Starting phenix.real_space_refine (version: dev) on Thu Feb 23 16:15:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/02_2023/6x6k_22076.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/02_2023/6x6k_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_22076/02_2023/6x6k_22076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/02_2023/6x6k_22076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/02_2023/6x6k_22076.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/02_2023/6x6k_22076.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 25.53, per 1000 atoms: 0.42 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: 19.99 Conformation dependent library (CDL) restraints added in 6.7 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: 2.74 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: 22.75 Time building geometry restraints manager: 21.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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 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. 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: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 30.810 Check model and map are aligned: 0.720 Process input model: 123.230 Find NCS groups from input model: 3.710 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Set scattering table: 0.430 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 % 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 *********************** 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 : 5.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 2063 average time/residue: 0.5967 time to fit residues: 2053.7779 Evaluate side-chains 1517 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1517 time to evaluate : 5.833 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8682 ------------------------------------------------------------------------------- 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: 0.8980 chunk 220 optimal weight: 7.9990 chunk 346 optimal weight: 0.5980 chunk 424 optimal weight: 0.8980 chunk 661 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 197 GLN AT 204 GLN AX 386 GLN ** AX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1856 ASN ** AY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 204 GLN BX 373 GLN BX 386 GLN ** 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 ** CY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 204 GLN DX 373 GLN ** DX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 197 GLN ET 301 GLN EX 373 GLN EX 386 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 197 GLN FT 204 GLN FX 386 GLN ** FY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 197 GLN GT 301 GLN GX 386 GLN GY1856 ASN ** GY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HT 197 GLN HT 204 GLN ** HX 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HX 386 GLN ** HX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1856 ASN HY1857 GLN ** HY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 373 GLN IX 386 GLN ** IX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IY1726 ASN IY1856 ASN JT 64 GLN JT 204 GLN ** JX 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN KT 204 GLN ** 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** ** KY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 197 GLN LT 301 GLN LX 373 GLN LX 386 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** MT 197 GLN MX 373 GLN MX 386 GLN ** MY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 61992 Z= 0.206 Angle : 0.621 7.776 83594 Z= 0.329 Chirality : 0.045 0.169 9520 Planarity : 0.005 0.055 10598 Dihedral : 5.581 30.940 8134 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 1.24 % 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: -1.04 (0.09), residues: 7406 helix: 0.25 (0.10), residues: 2212 sheet: -1.09 (0.12), residues: 1624 loop : -1.00 (0.10), residues: 3570 *********************** 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 1913 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1829 time to evaluate : 5.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 48 residues processed: 1863 average time/residue: 0.5947 time to fit residues: 1852.8578 Evaluate side-chains 1636 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1588 time to evaluate : 6.017 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4858 time to fit residues: 51.9367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 550 optimal weight: 6.9990 chunk 450 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 662 optimal weight: 0.8980 chunk 715 optimal weight: 0.8980 chunk 589 optimal weight: 4.9990 chunk 656 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 531 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AT 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1743 GLN AY1856 ASN AY1907 GLN ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN BY1726 ASN BY1856 ASN CX 386 GLN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN ** DY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 301 GLN EX 386 GLN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EY1694 GLN EY1856 ASN EY1857 GLN ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FX 386 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 301 GLN GX 443 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 197 GLN ** HX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN HY1856 ASN HY1857 GLN IX 413 HIS IX 443 GLN IY1726 ASN ** IY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 204 GLN JT 208 GLN JX 386 GLN ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN ** JY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KT 197 GLN KX 413 HIS ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 301 GLN LX 386 GLN ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LY1856 ASN LY1857 GLN ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MX 386 GLN ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 196 ASN NX 386 GLN NX 443 GLN NY1694 GLN NY1856 ASN ** NY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 61992 Z= 0.280 Angle : 0.611 12.484 83594 Z= 0.327 Chirality : 0.046 0.171 9520 Planarity : 0.004 0.049 10598 Dihedral : 5.242 29.333 8134 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 