_final: 0.8407 (m) REVERT: KT 194 LYS cc_start: 0.8230 (pttm) cc_final: 0.7734 (tptp) REVERT: KT 209 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7753 (tp30) REVERT: KT 216 ASN cc_start: 0.7690 (m110) cc_final: 0.7344 (m110) REVERT: KT 292 GLU cc_start: 0.8023 (tp30) cc_final: 0.6942 (mt-10) REVERT: KT 296 GLU cc_start: 0.7727 (tm-30) cc_final: 0.6848 (tm-30) REVERT: KT 300 ASN cc_start: 0.6887 (m-40) cc_final: 0.6400 (m-40) REVERT: KX 371 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7356 (tm-30) REVERT: KX 386 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8049 (tp40) REVERT: KX 509 LEU cc_start: 0.9210 (mt) cc_final: 0.8825 (mt) REVERT: KY 1739 TYR cc_start: 0.9114 (m-80) cc_final: 0.8806 (m-80) REVERT: KY 1772 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8236 (pp) REVERT: KY 1873 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8131 (pm20) REVERT: LT 194 LYS cc_start: 0.7936 (pttm) cc_final: 0.7608 (tptp) REVERT: LT 210 TYR cc_start: 0.8238 (t80) cc_final: 0.7934 (t80) REVERT: LT 216 ASN cc_start: 0.7748 (m110) cc_final: 0.7309 (m110) REVERT: LT 292 GLU cc_start: 0.7684 (tp30) cc_final: 0.6867 (mt-10) REVERT: LX 386 GLN cc_start: 0.8575 (tp40) cc_final: 0.8266 (tp40) REVERT: LX 387 TYR cc_start: 0.8453 (t80) cc_final: 0.7922 (t80) REVERT: LY 1739 TYR cc_start: 0.9096 (m-80) cc_final: 0.8637 (m-80) REVERT: MT 194 LYS cc_start: 0.7921 (pttm) cc_final: 0.7579 (tptp) REVERT: MT 208 GLN cc_start: 0.7567 (tp-100) cc_final: 0.7365 (tp40) REVERT: MT 216 ASN cc_start: 0.7554 (m110) cc_final: 0.7230 (m110) REVERT: MT 296 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6708 (tm-30) REVERT: MT 300 ASN cc_start: 0.6651 (m-40) cc_final: 0.6224 (m-40) REVERT: MY 1685 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7337 (mmtm) REVERT: NT 27 LYS cc_start: 0.7529 (mmtt) cc_final: 0.7322 (mmtm) REVERT: NT 216 ASN cc_start: 0.7694 (m110) cc_final: 0.7254 (m110) REVERT: NT 296 GLU cc_start: 0.7569 (tm-30) cc_final: 0.6865 (tm-30) REVERT: NT 300 ASN cc_start: 0.6552 (m-40) cc_final: 0.5901 (m-40) REVERT: NX 374 LYS cc_start: 0.7840 (ptmm) cc_final: 0.7491 (ptpp) REVERT: NX 459 MET cc_start: 0.8800 (mtp) cc_final: 0.8455 (mtp) REVERT: NY 1685 LYS cc_start: 0.7056 (mmtm) cc_final: 0.6705 (mmtt) outliers start: 205 outliers final: 163 residues processed: 1639 average time/residue: 0.5727 time to fit residues: 1576.6669 Evaluate side-chains 1622 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1452 time to evaluate : 5.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AX residue 424 THR Chi-restraints excluded: chain AY residue 1694 GLN Chi-restraints excluded: chain AY residue 1711 THR Chi-restraints excluded: chain AY residue 1724 ASN Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1873 GLU Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BX residue 508 GLU Chi-restraints excluded: chain BY residue 1694 GLN Chi-restraints excluded: chain BY residue 1711 THR Chi-restraints excluded: chain BY residue 1724 ASN Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1813 THR Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 82 LEU Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CT residue 197 GLN Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 424 THR Chi-restraints excluded: chain CX residue 451 THR Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain CY residue 1694 GLN Chi-restraints excluded: chain CY residue 1711 THR Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 52 LEU Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1711 THR Chi-restraints excluded: chain DY residue 1724 ASN Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1880 LEU Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 383 LEU Chi-restraints excluded: chain EX residue 424 THR Chi-restraints excluded: chain EX residue 460 THR Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1694 GLN Chi-restraints excluded: chain EY residue 1711 THR Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1724 