Starting phenix.real_space_refine on Tue Mar 12 08:10:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/03_2024/8jou_36462.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/03_2024/8jou_36462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/03_2024/8jou_36462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/03_2024/8jou_36462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/03_2024/8jou_36462.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/03_2024/8jou_36462.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.105 sd= 2.608 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 39340 2.51 5 N 10805 2.21 5 O 12250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ASP 126": "OD1" <-> "OD2" Residue "b TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 126": "OD1" <-> "OD2" Residue "d GLU 9": "OE1" <-> "OE2" Residue "d TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 58": "OE1" <-> "OE2" Residue "f PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 36": "OD1" <-> "OD2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 9": "OE1" <-> "OE2" Residue "h GLU 58": "OE1" <-> "OE2" Residue "h TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 60": "OE1" <-> "OE2" Residue "j TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "F TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "H GLU 9": "OE1" <-> "OE2" Residue "H TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "J PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 9": "OE1" <-> "OE2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 60": "OE1" <-> "OE2" Residue "N TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 18": "OD1" <-> "OD2" Residue "P TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 51": "OD1" <-> "OD2" Residue "Q TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 39": "OD1" <-> "OD2" Residue "R GLU 49": "OE1" <-> "OE2" Residue "S ASP 126": "OD1" <-> "OD2" Residue "T TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 126": "OD1" <-> "OD2" Residue "V GLU 9": "OE1" <-> "OE2" Residue "V TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 36": "OD1" <-> "OD2" Residue "Y TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 9": "OE1" <-> "OE2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "Z TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 60": "OE1" <-> "OE2" Residue "1 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 18": "OD1" <-> "OD2" Residue "3 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 51": "OD1" <-> "OD2" Residue "4 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 39": "OD1" <-> "OD2" Residue "5 GLU 49": "OE1" <-> "OE2" Residue "6 ASP 126": "OD1" <-> "OD2" Residue "7 TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 126": "OD1" <-> "OD2" Residue "9 GLU 9": "OE1" <-> "OE2" Residue "9 TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 58": "OE1" <-> "OE2" Residue "l PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 36": "OD1" <-> "OD2" Residue "m TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 9": "OE1" <-> "OE2" Residue "n GLU 58": "OE1" <-> "OE2" Residue "n TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 60": "OE1" <-> "OE2" Residue "p TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 18": "OD1" <-> "OD2" Residue "r TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 51": "OD1" <-> "OD2" Residue "s TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 39": "OD1" <-> "OD2" Residue "t GLU 49": "OE1" <-> "OE2" Residue "u ASP 126": "OD1" <-> "OD2" Residue "v TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 126": "OD1" <-> "OD2" Residue "x GLU 9": "OE1" <-> "OE2" Residue "x TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 58": "OE1" <-> "OE2" Residue "z PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ASP 36": "OD1" <-> "OD2" Residue "AA TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB GLU 9": "OE1" <-> "OE2" Residue "AB GLU 58": "OE1" <-> "OE2" Residue "AB TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD GLU 60": "OE1" <-> "OE2" Residue "AD TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF ASP 18": "OD1" <-> "OD2" Residue "AF TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG ASP 51": "OD1" <-> "OD2" Residue "AG TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AH PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AH ASP 39": "OD1" <-> "OD2" Residue "AH GLU 49": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 62425 Number of models: 1 Model: "" Number of chains: 70 Chain: "a" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "b" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "c" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "d" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "e" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "f" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "g" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "h" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "i" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "j" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "A" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "B" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "C" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "E" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "G" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "I" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "K" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "L" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "M" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "N" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "O" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "P" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "Q" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "R" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "S" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "T" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "U" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "V" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "W" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "X" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "Y" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "Z" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "0" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "1" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "2" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "3" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "4" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "5" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "6" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "7" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "8" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "9" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "k" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "l" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "m" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "n" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "o" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "p" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "q" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "r" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "s" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "u" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "v" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "w" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "x" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "y" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "z" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "AA" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "AB" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "AC" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "AD" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "AE" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "AF" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "AG" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "AH" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Time building chain proxies: 24.09, per 1000 atoms: 0.39 Number of scatterers: 62425 At special positions: 0 Unit cell: (698.5, 670.56, 199.39, 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 30 16.00 O 12250 8.00 N 10805 7.00 C 39340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.50 Conformation dependent library (CDL) restraints added in 8.4 seconds 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15680 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 160 sheets defined 8.5% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain 'a' and resid 5 through 17 Processing helix chain 'b' and resid 5 through 17 Processing helix chain 'c' and resid 5 through 17 Processing helix chain 'd' and resid 5 through 17 Processing helix chain 'e' and resid 5 through 17 Processing helix chain 'f' and resid 5 through 17 Processing helix chain 'g' and resid 5 through 18 Processing helix chain 'h' and resid 5 through 17 Processing helix chain 'i' and resid 5 through 17 Processing helix chain 'j' and resid 5 through 17 Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'B' and resid 20 through 23 Processing helix chain 'E' and resid 5 through 17 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'J' and resid 5 through 17 Processing helix chain 'K' and resid 5 through 18 Processing helix chain 'L' and resid 5 through 17 Processing helix chain 'M' and resid 5 through 17 Processing helix chain 'N' and resid 5 through 17 Processing helix chain 'P' and resid 38 through 40 No H-bonds generated for 'chain 'P' and resid 38 through 40' Processing helix chain 'Q' and resid 20 through 23 Processing helix chain 'S' and resid 5 through 17 Processing helix chain 'T' and resid 5 through 17 Processing helix chain 'U' and resid 5 through 17 Processing helix chain 'V' and resid 5 through 17 Processing helix chain 'W' and resid 5 through 17 Processing helix chain 'X' and resid 5 through 17 Processing helix chain 'Y' and resid 5 through 18 Processing helix chain 'Z' and resid 5 through 17 Processing helix chain '0' and resid 5 through 17 Processing helix chain '1' and resid 5 through 17 Processing helix chain '3' and resid 38 through 40 No H-bonds generated for 'chain '3' and resid 38 through 40' Processing helix chain '4' and resid 20 through 23 Processing helix chain '6' and resid 5 through 17 Processing helix chain '7' and resid 5 through 17 Processing helix chain '8' and resid 5 through 17 Processing helix chain '9' and resid 5 through 17 Processing helix chain 'k' and resid 5 through 17 Processing helix chain 'l' and resid 5 through 17 Processing helix chain 'm' and resid 5 through 18 Processing helix chain 'n' and resid 5 through 17 Processing helix chain 'o' and resid 5 through 17 Processing helix chain 'p' and resid 5 through 17 Processing helix chain 'r' and resid 38 through 40 No H-bonds generated for 'chain 'r' and resid 38 through 40' Processing