2.65 % 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: -0.60 (0.10), residues: 7406 helix: 0.97 (0.11), residues: 2212 sheet: -1.08 (0.12), residues: 1666 loop : -0.86 (0.10), residues: 3528 *********************** 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 1867 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1687 time to evaluate : 5.888 Fit side-chains outliers start: 180 outliers final: 89 residues processed: 1802 average time/residue: 0.6367 time to fit residues: 1952.7175 Evaluate side-chains 1617 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1528 time to evaluate : 5.827 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 0.4725 time to fit residues: 88.4525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 4.9990 chunk 497 optimal weight: 5.9990 chunk 343 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 444 optimal weight: 0.9980 chunk 664 optimal weight: 3.9990 chunk 703 optimal weight: 0.8980 chunk 347 optimal weight: 4.9990 chunk 629 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** AY1743 GLN AY1856 ASN AY1857 GLN ** AY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 301 GLN ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BY1694 GLN ** BY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CX 413 HIS CY1694 GLN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN DT 301 GLN ** DY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 413 HIS ** 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 386 GLN FY1694 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 301 GLN ** GX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** GY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN HY1857 GLN IX 443 GLN IY1694 GLN ** JT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 413 HIS JY1694 GLN ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN ** KY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 301 GLN ** LX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LY1694 GLN LY1856 ASN ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MX 386 GLN MY1694 GLN ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 301 GLN ** NX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NY1857 GLN ** NY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 61992 Z= 0.321 Angle : 0.632 14.265 83594 Z= 0.332 Chirality : 0.047 0.176 9520 Planarity : 0.004 0.046 10598 Dihedral : 5.164 28.476 8134 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 1.55 % 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: -0.44 (0.10), residues: 7406 helix: 1.15 (0.11), residues: 2226 sheet: -1.05 (0.12), residues: 1666 loop : -0.78 (0.10), residues: 3514 *********************** 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 1734 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1629 time to evaluate : 5.949 Fit side-chains revert: symmetry clash outliers start: 105 outliers final: 36 residues processed: 1691 average time/residue: 0.6151 time to fit residues: 1740.7166 Evaluate side-chains 1555 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1519 time to evaluate : 5.933 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4860 time to fit residues: 40.5491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 5.9990 chunk 399 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 523 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 600 optimal weight: 3.9990 chunk 486 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 359 optimal weight: 1.9990 chunk 631 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 ** AY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1743 GLN AY1857 GLN ** AY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN CT 41 ASN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN DT 197 GLN ** DT 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 443 GLN ** DY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ET 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 443 GLN EY1856 ASN ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FT 216 ASN FX 386 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** GY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1694 GLN HY1743 GLN HY1857 GLN ** IT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 443 GLN ** JT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN KX 443 GLN ** KY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 301 GLN ** LX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 208 GLN MX 386 GLN ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 216 ASN ** NX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.079 61992 Z= 0.419 Angle : 0.672 14.349 83594 Z= 0.355 Chirality : 0.048 0.178 9520 Planarity : 0.004 0.047 10598 Dihedral : 5.284 28.394 8134 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 2.34 % 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: -0.58 (0.10), residues: 7406 helix: 1.06 (0.11), residues: 2310 sheet: -1.11 (0.12), residues: 1666 loop : -0.93 (0.10), residues: 3430 *********************** 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 1732 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1573 time to evaluate : 6.119 Fit side-chains outliers start: 159 outliers final: 77 residues processed: 1669 average time/residue: 0.6038 time to fit residues: 1687.2836 Evaluate side-chains 1532 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1455 time to evaluate : 6.014 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 0.4458 time to fit residues: 72.8154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 0.7980 chunk 633 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 413 optimal weight: 0.6980 chunk 173 optimal weight: 10.0000 chunk 704 optimal weight: 1.9990 chunk 584 optimal weight: 8.9990 chunk 326 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 232 optimal weight: 0.7980 chunk 369 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** ** AY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1743 GLN ** AY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN DX 373 GLN ** DY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 443 GLN EY1856 ASN ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FX 386 GLN FX 443 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 31 