ASN Chi-restraints excluded: chain EY residue 1813 THR Chi-restraints excluded: chain EY residue 1873 GLU Chi-restraints excluded: chain FT residue 52 LEU Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 471 GLU Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1711 THR Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain FY residue 1813 THR Chi-restraints excluded: chain FY residue 1873 GLU Chi-restraints excluded: chain FY residue 1879 ILE Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 93 ILE Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1711 THR Chi-restraints excluded: chain GY residue 1751 ILE Chi-restraints excluded: chain GY residue 1873 GLU Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 424 THR Chi-restraints excluded: chain HY residue 1711 THR Chi-restraints excluded: chain HY residue 1724 ASN Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain HY residue 1873 GLU Chi-restraints excluded: chain HY residue 1894 LYS Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 377 LEU Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 508 GLU Chi-restraints excluded: chain IY residue 1694 GLN Chi-restraints excluded: chain IY residue 1711 THR Chi-restraints excluded: chain IY residue 1724 ASN Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1813 THR Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 94 THR Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 196 ASN Chi-restraints excluded: chain JX residue 424 THR Chi-restraints excluded: chain JX residue 451 THR Chi-restraints excluded: chain JX residue 488 ILE Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1694 GLN Chi-restraints excluded: chain JY residue 1711 THR Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 377 LEU Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 418 GLU Chi-restraints excluded: chain KX residue 449 SER Chi-restraints excluded: chain KX residue 460 THR Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1711 THR Chi-restraints excluded: chain KY residue 1724 ASN Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1809 SER Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1880 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 383 LEU Chi-restraints excluded: chain LX residue 424 THR Chi-restraints excluded: chain LX residue 460 THR Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1711 THR Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1724 ASN Chi-restraints excluded: chain LY residue 1813 THR Chi-restraints excluded: chain LY residue 1857 GLN Chi-restraints excluded: chain MT residue 52 LEU Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 424 THR Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1711 THR Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain MY residue 1813 THR Chi-restraints excluded: chain MY residue 1873 GLU Chi-restraints excluded: chain MY residue 1879 ILE Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1711 THR Chi-restraints excluded: chain NY residue 1751 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 0.9980 chunk 691 optimal weight: 5.9990 chunk 422 optimal weight: 5.9990 chunk 328 optimal weight: 0.5980 chunk 480 optimal weight: 8.9990 chunk 725 optimal weight: 0.9990 chunk 667 optimal weight: 0.6980 chunk 577 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 446 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 64 GLN AT 300 ASN AY1743 GLN AY1857 GLN ** BT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN CT 197 GLN ** CX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN ** DT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 443 GLN ** DX 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ET 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FX 443 GLN ** GY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HT 64 GLN HY1743 GLN HY1856 ASN HY1857 GLN ** HY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 443 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 196 ASN JT 