helix chain 's' and resid 20 through 23 Processing helix chain 'u' and resid 5 through 17 Processing helix chain 'v' and resid 5 through 17 Processing helix chain 'w' and resid 5 through 17 Processing helix chain 'x' and resid 5 through 17 Processing helix chain 'y' and resid 5 through 17 Processing helix chain 'z' and resid 5 through 17 Processing helix chain 'AA' and resid 5 through 18 Processing helix chain 'AB' and resid 5 through 17 Processing helix chain 'AC' and resid 5 through 17 Processing helix chain 'AD' and resid 5 through 17 Processing helix chain 'AF' and resid 38 through 40 No H-bonds generated for 'chain 'AF' and resid 38 through 40' Processing helix chain 'AG' and resid 20 through 23 Processing sheet with id= 1, first strand: chain 'a' and resid 29 through 33 removed outlier: 3.552A pdb=" N TYR a 99 " --> pdb=" O ALA a 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE a 112 " --> pdb=" O VAL a 101 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'a' and resid 83 through 84 Processing sheet with id= 3, first strand: chain 'a' and resid 94 through 95 Processing sheet with id= 4, first strand: chain 'a' and resid 136 through 137 Processing sheet with id= 5, first strand: chain 'b' and resid 29 through 33 removed outlier: 6.772A pdb=" N HIS b 98 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N VAL b 118 " --> pdb=" O HIS b 98 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA b 100 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N LEU b 116 " --> pdb=" O ALA b 100 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE b 102 " --> pdb=" O ALA b 114 " (cutoff:3.500A) removed outlier: 12.570A pdb=" N ALA b 114 " --> pdb=" O PHE b 102 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 29 through 33 removed outlier: 7.143A pdb=" N HIS c 98 " --> pdb=" O VAL c 118 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N VAL c 118 " --> pdb=" O HIS c 98 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N ALA c 100 " --> pdb=" O LEU c 116 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LEU c 116 " --> pdb=" O ALA c 100 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N PHE c 102 " --> pdb=" O ALA c 114 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N ALA c 114 " --> pdb=" O PHE c 102 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 83 through 84 Processing sheet with id= 8, first strand: chain 'c' and resid 136 through 137 Processing sheet with id= 9, first strand: chain 'd' and resid 57 through 58 removed outlier: 3.931A pdb=" N ARG d 57 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N THR d 95 " --> pdb=" O VAL d 118 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL d 118 " --> pdb=" O THR d 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR d 97 " --> pdb=" O LEU d 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE d 112 " --> pdb=" O VAL d 101 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'd' and resid 83 through 84 Processing sheet with id= 11, first strand: chain 'e' and resid 29 through 33 removed outlier: 3.640A pdb=" N HIS e 98 " --> pdb=" O HIS e 33 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG e 120 " --> pdb=" O VAL e 96 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N HIS e 98 " --> pdb=" O VAL e 118 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL e 118 " --> pdb=" O HIS e 98 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N ALA e 100 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU e 116 " --> pdb=" O ALA e 100 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE e 102 " --> pdb=" O ALA e 114 " (cutoff:3.500A) removed outlier: 12.476A pdb=" N ALA e 114 " --> pdb=" O PHE e 102 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'e' and resid 83 through 84 Processing sheet with id= 13, first strand: chain 'e' and resid 136 through 137 Processing sheet with id= 14, first strand: chain 'f' and resid 29 through 33 removed outlier: 7.215A pdb=" N TYR f 99 " --> pdb=" O LYS f 113 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS f 113 " --> pdb=" O TYR f 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL f 101 " --> pdb=" O LEU f 111 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'f' and resid 83 through 84 Processing sheet with id= 16, first strand: chain 'f' and resid 94 through 95 Processing sheet with id= 17, first strand: chain 'g' and resid 57 through 58 removed outlier: 3.904A pdb=" N ARG g 57 " --> pdb=" O VAL g 30 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL g 94 " --> pdb=" O LEU g 122 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS g 98 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N VAL g 118 " --> pdb=" O HIS g 98 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N ALA g 100 " --> pdb=" O LEU g 116 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N LEU g 116 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N PHE g 102 " --> pdb=" O ALA g 114 " (cutoff:3.500A) removed outlier: 13.048A pdb=" N ALA g 114 " --> pdb=" O PHE g 102 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'g' and resid 83 through 84 removed outlier: 3.810A pdb=" N LEU g 83 " --> pdb=" O PHE g 130 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'h' and resid 29 through 33 removed outlier: 10.300A pdb=" N THR h 95 " --> pdb=" O VAL h 118 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VAL h 118 " --> pdb=" O THR h 95 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR h 97 " --> pdb=" O LEU h 116 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'h' and resid 83 through 84 removed outlier: 3.913A pdb=" N LEU h 83 " --> pdb=" O PHE h 130 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'i' and resid 29 through 33 removed outlier: 7.008A pdb=" N HIS i 98 " --> pdb=" O VAL i 118 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N VAL i 118 " --> pdb=" O HIS i 98 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA i 100 " --> pdb=" O LEU i 116 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEU i 116 " --> pdb=" O ALA i 100 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHE i 102 " --> pdb=" O ALA i 114 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N ALA i 114 " --> pdb=" O PHE i 102 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'i' and resid 83 through 84 removed outlier: 4.159A pdb=" N LEU i 83 " --> pdb=" O PHE i 130 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'i' and resid 136 through 137 Processing sheet with id= 24, first strand: chain 'j' and resid 29 through 33 removed outlier: 3.657A pdb=" N HIS j 98 " --> pdb=" O HIS j 33 " (cutoff:3.500A) removed outlier: 15.203A pdb=" N THR j 95 " --> pdb=" O THR j 117 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THR j 117 " --> pdb=" O THR j 95 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR j 97 " --> pdb=" O PRO j 115 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR j 99 " --> pdb=" O LYS j 113 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS j 113 " --> pdb=" O TYR j 99 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL j 101 " --> pdb=" O LEU j 111 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'j' and resid 83 through 84 removed outlier: 3.740A pdb=" N LEU j 83 " --> pdb=" O PHE j 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL j 129 " --> pdb=" O UNK A 101 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'j' and resid 136 through 138 removed outlier: 5.770A pdb=" N THR j 136 " --> pdb=" O UNK A 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'A' and resid 3 through 4 removed outlier: 3.537A pdb=" N ASP D 18 " --> pdb=" O UNK A 3 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 5 through 8 removed outlier: 5.796A pdb=" N GLN D 6 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA D 75 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER D 31 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 5 through 8 removed outlier: 5.781A pdb=" N GLN B 6 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA B 75 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER B 31 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 16 through 18 removed outlier: 3.563A pdb=" N ASP B 51 " --> pdb=" O VAL B 54 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 5 through 8 removed outlier: 6.104A pdb=" N GLN C 6 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA C 75 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER C 31 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'C' and resid 16 through 18 Processing sheet with id= 33, first strand: chain 'E' and resid 29 through 33 removed outlier: 3.553A pdb=" N TYR E 99 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 112 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 83 through 84 Processing sheet with id= 35, first strand: chain 'E' and resid 94 through 95 Processing sheet with id= 36, first strand: chain 'E' and resid 136 through 137 Processing sheet with id= 37, first strand: chain 'F' and resid 29 through 33 removed outlier: 6.772A pdb=" N HIS F 98 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N VAL F 118 " --> pdb=" O HIS F 98 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA F 100 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N LEU F 116 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE F 102 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 12.570A pdb=" N ALA F 114 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'G' and resid 29 through 33 removed outlier: 7.143A pdb=" N HIS G 98 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N VAL G 118 " --> pdb=" O HIS G 98 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N ALA G 100 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LEU G 116 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N PHE G 102 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N ALA G 114 " --> pdb=" O PHE G 102 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'G' and resid 83 through 84 Processing sheet with id= 40, first strand: chain 'G' and resid 136 through 137 Processing sheet with id= 41, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.931A pdb=" N ARG H 57 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N THR H 95 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL H 118 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR H 97 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE H 112 " --> pdb=" O VAL H 101 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'H' and resid 83 through 84 Processing sheet with id= 43, first strand: chain 'I' and resid 29 through 33 removed outlier: 3.640A pdb=" N HIS I 98 " --> pdb=" O HIS I 33 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG I 120 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N HIS I 98 " --> pdb=" O VAL I 118 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL I 118 " --> pdb=" O HIS I 98 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N ALA I 100 " --> pdb=" O LEU I 116 " (cutoff:3.500A) removed outlier: 10.914A pdb=" N LEU I 116 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE I 102 