GLN ** GT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN ** IT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 443 GLN ** JT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 197 GLN ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN ** JY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN ** LY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MX 443 GLN MY1726 ASN ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 61992 Z= 0.229 Angle : 0.611 15.746 83594 Z= 0.321 Chirality : 0.046 0.186 9520 Planarity : 0.004 0.043 10598 Dihedral : 5.059 27.444 8134 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 1.50 % 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: -0.46 (0.10), residues: 7406 helix: 1.23 (0.11), residues: 2310 sheet: -1.18 (0.12), residues: 1666 loop : -0.84 (0.10), residues: 3430 *********************** 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 1706 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1604 time to evaluate : 6.027 Fit side-chains outliers start: 102 outliers final: 35 residues processed: 1671 average time/residue: 0.6541 time to fit residues: 1849.7075 Evaluate side-chains 1517 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1482 time to evaluate : 5.862 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.5360 time to fit residues: 42.0680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 401 optimal weight: 0.8980 chunk 514 optimal weight: 8.9990 chunk 398 optimal weight: 0.7980 chunk 592 optimal weight: 4.9990 chunk 393 optimal weight: 4.9990 chunk 701 optimal weight: 0.3980 chunk 439 optimal weight: 0.7980 chunk 427 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 197 GLN AT 300 ASN ** AY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1743 GLN AY1907 GLN ** BT 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN CT 300 ASN CY1856 ASN DT 301 GLN ** DX 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ET 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 196 ASN ET 300 ASN EX 443 GLN EY1856 ASN ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FX 386 GLN FX 443 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 64 GLN ** GT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 300 ASN GX 413 HIS ** GY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HT 300 ASN HY1743 GLN ** IT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IT 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 373 GLN IX 443 GLN ** JX 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN ** JY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KT 300 ASN ** KY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN MT 196 ASN MT 300 ASN MX 386 GLN MX 413 HIS NT 300 ASN NX 373 GLN ** NX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 61992 Z= 0.188 Angle : 0.605 15.011 83594 Z= 0.317 Chirality : 0.045 0.198 9520 Planarity : 0.004 0.051 10598 Dihedral : 4.885 27.487 8134 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 1.38 % 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: -0.29 (0.10), residues: 7406 helix: 1.38 (0.11), residues: 2324 sheet: -1.13 (0.12), residues: 1666 loop : -0.73 (0.11), residues: 3416 *********************** 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 1732 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1638 time to evaluate : 7.121 Fit side-chains outliers start: 94 outliers final: 38 residues processed: 1689 average time/residue: 0.6011 time to fit residues: 1700.9035 Evaluate side-chains 1556 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1518 time to evaluate : 5.837 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4506 time to fit residues: 39.9880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 419 optimal weight: 8.9990 chunk 211 optimal weight: 0.0770 chunk 137 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 446 optimal weight: 6.9990 chunk 478 optimal weight: 10.0000 chunk 346 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 551 optimal weight: 4.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- 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 301 GLN ** AY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1743 GLN ** BX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 300 ASN ** CY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN DT 301 GLN ** DX 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 443 GLN ** DY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ET 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 300 ASN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 443 GLN EX 505 ASN EY1856 ASN ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FT 41 ASN FX 373 GLN FX 386 GLN FY1726 ASN ** GT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 64 GLN ** GT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 300 ASN ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HT 301 GLN ** HY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN IT 197 GLN IT 300 ASN ** IY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN ** JY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN ** LY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 31 GLN ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 300 ASN MX 443 GLN ** NX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 61992 Z= 0.327 Angle : 0.666 16.428 83594 Z= 0.345 Chirality : 0.048 0.208 9520 Planarity : 0.004 0.042 10598 Dihedral : 5.012 27.364 8134 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.03 % 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: -0.33 (0.10), residues: 7406 helix: 1.32 (0.11), residues: 2324 sheet: -1.09 (0.12), residues: 1666 loop : -0.76 (0.10), residues: 3416 *********************** 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 1587 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1517 time to evaluate : 6.008 Fit side-chains revert: symmetry clash outliers start: 70 outliers final: 28 residues processed: 1550 average time/residue: 0.6255 time to fit residues: 1622.0417 Evaluate side-chains 1473 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1445 time to evaluate : 6.022 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.4911 time to fit residues: 33.0108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 