204 GLN ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN KT 301 GLN KX 443 GLN ** LT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 300 ASN ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 31 GLN ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MX 443 GLN ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 64 GLN ** NY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 61992 Z= 0.211 Angle : 0.638 15.473 83594 Z= 0.333 Chirality : 0.046 0.218 9520 Planarity : 0.004 0.042 10598 Dihedral : 5.022 26.364 8134 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.50 % Allowed : 18.72 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.10), residues: 7406 helix: 1.37 (0.11), residues: 2310 sheet: -0.95 (0.12), residues: 1624 loop : -0.82 (0.10), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPJX 466 HIS 0.002 0.000 HISLT 169 PHE 0.016 0.001 PHEBY1810 TYR 0.021 0.001 TYRNY1695 ARG 0.007 0.000 ARGNT 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1745 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1575 time to evaluate : 5.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AT 194 LYS cc_start: 0.7870 (pttm) cc_final: 0.7322 (tptp) REVERT: AT 216 ASN cc_start: 0.7588 (m110) cc_final: 0.7372 (m110) REVERT: AX 369 ARG cc_start: 0.7678 (mmm160) cc_final: 0.7277 (mtt180) REVERT: AX 386 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8179 (tp40) REVERT: AX 484 LEU cc_start: 0.9125 (tp) cc_final: 0.8924 (tp) REVERT: BT 64 GLN cc_start: 0.8055 (tt0) cc_final: 0.7431 (mt0) REVERT: BT 67 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9064 (mt) REVERT: BT 209 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6585 (tp30) REVERT: BT 216 ASN cc_start: 0.7756 (m110) cc_final: 0.7372 (m110) REVERT: BT 296 GLU cc_start: 0.7666 (tm-30) cc_final: 0.6995 (tm-30) REVERT: BT 300 ASN cc_start: 0.6768 (m-40) cc_final: 0.6274 (m-40) REVERT: BX 369 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7502 (mtt-85) REVERT: BX 384 GLU cc_start: 0.8188 (tt0) cc_final: 0.7806 (tt0) REVERT: BY 1715 SER cc_start: 0.8195 (p) cc_final: 0.7942 (p) REVERT: CT 208 GLN cc_start: 0.7748 (tp-100) cc_final: 0.7539 (tp40) REVERT: CT 209 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7690 (tp30) REVERT: CT 216 ASN cc_start: 0.7673 (m110) cc_final: 0.7403 (m-40) REVERT: CT 292 GLU cc_start: 0.8073 (tp30) cc_final: 0.7078 (mt-10) REVERT: CT 296 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7450 (tm-30) REVERT: CT 300 ASN cc_start: 0.6427 (m-40) cc_final: 0.6165 (m110) REVERT: CX 369 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7547 (mtt180) REVERT: CX 374 LYS cc_start: 0.7698 (ptmm) cc_final: 0.7298 (ptpp) REVERT: CX 401 TYR cc_start: 0.9000 (m-80) cc_final: 0.8662 (m-80) REVERT: DT 59 THR cc_start: 0.8575 (m) cc_final: 0.8274 (m) REVERT: DT 194 LYS cc_start: 0.8207 (pttm) cc_final: 0.7658 (tptp) REVERT: DT 292 GLU cc_start: 0.7967 (tp30) cc_final: 0.6826 (mt-10) REVERT: DT 296 GLU cc_start: 0.7717 (tm-30) cc_final: 0.6689 (tm-30) REVERT: DT 297 TYR cc_start: 0.7737 (t80) cc_final: 0.7452 (t80) REVERT: DT 300 ASN cc_start: 0.6994 (m-40) cc_final: 0.6342 (m110) REVERT: DX 374 LYS cc_start: 0.7951 (ptmm) cc_final: 0.7464 (ptpp) REVERT: DX 410 ARG cc_start: 0.7327 (mtm110) cc_final: 0.6967 (mtm110) REVERT: DY 1739 TYR cc_start: 0.9032 (m-80) cc_final: 0.8701 (m-80) REVERT: DY 1772 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8096 (pp) REVERT: DY 1903 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8225 (mt) cc_final: 0.7823 (mt) REVERT: ET 59 THR cc_start: 0.8677 (m) cc_final: 0.8361 (m) REVERT: ET 64 GLN cc_start: 0.8019 (tt0) cc_final: 0.7431 (mt0) REVERT: ET 194 LYS cc_start: 0.7795 (pttm) cc_final: 0.7441 (tptp) REVERT: ET 210 TYR cc_start: 0.8184 (t80) cc_final: 0.7793 (t80) REVERT: ET 292 GLU cc_start: 0.7668 (tp30) cc_final: 0.6876 (mt-10) REVERT: ET 296 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7269 (tm-30) REVERT: ET 300 ASN cc_start: 0.6679 (m-40) cc_final: 0.6339 (m110) REVERT: ET 301 GLN cc_start: 0.7415 (tp40) cc_final: 0.6818 (mm110) REVERT: EX 387 TYR cc_start: 0.8355 (t80) cc_final: 0.7847 (t80) REVERT: EY 1739 TYR cc_start: 0.9009 (m-80) cc_final: 0.8551 (m-80) REVERT: FT 194 LYS cc_start: 0.7911 (pttm) cc_final: 0.7529 (tptp) REVERT: FT 213 ARG cc_start: 0.6501 (ttp-170) cc_final: 0.6204 (ttp-170) REVERT: FT 216 ASN cc_start: 0.7869 (m110) cc_final: 0.7611 (m110) REVERT: FT 292 GLU cc_start: 0.7735 (tp30) cc_final: 0.6887 (mt-10) REVERT: FT 296 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7286 (tm-30) REVERT: FT 300 ASN cc_start: 0.6856 (m-40) cc_final: 0.6583 (m110) REVERT: FX 386 GLN cc_start: 0.8547 (tp40) cc_final: 0.8236 (tp40) REVERT: FX 474 GLU cc_start: 0.7844 (tp30) cc_final: 0.7433 (mp0) REVERT: GT 215 ASN cc_start: 0.7558 (m-40) cc_final: 0.7249 (p0) REVERT: GT 216 ASN cc_start: 0.7657 (m110) cc_final: 0.7133 (m110) REVERT: GT 296 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7612 (tm-30) REVERT: GT 300 ASN cc_start: 0.6526 (m-40) cc_final: 0.6229 (m110) REVERT: GT 301 GLN cc_start: 0.7198 (tp40) cc_final: 0.6656 (mm110) REVERT: GX 369 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7425 (mtt180) REVERT: GX 374 LYS cc_start: 0.7829 (ptmm) cc_final: 0.7434 (ptpp) REVERT: GX 459 MET cc_start: 0.8709 (mtp) cc_final: 0.8372 (mtp) REVERT: GY 1685 LYS cc_start: 0.6961 (mmtm) cc_final: 0.6634 (mmtt) REVERT: HT 49 GLU cc_start: 0.7515 (mp0) cc_final: 0.7188 (mp0) REVERT: HT 64 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: HT 194 LYS cc_start: 0.7980 (pttm) cc_final: 0.7520 (tptp) REVERT: HT 201 THR cc_start: 0.8254 (p) cc_final: 0.7879 (t) REVERT: HT 292 GLU cc_start: 0.7769 (tp30) cc_final: 0.6810 (mt-10) REVERT: HT 296 GLU cc_start: 0.7696 (tm-30) cc_final: 0.6807 (tm-30) REVERT: HT 300 ASN cc_start: 0.6732 (m-40) cc_final: 0.6315 (m-40) REVERT: HT 301 GLN cc_start: 0.7325 (tp40) cc_final: 0.6791 (mm-40) REVERT: HX 369 ARG cc_start: 0.7819 (mmm160) cc_final: 0.7282 (mtt180) REVERT: HX 374 LYS cc_start: 0.8039 (ptmm) cc_final: 0.7526 (ptpp) REVERT: HX 386 GLN cc_start: 0.8325 (tm-30) cc_final: 0.8082 (tp40) REVERT: HX 410 ARG cc_start: 0.7667 (mtm110) cc_final: 0.7112 (mtm110) REVERT: IT 64 GLN cc_start: 0.8042 (tt0) cc_final: 0.7405 (mt0) REVERT: IT 67 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9046 (mt) REVERT: IT 209 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6551 (tp30) REVERT: IT 216 ASN cc_start: 0.7704 (m110) cc_final: 0.7316 (m110) REVERT: IT 300 ASN cc_start: 0.6772 (m-40) cc_final: 0.6513 (m110) REVERT: IX 384 GLU cc_start: 0.8255 (tt0) cc_final: 0.7848 (tt0) REVERT: IY 1715 SER cc_start: 0.8220 (p) cc_final: 0.7958 (p) REVERT: IY 1903 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7842 (tm-30) REVERT: JT 210 TYR cc_start: 0.8158 (t80) cc_final: 0.7759 (t80) REVERT: JT 216 ASN cc_start: 0.7827 (m110) cc_final: 0.7414 (m110) REVERT: JT 292 GLU cc_start: 0.8029 (tp30) cc_final: 0.6967 (mt-10) REVERT: JT 296 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6926 (tm-30) REVERT: JT 300 ASN cc_start: 0.6375 (m-40) cc_final: 0.5843 (m-40) REVERT: JX 369 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7892 (mtt180) REVERT: JX 371 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7098 (tm-30) REVERT: JX 401 TYR cc_start: 0.9025 (m-80) cc_final: 0.8705 (m-80) REVERT: KT 59 THR cc_start: 0.8633 (m) cc_final: 0.8349 (m) REVERT: KT 194 LYS cc_start: 0.8204 (pttm) cc_final: 0.7517 (tptp) REVERT: KT 201 THR cc_start: 0.8333 (p) cc_final: 0.7926 (t) REVERT: KT 209 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7739 (tp30) REVERT: KT 216 ASN cc_start: 0.7780 (m110) cc_final: 0.7452 (m110) REVERT: KT 292 GLU cc_start: 0.8047 (tp30) cc_final: 0.6911 (mt-10) REVERT: KT 296 GLU cc_start: 0.7709 (tm-30) cc_final: 0.6808 (tm-30) REVERT: KT 300 ASN cc_start: 0.6796 (m-40) cc_final: 0.6363 (m-40) REVERT: KX 371 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7351 (tm-30) REVERT: KX 386 GLN cc_start: 0.8323 (tm-30) cc_final: 0.8030 (tp40) REVERT: KX 410 ARG cc_start: 0.7409 (mtm110) cc_final: 0.7113 (mtm110) REVERT: KX 509 LEU cc_start: 0.9116 (mt) cc_final: 0.8774 (mt) REVERT: KY 1739 TYR cc_start: 0.9043 (m-80) cc_final: 0.8711 (m-80) REVERT: KY 1772 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8097 (pp) REVERT: LT 168 LEU cc_start: 0.8140 (pp) cc_final: 0.7681 (tt) REVERT: LT 194 LYS cc_start: 0.7759 (pttm) cc_final: 0.7450 (tptp) REVERT: LT 210 TYR cc_start: 0.8230 (t80) cc_final: 0.7919 (t80) REVERT: LT 216 ASN cc_start: 0.7791 (m110) cc_final: 0.7369 (m110) REVERT: LT 292 GLU cc_start: 0.7672 (tp30) cc_final: 0.6922 (mt-10) REVERT: LX 386 GLN cc_start: 0.8547 (tp40) cc_final: 0.8199 (tp40) REVERT: LX 387 TYR cc_start: 0.8377 (t80) cc_final: 0.7752 (t80) REVERT: LY 1739 TYR cc_start: 0.9021 (m-80) cc_final: 0.8568 (m-80) REVERT: LY 1854 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7641 (mpp) REVERT: MT 194 LYS cc_start: 0.7811 (pttm) cc_final: 0.7470 (tptp) REVERT: MT 216 ASN cc_start: 0.7763 (m110) cc_final: 0.7530 (m110) REVERT: MT 296 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6696 (tm-30) REVERT: MT 300 ASN cc_start: 0.6976 (m-40) cc_final: 0.6589 (m-40) REVERT: MX 386 GLN cc_start: 0.8548 (tp40) cc_final: 0.8238 (tp40) REVERT: MY 1685 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7332 (mmtm) REVERT: NT 27 LYS cc_start: 0.7533 (mmtt) cc_final: 0.7311 (mmtm) REVERT: NT 209 GLU cc_start: 0.7293 (pp20) cc_final: 0.6249 (tm-30) REVERT: NT 216 ASN cc_start: 0.7766 (m110) cc_final: 0.7461 (m-40) REVERT: NT 296 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7111 (tm-30) REVERT: NT 300 ASN cc_start: 0.6512 (m-40) cc_final: 0.5915 (m-40) REVERT: NX 459 MET cc_start: 0.8694 (mtp) cc_final: 0.8341 (mtp) REVERT: NX 471 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6752 (mt-10) REVERT: NY 1685 LYS cc_start: 0.6960 (mmtm) cc_final: 0.6632 (mmtt) REVERT: NY 1873 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6801 (mt-10) outliers start: 170 outliers final: 135 residues processed: 1676 average time/residue: 0.5755 time to fit residues: 1614.5645 Evaluate side-chains 1650 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1508 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 424 THR Chi-restraints excluded: chain AY residue 1711 THR Chi-restraints excluded: chain AY residue 1724 ASN Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1813 THR Chi-restraints excluded: chain AY residue 1873 GLU Chi-restraints excluded: chain AY residue 1894 LYS Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BX residue 508 GLU Chi-restraints excluded: chain BY residue 1724 ASN Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1813 THR Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CT residue 197 GLN Chi-restraints excluded: chain CX residue 383 LEU Chi-restraints excluded: chain CX residue 424 THR Chi-restraints excluded: chain CX residue 459 MET Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain CY residue 1711 THR Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1724 ASN Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1880 LEU Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 383 LEU Chi-restraints excluded: chain EX residue 460 THR Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1711 THR Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1724 ASN Chi-restraints excluded: chain EY residue 1813 THR Chi-restraints excluded: chain EY residue 1873 GLU Chi-restraints excluded: chain FT residue 52 LEU Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 471 GLU Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1711 THR Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain FY residue 1813 THR Chi-restraints excluded: chain FY residue 1873 GLU Chi-restraints excluded: chain FY residue 1879 ILE Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 93 ILE Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1711 