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 12.476A pdb=" N ALA I 114 " --> pdb=" O PHE I 102 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'I' and resid 83 through 84 Processing sheet with id= 45, first strand: chain 'I' and resid 136 through 137 Processing sheet with id= 46, first strand: chain 'J' and resid 29 through 33 removed outlier: 7.214A pdb=" N TYR J 99 " --> pdb=" O LYS J 113 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS J 113 " --> pdb=" O TYR J 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL J 101 " --> pdb=" O LEU J 111 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'J' and resid 83 through 84 Processing sheet with id= 48, first strand: chain 'J' and resid 94 through 95 Processing sheet with id= 49, first strand: chain 'K' and resid 57 through 58 removed outlier: 3.903A pdb=" N ARG K 57 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL K 94 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS K 98 " --> pdb=" O VAL K 118 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N VAL K 118 " --> pdb=" O HIS K 98 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N ALA K 100 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N LEU K 116 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N PHE K 102 " --> pdb=" O ALA K 114 " (cutoff:3.500A) removed outlier: 13.047A pdb=" N ALA K 114 " --> pdb=" O PHE K 102 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'K' and resid 83 through 84 removed outlier: 3.810A pdb=" N LEU K 83 " --> pdb=" O PHE K 130 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'L' and resid 29 through 33 removed outlier: 10.300A pdb=" N THR L 95 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VAL L 118 " --> pdb=" O THR L 95 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR L 97 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'L' and resid 83 through 84 removed outlier: 3.913A pdb=" N LEU L 83 " --> pdb=" O PHE L 130 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'M' and resid 29 through 33 removed outlier: 7.008A pdb=" N HIS M 98 " --> pdb=" O VAL M 118 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N VAL M 118 " --> pdb=" O HIS M 98 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA M 100 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEU M 116 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHE M 102 " --> pdb=" O ALA M 114 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N ALA M 114 " --> pdb=" O PHE M 102 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'M' and resid 83 through 84 removed outlier: 4.159A pdb=" N LEU M 83 " --> pdb=" O PHE M 130 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'M' and resid 136 through 137 Processing sheet with id= 56, first strand: chain 'N' and resid 29 through 33 removed outlier: 3.657A pdb=" N HIS N 98 " --> pdb=" O HIS N 33 " (cutoff:3.500A) removed outlier: 15.203A pdb=" N THR N 95 " --> pdb=" O THR N 117 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THR N 117 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N THR N 97 " --> pdb=" O PRO N 115 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR N 99 " --> pdb=" O LYS N 113 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS N 113 " --> pdb=" O TYR N 99 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL N 101 " --> pdb=" O LEU N 111 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'N' and resid 83 through 84 removed outlier: 3.740A pdb=" N LEU N 83 " --> pdb=" O PHE N 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL N 129 " --> pdb=" O UNK O 101 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'N' and resid 136 through 138 removed outlier: 5.770A pdb=" N THR N 136 " --> pdb=" O UNK O 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'O' and resid 3 through 4 removed outlier: 3.538A pdb=" N ASP P 18 " --> pdb=" O UNK O 3 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'P' and resid 5 through 8 removed outlier: 5.796A pdb=" N GLN P 6 " --> pdb=" O ARG P 89 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA P 75 " --> pdb=" O SER P 31 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER P 31 " --> pdb=" O ALA P 75 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Q' and resid 5 through 8 removed outlier: 5.780A pdb=" N GLN Q 6 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA Q 75 " --> pdb=" O SER Q 31 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER Q 31 " --> pdb=" O ALA Q 75 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Q' and resid 16 through 18 removed outlier: 3.563A pdb=" N ASP Q 51 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'R' and resid 5 through 8 removed outlier: 6.104A pdb=" N GLN R 6 " --> pdb=" O ARG R 89 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA R 75 " --> pdb=" O SER R 31 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER R 31 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'R' and resid 16 through 18 Processing sheet with id= 65, first strand: chain 'S' and resid 29 through 33 removed outlier: 3.552A pdb=" N TYR S 99 " --> pdb=" O ALA S 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE S 112 " --> pdb=" O VAL S 101 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'S' and resid 83 through 84 Processing sheet with id= 67, first strand: chain 'S' and resid 94 through 95 Processing sheet with id= 68, first strand: chain 'S' and resid 136 through 137 Processing sheet with id= 69, first strand: chain 'T' and resid 29 through 33 removed outlier: 6.772A pdb=" N HIS T 98 " --> pdb=" O VAL T 118 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N VAL T 118 " --> pdb=" O HIS T 98 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA T 100 " --> pdb=" O LEU T 116 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N LEU T 116 " --> pdb=" O ALA T 100 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE T 102 " --> pdb=" O ALA T 114 " (cutoff:3.500A) removed outlier: 12.569A pdb=" N ALA T 114 " --> pdb=" O PHE T 102 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'U' and resid 29 through 33 removed outlier: 7.143A pdb=" N HIS U 98 " --> pdb=" O VAL U 118 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N VAL U 118 " --> pdb=" O HIS U 98 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N ALA U 100 " --> pdb=" O LEU U 116 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LEU U 116 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N PHE U 102 " --> pdb=" O ALA U 114 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N ALA U 114 " --> pdb=" O PHE U 102 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'U' and resid 83 through 84 Processing sheet with id= 72, first strand: chain 'U' and resid 136 through 137 Processing sheet with id= 73, first strand: chain 'V' and resid 57 through 58 removed outlier: 3.931A pdb=" N ARG V 57 " --> pdb=" O VAL V 30 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N THR V 95 " --> pdb=" O VAL V 118 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL V 118 " --> pdb=" O THR V 95 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR V 97 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE V 112 " --> pdb=" O VAL V 101 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'V' and resid 83 through 84 Processing sheet with id= 75, first strand: chain 'W' and resid 29 through 33 removed outlier: 3.639A pdb=" N HIS W 98 " --> pdb=" O HIS W 33 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG W 120 " --> pdb=" O VAL W 96 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N HIS W 98 " --> pdb=" O VAL W 118 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL W 118 " --> pdb=" O HIS W 98 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N ALA W 100 " --> pdb=" O LEU W 116 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU W 116 " --> pdb=" O ALA W 100 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE W 102 " --> pdb=" O ALA W 114 " (cutoff:3.500A) removed outlier: 12.477A pdb=" N ALA W 114 " --> pdb=" O PHE W 102 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'W' and resid 83 through 84 Processing sheet with id= 77, first strand: chain 'W' and resid 136 through 137 Processing sheet with id= 78, first strand: chain 'X' and resid 29 through 33 removed outlier: 7.215A pdb=" N TYR X 99 " --> pdb=" O LYS X 113 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS X 113 " --> pdb=" O TYR X 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL X 101 " --> pdb=" O LEU X 111 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'X' and resid 83 through 84 Processing sheet with id= 80, first strand: chain 'X' and resid 94 through 95 Processing sheet with id= 81, first strand: chain 'Y' and resid 57 through 58 removed outlier: 3.904A pdb=" N ARG Y 57 " --> pdb=" O VAL Y 30 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL Y 94 " --> pdb=" O LEU Y 122 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS Y 98 " --> pdb=" O VAL Y 118 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N VAL Y 118 " --> pdb=" O HIS Y 98 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N ALA Y 100 " --> pdb=" O LEU Y 116 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N LEU Y 116 " --> pdb=" O ALA Y 100 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N PHE Y 102 " --> pdb=" O ALA Y 114 " (cutoff:3.500A) removed outlier: 13.047A pdb=" N ALA Y 114 " --> pdb=" O PHE Y 102 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'Y' and resid 83 through 84 removed outlier: 3.810A pdb=" N LEU Y 83 " --> pdb=" O PHE Y 130 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'Z' and resid 29 through 33 removed outlier: 10.300A pdb=" N THR Z 95 " --> pdb=" O VAL Z 118 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VAL Z 118 " --> pdb=" O THR Z 95 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR Z 97 " --> pdb=" O LEU Z 116 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'Z' and resid 83 through 84 removed outlier: 3.912A pdb=" N LEU Z 83 " --> pdb=" O PHE Z 130 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain '0' and resid 29 through 33 removed outlier: 7.007A pdb=" N HIS 0 98 " --> pdb=" O VAL 0 118 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N VAL 0 118 " --> pdb=" O HIS 0 98 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA 0 100 " --> pdb=" O LEU 0 116 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEU 0 116 " --> pdb=" O ALA 0 100 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHE 0 102 " --> pdb=" O ALA 0 114 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N ALA 0 114 " --> pdb=" O PHE 0 102 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain '0' and resid 83 through 84 removed outlier: 4.159A pdb=" N LEU 0 83 " --> pdb=" O PHE 0 130 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain '0' and resid 136 through 137 Processing sheet with id= 88, first strand: chain '1' and resid 29 through 33 removed outlier: 3.657A pdb=" N HIS 1 98 " --> pdb=" O HIS 1 33 " (cutoff:3.500A) removed outlier: 15.204A pdb=" N THR 1 95 " --> pdb=" O THR 1 117 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THR 