7.9990 chunk 672 optimal weight: 0.7980 chunk 613 optimal weight: 0.9980 chunk 653 optimal weight: 0.9980 chunk 393 optimal weight: 3.9990 chunk 284 optimal weight: 0.0370 chunk 513 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 590 optimal weight: 0.9990 chunk 618 optimal weight: 6.9990 chunk 651 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1743 GLN ** BX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 300 ASN ** CX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN ** DX 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 443 GLN ** DX 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ET 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 169 HIS ET 300 ASN ** 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** FT 300 ASN GT 64 GLN ** GT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 300 ASN GT 301 GLN HT 31 GLN ** HY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN IT 300 ASN IX 443 GLN ** JX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN KX 443 GLN ** LT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN LY1856 ASN ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 300 ASN ** NX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 61992 Z= 0.200 Angle : 0.627 16.429 83594 Z= 0.326 Chirality : 0.046 0.204 9520 Planarity : 0.004 0.042 10598 Dihedral : 4.893 26.849 8134 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.71 % 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: -0.22 (0.10), residues: 7406 helix: 1.47 (0.11), residues: 2324 sheet: -0.96 (0.12), residues: 1624 loop : -0.79 (0.11), residues: 3458 *********************** 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 1613 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1565 time to evaluate : 5.952 Fit side-chains outliers start: 48 outliers final: 19 residues processed: 1586 average time/residue: 0.6110 time to fit residues: 1643.3082 Evaluate side-chains 1506 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1487 time to evaluate : 5.996 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4858 time to fit residues: 25.4509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 5.9990 chunk 691 optimal weight: 0.7980 chunk 422 optimal weight: 5.9990 chunk 328 optimal weight: 10.0000 chunk 480 optimal weight: 9.9990 chunk 725 optimal weight: 0.8980 chunk 667 optimal weight: 4.9990 chunk 577 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 446 optimal weight: 0.5980 chunk 354 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AY1743 GLN ** AY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY1694 GLN CT 300 ASN CX 386 GLN ** CY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 379 GLN ** 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** ** DY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ET 33 ASN ** 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** FT 300 ASN ** FX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FX 413 HIS ** GT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 64 GLN ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN ** HY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IT 300 ASN JX 386 GLN JY1856 ASN JY1907 GLN KT 34 HIS 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 ** MT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 300 ASN ** MX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MY1774 ASN NT 127 ASN ** NX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NY1694 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 61992 Z= 0.199 Angle : 0.641 17.014 83594 Z= 0.331 Chirality : 0.046 0.207 9520 Planarity : 0.004 0.042 10598 Dihedral : 4.854 27.626 8134 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 0.31 % 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: -0.18 (0.10), residues: 7406 helix: 1.48 (0.11), residues: 2324 sheet: -0.90 (0.12), residues: 1624 loop : -0.78 (0.10), residues: 3458 ********************** 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 1600 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1579 time to evaluate : 6.075 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 1586 average time/residue: 0.6096 time to fit residues: 1618.6501 Evaluate side-chains 1471 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1461 time to evaluate : 5.950 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5251 time to fit residues: 17.1025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 0.6980 chunk 615 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 532 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 578 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 593 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** AY1743 GLN AY1857 GLN ** BT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CX 386 GLN ** CY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 379 GLN ** 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** ** DY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ET 33 ASN ** 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** FT 300 ASN ** FY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 64 GLN ** GX 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1743 GLN HY1857 GLN ** HY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IT 196 ASN IT 300 ASN ** IX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 197 GLN 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 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NY1694 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097602 restraints weight = 107731.463| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.96 r_work: 0.3153 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 61992 Z= 0.241 Angle : 0.656 17.280 83594 Z= 0.340 Chirality : 0.046 0.230 9520 Planarity : 0.004 0.042 10598 Dihedral : 4.886 27.406 8134 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.22 % 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: -0.16 (0.10), residues: 7406 helix: 1.46 (0.11), residues: 2324 sheet: -0.85 (0.12), residues: 1624 loop : -0.76 (0.11), residues: 3458 =============================================================================== Job complete usr+sys time: 23195.34 seconds wall clock time: 404 minutes 35.42 seconds (24275.42 seconds total)