THR Chi-restraints excluded: chain GY residue 1751 ILE Chi-restraints excluded: chain GY residue 1873 GLU Chi-restraints excluded: chain HT residue 64 GLN Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 424 THR Chi-restraints excluded: chain HY residue 1711 THR Chi-restraints excluded: chain HY residue 1724 ASN Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 508 GLU Chi-restraints excluded: chain IY residue 1694 GLN Chi-restraints excluded: chain IY residue 1724 ASN Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1813 THR Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 196 ASN Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1711 THR Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 377 LEU Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 418 GLU Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1724 ASN Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1809 SER Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 383 LEU Chi-restraints excluded: chain LX residue 460 THR Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1711 THR Chi-restraints excluded: chain LY residue 1724 ASN Chi-restraints excluded: chain LY residue 1813 THR Chi-restraints excluded: chain LY residue 1854 MET Chi-restraints excluded: chain MT residue 52 LEU Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1711 THR Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain MY residue 1813 THR Chi-restraints excluded: chain MY residue 1873 GLU Chi-restraints excluded: chain MY residue 1879 ILE Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1711 THR Chi-restraints excluded: chain NY residue 1751 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 2.9990 chunk 615 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 532 optimal weight: 8.9990 chunk 85 optimal weight: 0.3980 chunk 160 optimal weight: 3.9990 chunk 578 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 593 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 300 ASN AY1743 GLN AY1856 ASN ** BT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CX 386 GLN ** CX 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN ** DT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 443 GLN ** DX 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ET 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 196 ASN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 505 ASN ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FT 196 ASN FX 443 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HT 64 GLN ** HY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN HY1856 ASN ** HY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IY1726 ASN JT 196 ASN ** JX 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN ** JY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KT 197 GLN ** LT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 300 ASN ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN LX 505 ASN LY1857 GLN ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MY1694 GLN ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MY1856 ASN NT 64 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095840 restraints weight = 107666.754| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.95 r_work: 0.3126 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 61992 Z= 0.240 Angle : 0.645 15.166 83594 Z= 0.335 Chirality : 0.046 0.205 9520 Planarity : 0.004 0.057 10598 Dihedral : 4.972 27.091 8134 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.47 % Allowed : 19.19 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.10), residues: 7406 helix: 1.37 (0.11), residues: 2324 sheet: -0.90 (0.12), residues: 1624 loop : -0.79 (0.10), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPKX 466 HIS 0.002 0.000 HISNT 169 PHE 0.016 0.001 PHENY1759 TYR 0.033 0.001 TYRJT 36 ARG 0.009 0.001 ARGNT 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23208.12 seconds wall clock time: 404 minutes 51.37 seconds (24291.37 seconds total)