1 117 " --> pdb=" O THR 1 95 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR 1 97 " --> pdb=" O PRO 1 115 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR 1 99 " --> pdb=" O LYS 1 113 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS 1 113 " --> pdb=" O TYR 1 99 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL 1 101 " --> pdb=" O LEU 1 111 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain '1' and resid 83 through 84 removed outlier: 3.740A pdb=" N LEU 1 83 " --> pdb=" O PHE 1 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL 1 129 " --> pdb=" O UNK 2 101 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain '1' and resid 136 through 138 removed outlier: 5.770A pdb=" N THR 1 136 " --> pdb=" O UNK 2 105 " (cutoff:3.500A) No H-bonds generated for sheet with id= 90 Processing sheet with id= 91, first strand: chain '2' and resid 3 through 4 removed outlier: 3.537A pdb=" N ASP 3 18 " --> pdb=" O UNK 2 3 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain '3' and resid 5 through 8 removed outlier: 5.797A pdb=" N GLN 3 6 " --> pdb=" O ARG 3 89 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA 3 75 " --> pdb=" O SER 3 31 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER 3 31 " --> pdb=" O ALA 3 75 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain '4' and resid 5 through 8 removed outlier: 5.781A pdb=" N GLN 4 6 " --> pdb=" O ARG 4 89 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA 4 75 " --> pdb=" O SER 4 31 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER 4 31 " --> pdb=" O ALA 4 75 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain '4' and resid 16 through 18 removed outlier: 3.563A pdb=" N ASP 4 51 " --> pdb=" O VAL 4 54 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain '5' and resid 5 through 8 removed outlier: 6.104A pdb=" N GLN 5 6 " --> pdb=" O ARG 5 89 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA 5 75 " --> pdb=" O SER 5 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER 5 31 " --> pdb=" O ALA 5 75 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain '5' and resid 16 through 18 Processing sheet with id= 97, first strand: chain '6' and resid 29 through 33 removed outlier: 3.553A pdb=" N TYR 6 99 " --> pdb=" O ALA 6 114 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE 6 112 " --> pdb=" O VAL 6 101 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain '6' and resid 83 through 84 Processing sheet with id= 99, first strand: chain '6' and resid 94 through 95 Processing sheet with id=100, first strand: chain '6' and resid 136 through 137 Processing sheet with id=101, first strand: chain '7' and resid 29 through 33 removed outlier: 6.771A pdb=" N HIS 7 98 " --> pdb=" O VAL 7 118 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N VAL 7 118 " --> pdb=" O HIS 7 98 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA 7 100 " --> pdb=" O LEU 7 116 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N LEU 7 116 " --> pdb=" O ALA 7 100 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE 7 102 " --> pdb=" O ALA 7 114 " (cutoff:3.500A) removed outlier: 12.570A pdb=" N ALA 7 114 " --> pdb=" O PHE 7 102 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain '8' and resid 29 through 33 removed outlier: 7.143A pdb=" N HIS 8 98 " --> pdb=" O VAL 8 118 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N VAL 8 118 " --> pdb=" O HIS 8 98 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N ALA 8 100 " --> pdb=" O LEU 8 116 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LEU 8 116 " --> pdb=" O ALA 8 100 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N PHE 8 102 " --> pdb=" O ALA 8 114 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N ALA 8 114 " --> pdb=" O PHE 8 102 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain '8' and resid 83 through 84 Processing sheet with id=104, first strand: chain '8' and resid 136 through 137 Processing sheet with id=105, first strand: chain '9' and resid 57 through 58 removed outlier: 3.931A pdb=" N ARG 9 57 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N THR 9 95 " --> pdb=" O VAL 9 118 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL 9 118 " --> pdb=" O THR 9 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR 9 97 " --> pdb=" O LEU 9 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE 9 112 " --> pdb=" O VAL 9 101 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain '9' and resid 83 through 84 Processing sheet with id=107, first strand: chain 'k' and resid 29 through 33 removed outlier: 3.639A pdb=" N HIS k 98 " --> pdb=" O HIS k 33 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG k 120 " --> pdb=" O VAL k 96 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N HIS k 98 " --> pdb=" O VAL k 118 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL k 118 " --> pdb=" O HIS k 98 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N ALA k 100 " --> pdb=" O LEU k 116 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU k 116 " --> pdb=" O ALA k 100 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE k 102 " --> pdb=" O ALA k 114 " (cutoff:3.500A) removed outlier: 12.476A pdb=" N ALA k 114 " --> pdb=" O PHE k 102 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'k' and resid 83 through 84 Processing sheet with id=109, first strand: chain 'k' and resid 136 through 137 Processing sheet with id=110, first strand: chain 'l' and resid 29 through 33 removed outlier: 7.215A pdb=" N TYR l 99 " --> pdb=" O LYS l 113 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS l 113 " --> pdb=" O TYR l 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL l 101 " --> pdb=" O LEU l 111 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'l' and resid 83 through 84 Processing sheet with id=112, first strand: chain 'l' and resid 94 through 95 Processing sheet with id=113, first strand: chain 'm' and resid 57 through 58 removed outlier: 3.903A pdb=" N ARG m 57 " --> pdb=" O VAL m 30 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL m 94 " --> pdb=" O LEU m 122 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS m 98 " --> pdb=" O VAL m 118 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N VAL m 118 " --> pdb=" O HIS m 98 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N ALA m 100 " --> pdb=" O LEU m 116 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N LEU m 116 " --> pdb=" O ALA m 100 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N PHE m 102 " --> pdb=" O ALA m 114 " (cutoff:3.500A) removed outlier: 13.047A pdb=" N ALA m 114 " --> pdb=" O PHE m 102 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'm' and resid 83 through 84 removed outlier: 3.810A pdb=" N LEU m 83 " --> pdb=" O PHE m 130 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'n' and resid 29 through 33 removed outlier: 10.300A pdb=" N THR n 95 " --> pdb=" O VAL n 118 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VAL n 118 " --> pdb=" O THR n 95 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR n 97 " --> pdb=" O LEU n 116 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'n' and resid 83 through 84 removed outlier: 3.913A pdb=" N LEU n 83 " --> pdb=" O PHE n 130 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'o' and resid 29 through 33 removed outlier: 7.007A pdb=" N HIS o 98 " --> pdb=" O VAL o 118 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N VAL o 118 " --> pdb=" O HIS o 98 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA o 100 " --> pdb=" O LEU o 116 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEU o 116 " --> pdb=" O ALA o 100 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHE o 102 " --> pdb=" O ALA o 114 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N ALA o 114 " --> pdb=" O PHE o 102 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'o' and resid 83 through 84 removed outlier: 4.159A pdb=" N LEU o 83 " --> pdb=" O PHE o 130 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain 'o' and resid 136 through 137 Processing sheet with id=120, first strand: chain 'p' and resid 29 through 33 removed outlier: 3.656A pdb=" N HIS p 98 " --> pdb=" O HIS p 33 " (cutoff:3.500A) removed outlier: 15.203A pdb=" N THR p 95 " --> pdb=" O THR p 117 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THR p 117 " --> pdb=" O THR p 95 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR p 97 " --> pdb=" O PRO p 115 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR p 99 " --> pdb=" O LYS p 113 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS p 113 " --> pdb=" O TYR p 99 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL p 101 " --> pdb=" O LEU p 111 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'p' and resid 83 through 84 removed outlier: 3.740A pdb=" N LEU p 83 " --> pdb=" O PHE p 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL p 129 " --> pdb=" O UNK q 101 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'p' and resid 136 through 138 removed outlier: 5.770A pdb=" N THR p 136 " --> pdb=" O UNK q 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=122 Processing sheet with id=123, first strand: chain 'q' and resid 3 through 4 removed outlier: 3.537A pdb=" N ASP r 18 " --> pdb=" O UNK q 3 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'r' and resid 5 through 8 removed outlier: 5.796A pdb=" N GLN r 6 " --> pdb=" O ARG r 89 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA r 75 " --> pdb=" O SER r 31 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER r 31 " --> pdb=" O ALA r 75 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 's' and resid 5 through 8 removed outlier: 5.781A pdb=" N GLN s 6 " --> pdb=" O ARG s 89 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA s 75 " --> pdb=" O SER s 31 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N SER s 31 " --> pdb=" O ALA s 75 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 's' and resid 16 through 18 removed outlier: 3.563A pdb=" N ASP s 51 " --> pdb=" O VAL s 54 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 't' and resid 5 through 8 removed outlier: 6.105A pdb=" N GLN t 6 " --> pdb=" O ARG t 89 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA t 75 " --> pdb=" O SER t 31 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER t 31 " --> pdb=" O ALA t 75 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain 't' and resid 16 through 18 Processing sheet with id=129, first strand: chain 'u' and resid 29 through 33 removed outlier: 3.552A pdb=" N TYR u 99 " --> pdb=" O ALA u 114 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE u 112 " --> pdb=" O VAL u 101 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'u' and resid 83 through 84 Processing sheet with id=131, first strand: chain 'u' and resid 94 through 95 Processing sheet with id=132, first strand: chain 'u' and resid 136 through 137 Processing sheet with id=133, first strand: chain 'v' and resid 29 through 33 removed outlier: 6.772A pdb=" N HIS v 98 " --> pdb=" O VAL v 118 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N VAL v 118 " --> pdb=" O HIS v 98 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA v 100 " --> pdb=" O LEU v 116 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N LEU v 116 " --> pdb=" O ALA v 100 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N PHE v 102 " --> pdb=" O ALA v 114 " (cutoff:3.500A) removed outlier: 12.570A pdb=" N ALA v 114 " --> pdb=" O PHE v 102 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain 'w' and resid 29 through 33 removed outlier: 7.143A pdb=" N HIS w 98 " --> pdb=" O VAL w 118 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N VAL w 118 " --> pdb=" O HIS w 98 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N ALA w 100 " --> pdb=" O LEU w 116 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LEU w 116 " --> pdb=" O ALA w 100 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N PHE w 102 " --> pdb=" O ALA w 114 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N ALA w 114 " --> pdb=" O PHE w 102 " (cutoff:3.500A) Processing sheet with id=135, first strand: chain 'w' and resid 83 through 84 Processing sheet with id=136, first strand: chain 'w' and resid 136 through 137 Processing sheet with id=137, first strand: chain 'x' and resid 57 through 58 removed outlier: 3.931A pdb=" N ARG x 57 " --> pdb=" O VAL x 30 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N THR x 95 " --> pdb=" O VAL x 118 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL x 118 " --> pdb=" O THR x 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR x 97 " --> pdb=" O LEU x 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE x 112 " --> pdb=" O VAL x 101 " (cutoff:3.500A) Processing sheet with id=138, first strand: chain 'x' and resid 83 through 84 Processing sheet with id=139, first strand: chain 'y' and resid 29 through 33 removed outlier: 3.640A pdb=" N HIS y 98 " --> pdb=" O HIS y 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG y 120 " --> pdb=" O VAL y 96 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N HIS y 98 " --> pdb=" O VAL y 118 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL y 118 " --> pdb=" O HIS y 98 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N ALA y 100 " --> pdb=" O LEU y 116 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU y 116 " --> pdb=" O ALA y 100 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE y 102 " --> pdb=" O ALA y 114 " (cutoff:3.500A) removed outlier: 12.477A pdb=" N ALA y 114 " --> pdb=" O PHE y 102 " (cutoff:3.500A) Processing sheet with id=140, first strand: chain 'y' and resid 83 through 84 Processing sheet with id=141, first strand: chain 'y' and resid 136 through 137 Processing sheet with id=142, first strand: chain 'z' and resid 29 through 33 removed outlier: 7.215A pdb=" N TYR z 99 " --> pdb=" O LYS z 113 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS z 113 " --> pdb=" O TYR z 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL z 101 " --> pdb=" O LEU z 111 " (cutoff:3.500A) Processing sheet with id=143, first strand: chain 'z' and resid 83 through 84 Processing sheet with id=144, first strand: chain 'z' and resid 94 through 95 Processing sheet with id=145, first strand: chain 'AA' and resid 57 through 58 removed outlier: 3.904A pdb=" N ARGAA 57 " --> pdb=" O VALAA 30 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VALAA 94 " --> pdb=" O LEUAA 122 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HISAA 98 " --> pdb=" O VALAA 118 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N VALAA 118 " --> pdb=" O HISAA 98 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N ALAAA 100 " --> pdb=" O LEUAA 116 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N LEUAA 116 " --> pdb=" O ALAAA 100 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N PHEAA 102 " --> pdb=" O ALAAA 114 " (cutoff:3.500A) removed outlier: 13.048A pdb=" N ALAAA 114 " --> pdb=" O PHEAA 102 " (cutoff:3.500A) Processing sheet with id=146, first strand: chain 'AA' and resid 83 through 84 removed outlier: 3.810A pdb=" N LEUAA 83 " --> pdb=" O PHEAA 130 " (cutoff:3.500A) Processing sheet with id=147, first strand: chain 'AB' and resid 29 through 33 removed outlier: 10.300A pdb=" N THRAB 95 " --> pdb=" O VALAB 118 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VALAB 118 " --> pdb=" O THRAB 95 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THRAB 97 " --> pdb=" O LEUAB 116 " (cutoff:3.500A) Processing sheet with id=148, first strand: chain 'AB' and resid 83 through 84 removed outlier: 3.913A pdb=" N LEUAB 83 " --> pdb=" O PHEAB 130 " (cutoff:3.500A) Processing sheet with id=149, first strand: chain 'AC' and resid 29 through 33 removed outlier: 7.007A pdb=" N HISAC 98 " --> pdb=" O VALAC 118 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N VALAC 118 " --> pdb=" O HISAC 98 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALAAC 100 " --> pdb=" O LEUAC 116 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEUAC 116 " --> pdb=" O ALAAC 100 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHEAC 102 " --> pdb=" O ALAAC 114 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N ALAAC 114 " --> pdb=" O PHEAC 102 " (cutoff:3.500A) Processing sheet with id=150, first strand: chain 'AC' and resid 83 through 84 removed outlier: 4.159A pdb=" N LEUAC 83 " --> pdb=" O PHEAC 130 " (cutoff:3.500A) Processing sheet with id=151, first strand: chain 'AC' and resid 136 through 137 Processing sheet with id=152, first strand: chain 'AD' and resid 29 through 33 removed outlier: 3.657A pdb=" N HISAD 98 " --> pdb=" O HISAD 33 " (cutoff:3.500A) removed outlier: 15.203A pdb=" N THRAD 95 " --> pdb=" O THRAD 117 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THRAD 117 " --> pdb=" O THRAD 95 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THRAD 97 " --> pdb=" O PROAD 115 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYRAD 99 " --> pdb=" O LYSAD 113 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYSAD 113 " --> pdb=" O TYRAD 99 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VALAD 101 " --> pdb=" O LEUAD 111 " (cutoff:3.500A) Processing sheet with id=153, first strand: chain 'AD' and resid 83 through 84 removed outlier: 3.740A pdb=" N LEUAD 83 " --> pdb=" O PHEAD 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VALAD 129 " --> pdb=" O UNKAE 101 " (cutoff:3.500A) Processing sheet with id=154, first strand: chain 'AD' and resid 136 through 138 removed outlier: 5.770A pdb=" N THRAD 136 " --> pdb=" O UNKAE 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=154 Processing sheet with id=155, first strand: chain 'AE' and resid 3 through 4 removed outlier: 3.538A pdb=" N ASPAF 18 " --> pdb=" O UNKAE 3 " (cutoff:3.500A) Processing sheet with id=156, first strand: chain 'AF' and resid 5 through 8 removed outlier: 5.796A pdb=" N GLNAF 6 " --> pdb=" O ARGAF 89 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALAAF 75 " --> pdb=" O SERAF 31 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SERAF 31 " --> pdb=" O ALAAF 75 " (cutoff:3.500A) Processing sheet with id=157, first strand: chain 'AG' and resid 5 through 8 removed outlier: 5.781A pdb=" N GLNAG 6 " --> pdb=" O ARGAG 89 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALAAG 75 " --> pdb=" O SERAG 31 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SERAG 31 " --> pdb=" O ALAAG 75 " (cutoff:3.500A) Processing sheet with id=158, first strand: chain 'AG' and resid 16 through 18 removed outlier: 3.563A pdb=" N ASPAG 51 " --> pdb=" O VALAG 54 " (cutoff:3.500A) Processing sheet with id=159, first strand: chain 'AH' and resid 5 through 8 removed outlier: 6.104A pdb=" N GLNAH 6 " --> pdb=" O ARGAH 89 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALAAH 75 " --> pdb=" O SERAH 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SERAH 31 " --> pdb=" O ALAAH 75 " (cutoff:3.500A) Processing sheet with id=160, first strand: chain 'AH' and resid 16 through 18 1275 hydrogen bonds defined for protein. 3330 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: 19.34 Time building geometry restraints manager: 20.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19053 1.33 - 1.45: 9916 1.45 - 1.57: 34716 1.57 - 1.69: 5 1.69 - 1.81: 45 Bond restraints: 63735 Sorted by residual: bond pdb=" CA UNK q 58 " pdb=" C UNK q 58 " ideal model delta sigma weight residual 1.525 1.462 0.063 2.10e-02 2.27e+03 9.13e+00 bond pdb=" CA UNKAE 58 " pdb=" C UNKAE 58 " ideal model delta sigma weight residual 1.525 1.462 0.063 2.10e-02 2.27e+03 9.13e+00 bond pdb=" CA UNK A 58 " pdb=" C UNK A 58 " ideal model delta sigma weight residual 1.525 1.462 0.063 2.10e-02 2.27e+03 9.09e+00 bond pdb=" CA UNK O 58 " pdb=" C UNK O 58 " ideal model delta sigma weight residual 1.525 1.462 0.063 2.10e-02 2.27e+03 9.06e+00 bond pdb=" CA UNK 2 58 " pdb=" C UNK 2 58 " ideal model delta sigma weight residual 1.525 1.462 0.063 2.10e-02 2.27e+03 8.98e+00 ... (remaining 63730 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.97: 2853 107.97 - 115.08: 37049 115.08 - 122.18: 34202 122.18 - 129.29: 13041 129.29 - 136.40: 415 Bond angle restraints: 87560 Sorted by residual: angle pdb=" N ASP s 39 " pdb=" CA ASP s 39 " pdb=" C ASP s 39 " ideal model delta sigma weight residual 111.02 125.43 -14.41 1.22e+00 6.72e-01 1.39e+02 angle pdb=" N ASP Q 39 " pdb=" CA ASP Q 39 " pdb=" C ASP Q 39 " ideal model delta sigma weight residual 111.02 125.40 -14.38 1.22e+00 6.72e-01 1.39e+02 angle pdb=" N ASP 4 39 " pdb=" CA ASP 4 39 " pdb=" C ASP 4 39 " ideal model delta sigma weight residual 111.02 125.39 -14.37 1.22e+00 6.72e-01 1.39e+02 angle pdb=" N ASP B 39 " pdb=" CA ASP B 39 " pdb=" C ASP B 39 " ideal model delta sigma weight residual 111.02 125.38 -14.36 1.22e+00 6.72e-01 1.39e+02 angle pdb=" N ASPAG 39 " pdb=" CA ASPAG 39 " pdb=" C ASPAG 39 " ideal model delta sigma weight residual 111.02 125.38 -14.36 1.22e+00 6.72e-01 1.39e+02 ... (remaining 87555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 34200 17.90 - 35.80: 2140 35.80 - 53.70: 335 53.70 - 71.60: 50 71.60 - 89.49: 15 Dihedral angle restraints: 36740 sinusoidal: 12110 harmonic: 24630 Sorted by residual: dihedral pdb=" CA THR t 63 " pdb=" C THR t 63 " pdb=" N ALA t 64 " pdb=" CA ALA t 64 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA THRAH 63 " pdb=" C THRAH 63 " pdb=" N ALAAH 64 " pdb=" CA ALAAH 64 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA THR C 63 " pdb=" C THR C 63 " pdb=" N ALA C 64 " pdb=" CA ALA C 64 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 36737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 9751 0.096 - 0.191: 605 0.191 - 0.287: 24 0.287 - 0.383: 10 0.383 - 0.478: 15 Chirality restraints: 10405 Sorted by residual: chirality pdb=" CA ASP Q 39 " pdb=" N ASP Q 39 " pdb=" C ASP Q 39 " pdb=" CB ASP Q 39 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CA ASP B 39 " pdb=" N ASP B 39 " pdb=" C ASP B 39 " pdb=" CB ASP B 39 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA ASPAG 39 " pdb=" N ASPAG 39 " pdb=" C ASPAG 39 " pdb=" CB ASPAG 39 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 10402 not shown) Planarity restraints: 11555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP I 51 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO I 52 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO I 52 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO I 52 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP W 51 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO W 52 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO W 52 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO W 52 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP e 51 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO e 52 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO e 52 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO e 52 " -0.058 5.00e-02 4.00e+02 ... (remaining 11552 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.59: 20 1.59 - 2.42: 355 2.42 - 3.24: 66034 3.24 - 4.07: 150760 4.07 - 4.90: 264705 Warning: very small nonbonded interaction distances. Nonbonded interactions: 481874 Sorted by model distance: nonbonded pdb=" N LEU 5 13 " pdb=" NH1 ARG r 80 " model vdw 0.759 3.200 nonbonded pdb=" NH1 ARG D 80 " pdb=" N LEUAH 13 " model vdw 0.759 3.200 nonbonded pdb=" N LEU R 13 " pdb=" NH1 ARG 3 80 " model vdw 0.759 3.200 nonbonded pdb=" N LEU t 13 " pdb=" NH1 ARGAF 80 " model vdw 0.759 3.200 nonbonded pdb=" N LEU C 13 " pdb=" NH1 ARG P 80 " model vdw 0.759 3.200 ... (remaining 481869 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 '0' selection = chain '1' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '2' selection = chain 'A' selection = chain 'AE' selection = chain 'O' selection = chain 'q' } ncs_group { reference = chain '3' selection = chain '4' selection = chain '5' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'r' selection = chain 's' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 34.210 Check model and map are aligned: 0.660 Set scattering table: 0.430 Process input model: 119.400 Find NCS groups from input model: 3.640 Set up NCS constraints: 0.970 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 63735 Z= 0.269 Angle : 0.832 14.407 87560 Z= 0.484 Chirality : 0.051 0.478 10405 Planarity : 0.007 0.108 11555 Dihedral : 12.095 89.494 21060 Min Nonbonded Distance : 0.759 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 1.87 % Allowed : 7.71 % Favored : 90.42 % Rotamer: Outliers : 0.49 % Allowed : 0.43 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.09), residues: 8005 helix: 1.04 (0.17), residues: 650 sheet: 1.15 (0.14), residues: 1235 loop : -1.91 (0.07), residues: 6120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP o 69 HIS 0.015 0.002 HIS x 98 PHE 0.042 0.002 PHE K 128 TYR 0.035 0.002 TYRAG 15 ARG 0.004 0.001 ARG V 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1136 time to evaluate : 4.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 48 LEU cc_start: 0.6713 (tp) cc_final: 0.6346 (mt) REVERT: i 97 THR cc_start: 0.7045 (p) cc_final: 0.6677 (p) REVERT: N 65 ILE cc_start: 0.4451 (tp) cc_final: 0.4229 (tp) REVERT: Z 65 ILE cc_start: 0.5157 (tp) cc_final: 0.4877 (tp) REVERT: 8 105 PRO cc_start: 0.5134 (Cg_exo) cc_final: 0.4877 (Cg_endo) REVERT: o 7 TYR cc_start: 0.5351 (t80) cc_final: 0.5088 (t80) outliers start: 30 outliers final: 6 residues processed: 1164 average time/residue: 0.6118 time to fit residues: 1200.2893 Evaluate side-chains 553 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 547 time to evaluate : 4.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 696 optimal weight: 0.2980 chunk 625 optimal weight: 50.0000 chunk 346 optimal weight: 6.9990 chunk 213 optimal weight: 20.0000 chunk 421 optimal weight: 4.9990 chunk 334 optimal weight: 10.0000 chunk 646 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 393 optimal weight: 20.0000 chunk 481 optimal weight: 0.0050 chunk 749 optimal weight: 2.9990 overall best weight: 2.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 138 GLN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN f 76 GLN ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 82 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN F 98 HIS G 89 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN K 98 HIS ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 ASN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS U 81 ASN U 89 ASN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 89 ASN W 61 GLN ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 HIS X 123 GLN Y 82 GLN ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 6 GLN ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 82 GLN 7 109 ASN 8 81 ASN 8 89 ASN 8 138 GLN 9 89 ASN ** l 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 14 ASN ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 138 GLN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 88 ASN r 6 GLN ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 76 GLN ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 109 ASN AD 14 ASN ** AD 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3903 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 63735 Z= 0.166 Angle : 0.642 10.594 87560 Z= 0.336 Chirality : 0.042 0.290 10405 Planarity : 0.006 0.071 11555 Dihedral : 4.457 22.777 9210 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 1.84 % Allowed : 6.70 % Favored : 91.47 % Rotamer: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.09), residues: 8005 helix: 1.55 (0.19), residues: 650 sheet: 1.46 (0.14), residues: 1210 loop : -1.78 (0.07), residues: 6145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP x 51 HIS 0.011 0.002 HIS L 98 PHE 0.024 0.001 PHE Z 112 TYR 0.028 0.002 TYRAA 85 ARG 0.023 0.001 ARG P 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 758 time to evaluate : 5.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 6 THR cc_start: 0.6595 (p) cc_final: 0.6374 (p) REVERT: e 36 ASP cc_start: 0.6295 (t0) cc_final: 0.6091 (t70) REVERT: h 48 LEU cc_start: 0.6767 (tp) cc_final: 0.6566 (mt) REVERT: j 106 THR cc_start: 0.7225 (p) cc_final: 0.6830 (t) REVERT: N 65 ILE cc_start: 0.3993 (tp) cc_final: 0.3759 (tp) REVERT: N 105 PRO cc_start: 0.7555 (Cg_endo) cc_final: 0.7255 (Cg_exo) REVERT: Z 65 ILE cc_start: 0.5169 (tp) cc_final: 0.4912 (tp) REVERT: 0 12 ILE cc_start: 0.6512 (mm) cc_final: 0.6272 (mm) REVERT: 1 97 THR cc_start: 0.4867 (t) cc_final: 0.4572 (t) REVERT: 8 105 PRO cc_start: 0.4972 (Cg_exo) cc_final: 0.4743 (Cg_endo) REVERT: o 84 THR cc_start: 0.7425 (p) cc_final: 0.6475 (p) REVERT: AD 126 ASP cc_start: 0.4182 (t0) cc_final: 0.3097 (t0) outliers start: 6 outliers final: 2 residues processed: 763 average time/residue: 0.6080 time to fit residues: 784.1428 Evaluate side-chains 498 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 496 time to evaluate : 4.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 416 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 623 optimal weight: 50.0000 chunk 510 optimal weight: 30.0000 chunk 206 optimal weight: 10.0000 chunk 750 optimal weight: 8.9990 chunk 810 optimal weight: 30.0000 chunk 668 optimal weight: 30.0000 chunk 744 optimal weight: 0.9980 chunk 255 optimal weight: 50.0000 chunk 602 optimal weight: 9.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN g 82 GLN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 14 ASN ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 HIS ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN J 123 GLN K 61 GLN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 ASN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 HIS ** W 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 HIS X 123 GLN ** Y 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 82 GLN ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 79 ASN ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 109 ASN ** 8 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 138 GLN ** m 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 82 GLN ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 138 GLN o 79 ASN ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 76 GLN ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 11 ASN AA 82 GLN ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 98 HIS AF 6 GLN ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 12 GLN ** AH 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4330 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 63735 Z= 0.234 Angle : 0.670 11.371 87560 Z= 0.347 Chirality : 0.042 0.323 10405 Planarity : 0.005 0.075 11555 Dihedral : 4.485 24.592 9210 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 1.86 % Allowed : 6.86 % Favored : 91.28 % Rotamer: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.09), residues: 8005 helix: 1.56 (0.20), residues: 650 sheet: 1.11 (0.14), residues: 1305 loop : -1.62 (0.07), residues: 6050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP p 51 HIS 0.012 0.002 HIS N 33 PHE 0.027 0.002 PHE N 102 TYR 0.050 0.002 TYR N 29 ARG 0.013 0.001 ARG S 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 709 time to evaluate : 4.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 36 ASP cc_start: 0.6821 (t0) cc_final: 0.6199 (t0) REVERT: f 36 ASP cc_start: 0.7045 (t0) cc_final: 0.6760 (t0) REVERT: h 48 LEU cc_start: 0.7211 (tp) cc_final: 0.6951 (mt) REVERT: N 34 THR cc_start: 0.5929 (p) cc_final: 0.5710 (p) REVERT: Y 36 ASP cc_start: 0.6834 (t0) cc_final: 0.6364 (t0) REVERT: Y 84 THR cc_start: 0.5831 (m) cc_final: 0.5584 (m) REVERT: Z 65 ILE cc_start: 0.5187 (tp) cc_final: 0.4907 (tp) REVERT: 8 105 PRO cc_start: 0.5631 (Cg_exo) cc_final: 0.5323 (Cg_endo) REVERT: AA 7 TYR cc_start: 0.5532 (t80) cc_final: 0.5245 (t80) REVERT: AH 73 THR cc_start: 0.5810 (m) cc_final: 0.5464 (t) outliers start: 2 outliers final: 0 residues processed: 710 average time/residue: 0.5935 time to fit residues: 712.3466 Evaluate side-chains 474 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 6.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 741 optimal weight: 50.0000 chunk 564 optimal weight: 0.8980 chunk 389 optimal weight: 9.9990 chunk 83 optimal weight: 0.4980 chunk 358 optimal weight: 7.9990 chunk 503 optimal weight: 30.0000 chunk 753 optimal weight: 2.9990 chunk 797 optimal weight: 50.0000 chunk 393 optimal weight: 20.0000 chunk 713 optimal weight: 50.0000 chunk 214 optimal weight: 7.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 HIS ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 61 GLN g 82 GLN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 138 GLN ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 HIS ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN J 123 GLN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 GLN ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 10 ASN ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 81 ASN ** 8 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 98 HIS ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN o 81 ASN ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN AA 11 ASN ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4379 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 63735 Z= 0.164 Angle : 0.605 10.723 87560 Z= 0.312 Chirality : 0.041 0.351 10405 Planarity : 0.005 0.057 11555 Dihedral : 4.180 23.090 9210 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 1.87 % Allowed : 6.62 % Favored : 91.51 % Rotamer: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.09), residues: 8005 helix: 1.55 (0.20), residues: 650 sheet: 1.48 (0.15), residues: 1155 loop : -1.57 (0.07), residues: 6200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP p 51 HIS 0.011 0.002 HISAD 98 PHE 0.019 0.001 PHE Z 112 TYR 0.015 0.001 TYR a 54 ARG 0.010 0.001 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 641 time to evaluate : 5.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.6613 (t0) cc_final: 0.6134 (t70) REVERT: c 36 ASP cc_start: 0.6544 (t0) cc_final: 0.5937 (t0) REVERT: f 36 ASP cc_start: 0.6751 (t0) cc_final: 0.6424 (t0) REVERT: P 25 ASP cc_start: 0.5201 (p0) cc_final: 0.4845 (p0) REVERT: W 136 THR cc_start: 0.6226 (m) cc_final: 0.5988 (t) REVERT: Y 36 ASP cc_start: 0.6832 (t0) cc_final: 0.6474 (t0) REVERT: 0 12 ILE cc_start: 0.6489 (mm) cc_final: 0.6273 (mm) REVERT: AA 7 TYR cc_start: 0.5297 (t80) cc_final: 0.4797 (t80) outliers start: 2 outliers final: 1 residues processed: 643 average time/residue: 0.5927 time to fit residues: 652.6819 Evaluate side-chains 454 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 453 time to evaluate : 4.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 664 optimal weight: 50.0000 chunk 452 optimal weight: 40.0000 chunk 11 optimal weight: 8.9990 chunk 593 optimal weight: 20.0000 chunk 329 optimal weight: 4.9990 chunk 680 optimal weight: 50.0000 chunk 551 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 407 optimal weight: 8.9990 chunk 715 optimal weight: 50.0000 chunk 201 optimal weight: 30.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 11 ASN e 109 ASN ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 82 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 138 GLN ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 44 ASN i 81 ASN ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 44 ASN ** j 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 GLN K 82 GLN ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 ASN ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 ASN ** S 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 82 GLN ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 98 HIS ** 1 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 61 GLN ** 6 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 109 ASN ** 8 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 89 ASN ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 11 ASN ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 109 ASN ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 89 ASN ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4970 moved from start: 0.8165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 63735 Z= 0.316 Angle : 0.753 15.386 87560 Z= 0.394 Chirality : 0.044 0.269 10405 Planarity : 0.006 0.158 11555 Dihedral : 5.012 25.817 9210 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 32.38 Ramachandran Plot: Outliers : 1.95 % Allowed : 8.04 % Favored : 90.01 % Rotamer: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.09), residues: 8005 helix: 0.97 (0.20), residues: 650 sheet: 0.71 (0.14), residues: 1253 loop : -1.64 (0.07), residues: 6102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP J 69 HIS 0.014 0.003 HIS W 98 PHE 0.031 0.002 PHE 0 102 TYR 0.040 0.003 TYR u 85 ARG 0.044 0.001 ARG 6 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 606 time to evaluate : 4.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.5807 (t0) cc_final: 0.4888 (t0) REVERT: h 36 ASP cc_start: 0.7853 (t0) cc_final: 0.7534 (t0) REVERT: i 69 TRP cc_start: 0.2338 (m-90) cc_final: 0.1837 (m-90) REVERT: B 18 ASP cc_start: 0.6351 (t0) cc_final: 0.6126 (t0) REVERT: P 25 ASP cc_start: 0.5094 (p0) cc_final: 0.4876 (p0) REVERT: 1 65 ILE cc_start: 0.4999 (tp) cc_final: 0.4751 (tp) REVERT: l 36 ASP cc_start: 0.6584 (t0) cc_final: 0.6052 (t0) REVERT: m 118 VAL cc_start: 0.7115 (t) cc_final: 0.6877 (t) REVERT: z 36 ASP cc_start: 0.6671 (t0) cc_final: 0.6416 (t0) outliers start: 2 outliers final: 0 residues processed: 608 average time/residue: 0.5809 time to fit residues: 609.2772 Evaluate side-chains 395 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 4.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 268 optimal weight: 8.9990 chunk 718 optimal weight: 0.9990 chunk 157 optimal weight: 30.0000 chunk 468 optimal weight: 50.0000 chunk 196 optimal weight: 40.0000 chunk 798 optimal weight: 50.0000 chunk 662 optimal weight: 10.0000 chunk 369 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 264 optimal weight: 9.9990 chunk 419 optimal weight: 9.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 11 ASN ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN g 82 GLN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN J 81 ASN L 76 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 ASN ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN X 76 GLN ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN ** Y 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 82 GLN ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 11 ASN 9 138 GLN ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 10 ASN ** o 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 81 ASN AA 11 ASN ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN ** AC 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 44 ASN ** AD 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 98 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4990 moved from start: 0.9037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 63735 Z= 0.214 Angle : 0.637 14.363 87560 Z= 0.328 Chirality : 0.042 0.235 10405 Planarity : 0.005 0.083 11555 Dihedral : 4.591 22.350 9210 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 1.97 % Allowed : 7.13 % Favored : 90.89 % Rotamer: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.09), residues: 8005 helix: 1.12 (0.21), residues: 650 sheet: 0.62 (0.14), residues: 1293 loop : -1.61 (0.07), residues: 6062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP n 51 HIS 0.011 0.002 HIS W 98 PHE 0.038 0.002 PHE j 112 TYR 0.030 0.002 TYR u 29 ARG 0.009 0.001 ARG E 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 570 time to evaluate : 5.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.6094 (t0) cc_final: 0.5320 (t0) REVERT: c 36 ASP cc_start: 0.6934 (t0) cc_final: 0.6327 (t0) REVERT: f 36 ASP cc_start: 0.6935 (t0) cc_final: 0.6358 (t0) REVERT: i 69 TRP cc_start: 0.2219 (m-90) cc_final: 0.1918 (m-90) REVERT: B 18 ASP cc_start: 0.5747 (t0) cc_final: 0.5449 (t70) REVERT: L 36 ASP cc_start: 0.7338 (t0) cc_final: 0.7137 (t0) REVERT: T 106 THR cc_start: 0.6200 (p) cc_final: 0.5967 (p) REVERT: U 36 ASP cc_start: 0.6691 (t70) cc_final: 0.6344 (t0) REVERT: 1 65 ILE cc_start: 0.4983 (tp) cc_final: 0.4648 (tp) REVERT: 8 36 ASP cc_start: 0.7081 (t0) cc_final: 0.6806 (t0) REVERT: l 36 ASP cc_start: 0.6186 (t0) cc_final: 0.5687 (t0) REVERT: z 36 ASP cc_start: 0.6923 (t0) cc_final: 0.6565 (t0) REVERT: AA 36 ASP cc_start: 0.8005 (t70) cc_final: 0.7453 (t0) outliers start: 2 outliers final: 0 residues processed: 571 average time/residue: 0.5777 time to fit residues: 571.9780 Evaluate side-chains 399 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 4.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 769 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 454 optimal weight: 8.9990 chunk 582 optimal weight: 8.9990 chunk 451 optimal weight: 4.9990 chunk 671 optimal weight: 1.9990 chunk 445 optimal weight: 50.0000 chunk 795 optimal weight: 70.0000 chunk 497 optimal weight: 7.9990 chunk 484 optimal weight: 40.0000 chunk 367 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 11 ASN g 81 ASN g 82 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN X 123 GLN ** Y 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 79 ASN ** 0 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 50 ASN ** 8 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 81 ASN AA 11 ASN ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN ** AC 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5051 moved from start: 0.9708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 63735 Z= 0.195 Angle : 0.615 12.576 87560 Z= 0.315 Chirality : 0.041 0.196 10405 Planarity : 0.005 0.104 11555 Dihedral : 4.431 23.158 9210 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 1.85 % Allowed : 7.92 % Favored : 90.23 % Rotamer: Outliers : 0.03 % Allowed : 2.05 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.09), residues: 8005 helix: 1.13 (0.21), residues: 650 sheet: 0.99 (0.15), residues: 1167 loop : -1.67 (0.07), residues: 6188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 22 HIS 0.010 0.002 HIS W 98 PHE 0.019 0.002 PHE G 130 TYR 0.029 0.002 TYR u 29 ARG 0.008 0.001 ARG 5 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 560 time to evaluate : 5.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.5891 (t0) cc_final: 0.4900 (t0) REVERT: c 36 ASP cc_start: 0.7198 (t0) cc_final: 0.6489 (t0) REVERT: d 36 ASP cc_start: 0.7359 (t0) cc_final: 0.7038 (t0) REVERT: f 36 ASP cc_start: 0.6878 (t0) cc_final: 0.6316 (t0) REVERT: h 36 ASP cc_start: 0.7799 (t0) cc_final: 0.7524 (t0) REVERT: i 69 TRP cc_start: 0.2331 (m-90) cc_final: 0.1950 (m-90) REVERT: j 113 LYS cc_start: 0.6149 (mmpt) cc_final: 0.5354 (mmtp) REVERT: F 36 ASP cc_start: 0.7191 (t0) cc_final: 0.6723 (t0) REVERT: G 36 ASP cc_start: 0.6904 (t0) cc_final: 0.6299 (t0) REVERT: J 36 ASP cc_start: 0.6676 (t0) cc_final: 0.5817 (t0) REVERT: T 36 ASP cc_start: 0.6851 (t0) cc_final: 0.6552 (t0) REVERT: 1 65 ILE cc_start: 0.5220 (tp) cc_final: 0.4835 (tp) REVERT: l 36 ASP cc_start: 0.6646 (t0) cc_final: 0.6160 (t0) REVERT: m 36 ASP cc_start: 0.8267 (t70) cc_final: 0.7984 (t0) REVERT: z 36 ASP cc_start: 0.6645 (t0) cc_final: 0.6300 (t0) REVERT: AA 36 ASP cc_start: 0.8393 (t70) cc_final: 0.7829 (t0) REVERT: AD 97 THR cc_start: 0.5592 (t) cc_final: 0.5363 (t) outliers start: 2 outliers final: 0 residues processed: 561 average time/residue: 0.5694 time to fit residues: 556.9254 Evaluate side-chains 411 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 6.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 491 optimal weight: 7.9990 chunk 317 optimal weight: 8.9990 chunk 474 optimal weight: 0.0010 chunk 239 optimal weight: 0.9990 chunk 156 optimal weight: 50.0000 chunk 154 optimal weight: 40.0000 chunk 505 optimal weight: 5.9990 chunk 541 optimal weight: 3.9990 chunk 393 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 625 optimal weight: 50.0000 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 11 ASN g 81 ASN g 82 GLN h 76 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 89 ASN h 138 GLN ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 HIS T 76 GLN ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN ** Y 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 89 ASN ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 138 GLN ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 98 HIS ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 33 HIS ** w 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 81 ASN AA 11 ASN ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 138 GLN ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN AC 14 ASN ** AD 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 98 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4997 moved from start: 0.9964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 63735 Z= 0.154 Angle : 0.590 11.387 87560 Z= 0.302 Chirality : 0.041 0.224 10405 Planarity : 0.005 0.095 11555 Dihedral : 4.203 21.946 9210 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 1.77 % Allowed : 7.37 % Favored : 90.86 % Rotamer: Outliers : 0.05 % Allowed : 1.16 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.09), residues: 8005 helix: 1.18 (0.21), residues: 650 sheet: 0.99 (0.15), residues: 1188 loop : -1.69 (0.07), residues: 6167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 22 HIS 0.009 0.002 HIS W 98 PHE 0.022 0.001 PHE j 130 TYR 0.020 0.002 TYRAB 85 ARG 0.007 0.001 ARG 5 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 566 time to evaluate : 5.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.6353 (t0) cc_final: 0.5500 (t0) REVERT: c 36 ASP cc_start: 0.7361 (t0) cc_final: 0.6880 (t0) REVERT: d 36 ASP cc_start: 0.7229 (t0) cc_final: 0.6884 (t0) REVERT: f 36 ASP cc_start: 0.7279 (t0) cc_final: 0.6574 (t0) REVERT: j 113 LYS cc_start: 0.6564 (mmpt) cc_final: 0.5522 (mmtp) REVERT: F 36 ASP cc_start: 0.6773 (t0) cc_final: 0.6421 (t0) REVERT: G 36 ASP cc_start: 0.6948 (t0) cc_final: 0.6493 (t0) REVERT: I 36 ASP cc_start: 0.7549 (t0) cc_final: 0.7193 (t0) REVERT: I 106 THR cc_start: 0.6333 (p) cc_final: 0.6066 (p) REVERT: J 36 ASP cc_start: 0.7033 (t0) cc_final: 0.6103 (t0) REVERT: Y 36 ASP cc_start: 0.8082 (t70) cc_final: 0.7721 (t70) REVERT: 1 65 ILE cc_start: 0.5129 (tp) cc_final: 0.4768 (tp) REVERT: 8 36 ASP cc_start: 0.6653 (t0) cc_final: 0.6390 (t0) REVERT: l 36 ASP cc_start: 0.6426 (t0) cc_final: 0.5996 (t0) REVERT: m 36 ASP cc_start: 0.8406 (t70) cc_final: 0.8131 (t0) REVERT: o 84 THR cc_start: 0.6952 (p) cc_final: 0.6166 (p) REVERT: z 36 ASP cc_start: 0.6963 (t0) cc_final: 0.6503 (t0) REVERT: AA 36 ASP cc_start: 0.8245 (t70) cc_final: 0.7717 (t0) outliers start: 3 outliers final: 0 residues processed: 568 average time/residue: 0.5740 time to fit residues: 568.5383 Evaluate side-chains 411 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 723 optimal weight: 9.9990 chunk 761 optimal weight: 4.9990 chunk 695 optimal weight: 20.0000 chunk 740 optimal weight: 7.9990 chunk 445 optimal weight: 8.9990 chunk 322 optimal weight: 8.9990 chunk 581 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 669 optimal weight: 40.0000 chunk 700 optimal weight: 40.0000 chunk 738 optimal weight: 40.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 11 ASN e 109 ASN g 81 ASN g 82 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN ** W 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN Y 82 GLN ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 81 ASN ** o 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 11 ASN ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 138 GLN ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN ** AD 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 69 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5142 moved from start: 1.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 63735 Z= 0.209 Angle : 0.617 12.124 87560 Z= 0.315 Chirality : 0.041 0.198 10405 Planarity : 0.005 0.112 11555 Dihedral : 4.317 21.689 9210 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 1.79 % Allowed : 8.37 % Favored : 89.84 % Rotamer: Outliers : 0.02 % Allowed : 0.79 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.09), residues: 8005 helix: 1.10 (0.21), residues: 650 sheet: 0.83 (0.15), residues: 1196 loop : -1.71 (0.07), residues: 6159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 22 HIS 0.009 0.002 HIS W 98 PHE 0.017 0.002 PHEAB 112 TYR 0.029 0.002 TYR u 29 ARG 0.012 0.001 ARG H 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 548 time to evaluate : 4.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.5691 (t0) cc_final: 0.4820 (t0) REVERT: c 36 ASP cc_start: 0.7358 (t0) cc_final: 0.6648 (t0) REVERT: d 36 ASP cc_start: 0.7393 (t0) cc_final: 0.6938 (t0) REVERT: f 36 ASP cc_start: 0.6586 (t0) cc_final: 0.6199 (t0) REVERT: h 36 ASP cc_start: 0.7885 (t0) cc_final: 0.7656 (t0) REVERT: j 27 LYS cc_start: 0.4174 (tmtt) cc_final: 0.3734 (tptp) REVERT: j 65 ILE cc_start: 0.5288 (tp) cc_final: 0.5028 (tp) REVERT: j 113 LYS cc_start: 0.7100 (mmpt) cc_final: 0.6296 (mmtp) REVERT: I 106 THR cc_start: 0.6240 (p) cc_final: 0.5978 (p) REVERT: J 36 ASP cc_start: 0.6842 (t0) cc_final: 0.6014 (t0) REVERT: X 36 ASP cc_start: 0.7375 (t0) cc_final: 0.6988 (t0) REVERT: Y 36 ASP cc_start: 0.8438 (t70) cc_final: 0.8024 (t70) REVERT: 1 65 ILE cc_start: 0.5231 (tp) cc_final: 0.4807 (tp) REVERT: 8 36 ASP cc_start: 0.6655 (t0) cc_final: 0.6384 (t0) REVERT: 8 44 ASN cc_start: 0.2922 (p0) cc_final: 0.2660 (p0) REVERT: l 36 ASP cc_start: 0.7242 (t0) cc_final: 0.6661 (t0) REVERT: m 36 ASP cc_start: 0.8214 (t70) cc_final: 0.7873 (t0) REVERT: z 36 ASP cc_start: 0.6410 (t0) cc_final: 0.6187 (t0) REVERT: AA 36 ASP cc_start: 0.8359 (t70) cc_final: 0.7826 (t0) outliers start: 1 outliers final: 0 residues processed: 549 average time/residue: 0.5381 time to fit residues: 522.3232 Evaluate side-chains 409 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 486 optimal weight: 40.0000 chunk 783 optimal weight: 50.0000 chunk 478 optimal weight: 6.9990 chunk 371 optimal weight: 9.9990 chunk 544 optimal weight: 9.9990 chunk 821 optimal weight: 30.0000 chunk 756 optimal weight: 20.0000 chunk 654 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 505 optimal weight: 7.9990 chunk 401 optimal weight: 50.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 11 ASN g 81 ASN g 82 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 ASN ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN ** W 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 44 ASN ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 76 GLN ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 82 GLN ** p 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 11 ASN ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN AC 14 ASN ** AD 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 98 HIS ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 69 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 moved from start: 1.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 63735 Z= 0.217 Angle : 0.627 13.120 87560 Z= 0.320 Chirality : 0.042 0.288 10405 Planarity : 0.005 0.100 11555 Dihedral : 4.417 30.292 9210 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 1.70 % Allowed : 8.48 % Favored : 89.82 % Rotamer: Outliers : 0.03 % Allowed : 0.44 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.09), residues: 8005 helix: 1.03 (0.21), residues: 650 sheet: 0.68 (0.15), residues: 1200 loop : -1.74 (0.07), residues: 6155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 22 HIS 0.010 0.002 HIS E 33 PHE 0.020 0.002 PHE N 128 TYR 0.033 0.002 TYR u 29 ARG 0.008 0.001 ARG 6 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 545 time to evaluate : 5.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.6176 (t0) cc_final: 0.5593 (t0) REVERT: c 36 ASP cc_start: 0.7511 (t0) cc_final: 0.6833 (t0) REVERT: i 69 TRP cc_start: 0.2059 (m-90) cc_final: 0.1757 (m-90) REVERT: j 61 GLN cc_start: 0.5357 (mp10) cc_final: 0.5073 (pp30) REVERT: j 65 ILE cc_start: 0.5034 (tp) cc_final: 0.4770 (tp) REVERT: J 36 ASP cc_start: 0.6789 (t0) cc_final: 0.5975 (t0) REVERT: U 36 ASP cc_start: 0.7135 (t0) cc_final: 0.6247 (t0) REVERT: W 50 ASN cc_start: 0.5022 (p0) cc_final: 0.4754 (p0) REVERT: X 36 ASP cc_start: 0.7745 (t0) cc_final: 0.7411 (t0) REVERT: 1 14 ASN cc_start: 0.8108 (p0) cc_final: 0.7905 (p0) REVERT: 9 36 ASP cc_start: 0.7108 (t0) cc_final: 0.6813 (t0) REVERT: l 36 ASP cc_start: 0.7482 (t0) cc_final: 0.6925 (t0) REVERT: m 36 ASP cc_start: 0.8148 (t70) cc_final: 0.7778 (t0) REVERT: x 36 ASP cc_start: 0.7196 (t0) cc_final: 0.6885 (t0) REVERT: z 36 ASP cc_start: 0.6948 (t0) cc_final: 0.6696 (t0) REVERT: AA 36 ASP cc_start: 0.8382 (t70) cc_final: 0.7947 (t0) outliers start: 2 outliers final: 0 residues processed: 547 average time/residue: 0.5747 time to fit residues: 560.6709 Evaluate side-chains 405 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 4.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 519 optimal weight: 10.0000 chunk 697 optimal weight: 8.9990 chunk 200 optimal weight: 50.0000 chunk 603 optimal weight: 50.0000 chunk 96 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 655 optimal weight: 5.9990 chunk 274 optimal weight: 30.0000 chunk 673 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 11 ASN g 81 ASN g 82 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 ASN L 76 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN ** W 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 ASN Z 76 GLN ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 44 ASN ** l 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 44 ASN ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 11 ASN ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 11 ASN ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN ** AD 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 98 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.056805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.045860 restraints weight = 1003595.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.045803 restraints weight = 843870.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.045196 restraints weight = 724014.448| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 1.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 63735 Z= 0.187 Angle : 0.602 12.653 87560 Z= 0.306 Chirality : 0.041 0.232 10405 Planarity : 0.005 0.080 11555 Dihedral : 4.326 25.736 9210 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 1.71 % Allowed : 8.46 % Favored : 89.83 % Rotamer: Outliers : 0.08 % Allowed : 0.28 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.09), residues: 8005 helix: 1.03 (0.21), residues: 650 sheet: 0.72 (0.15), residues: 1170 loop : -1.76 (0.07), residues: 6185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 22 HIS 0.010 0.002 HIS Z 98 PHE 0.027 0.002 PHEAC 102 TYR 0.028 0.002 TYR u 29 ARG 0.015 0.001 ARGAB 57 =============================================================================== Job complete usr+sys time: 15149.21 seconds wall clock time: 266 minutes 50.77 seconds (16010.77 seconds total)