Starting phenix.real_space_refine on Mon Mar 18 00:37:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/03_2024/6si7_10206.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/03_2024/6si7_10206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/03_2024/6si7_10206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/03_2024/6si7_10206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/03_2024/6si7_10206.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si7_10206/03_2024/6si7_10206.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 72 5.16 5 C 12321 2.51 5 N 3375 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 124": "OE1" <-> "OE2" Residue "P TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 170": "OE1" <-> "OE2" Residue "P GLU 201": "OE1" <-> "OE2" Residue "J GLU 124": "OE1" <-> "OE2" Residue "J TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J GLU 201": "OE1" <-> "OE2" Residue "K GLU 124": "OE1" <-> "OE2" Residue "K TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 170": "OE1" <-> "OE2" Residue "K GLU 201": "OE1" <-> "OE2" Residue "L GLU 124": "OE1" <-> "OE2" Residue "L TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 170": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 170": "OE1" <-> "OE2" Residue "M GLU 201": "OE1" <-> "OE2" Residue "N GLU 124": "OE1" <-> "OE2" Residue "N TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "N GLU 201": "OE1" <-> "OE2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 170": "OE1" <-> "OE2" Residue "O GLU 201": "OE1" <-> "OE2" Residue "Q GLU 124": "OE1" <-> "OE2" Residue "Q TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 170": "OE1" <-> "OE2" Residue "Q GLU 201": "OE1" <-> "OE2" Residue "R GLU 124": "OE1" <-> "OE2" Residue "R TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 170": "OE1" <-> "OE2" Residue "R GLU 201": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19476 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 269 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "P" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1895 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "B" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 269 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "J" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1895 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 269 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "K" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1895 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "D" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 269 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "L" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1895 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "E" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 269 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "M" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1895 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "F" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 269 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "N" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1895 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "G" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 269 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "O" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1895 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "H" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 269 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "Q" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1895 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Chain: "I" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 269 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "R" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1895 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 230} Chain breaks: 1 Time building chain proxies: 10.09, per 1000 atoms: 0.52 Number of scatterers: 19476 At special positions: 0 Unit cell: (127, 126, 112, 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 72 16.00 O 3708 8.00 N 3375 7.00 C 12321 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: 7.12 Conformation dependent library (CDL) restraints added in 3.6 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4626 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 19 sheets defined 28.1% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS P 22 " --> pdb=" O ALA P 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS P 26 " --> pdb=" O LYS P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL P 69 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR P 70 " --> pdb=" O ALA P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU P 92 " --> pdb=" O ASN P 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE P 95 " --> pdb=" O ASN P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 230 Processing helix chain 'P' and resid 251 through 256 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 74 removed outlier: 4.130A pdb=" N VAL J 69 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE J 95 " --> pdb=" O ASN J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 230 Processing helix chain 'J' and resid 251 through 256 Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS K 22 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL K 69 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU K 92 " --> pdb=" O ASN K 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE K 95 " --> pdb=" O ASN K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 230 Processing helix chain 'K' and resid 251 through 256 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL L 69 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU L 92 " --> pdb=" O ASN L 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE L 95 " --> pdb=" O ASN L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 230 Processing helix chain 'L' and resid 251 through 256 Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS M 26 " --> pdb=" O LYS M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL M 69 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 100 removed outlier: 3.778A pdb=" N GLU M 92 " --> pdb=" O ASN M 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE M 95 " --> pdb=" O ASN M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 230 Processing helix chain 'M' and resid 251 through 256 Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL N 69 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU N 92 " --> pdb=" O ASN N 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE N 95 " --> pdb=" O ASN N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 230 Processing helix chain 'N' and resid 251 through 256 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 18 through 29 removed outlier: 4.549A pdb=" N ASN G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 26 removed outlier: 3.880A pdb=" N LYS O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 74 removed outlier: 4.129A pdb=" N VAL O 69 " --> pdb=" O THR O 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR O 70 " --> pdb=" O ALA O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 100 removed outlier: 3.778A pdb=" N GLU O 92 " --> pdb=" O ASN O 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE O 95 " --> pdb=" O ASN O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 230 Processing helix chain 'O' and resid 251 through 256 Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS Q 22 " --> pdb=" O ALA Q 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS Q 26 " --> pdb=" O LYS Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 74 removed outlier: 4.130A pdb=" N VAL Q 69 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU Q 92 " --> pdb=" O ASN Q 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE Q 95 " --> pdb=" O ASN Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 230 Processing helix chain 'Q' and resid 251 through 256 Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 18 through 29 removed outlier: 4.550A pdb=" N ASN I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 26 removed outlier: 3.879A pdb=" N LYS R 22 " --> pdb=" O ALA R 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS R 26 " --> pdb=" O LYS R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 74 removed outlier: 4.130A pdb=" N VAL R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 100 removed outlier: 3.777A pdb=" N GLU R 92 " --> pdb=" O ASN R 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE R 95 " --> pdb=" O ASN R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 230 Processing helix chain 'R' and resid 251 through 256 Processing sheet with id=AA1, first strand: chain 'P' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE P 35 " --> pdb=" O ILE P 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL P 123 " --> pdb=" O PHE P 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER P 37 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY P 125 " --> pdb=" O SER P 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE P 34 " --> pdb=" O ILE P 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU P 81 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL P 36 " --> pdb=" O LEU P 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA P 158 " --> pdb=" O ILE P 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR P 130 " --> pdb=" O GLN P 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN P 156 " --> pdb=" O TYR P 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE P 157 " --> pdb=" O SER P 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER P 178 " --> pdb=" O ILE P 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL P 159 " --> pdb=" O ASN P 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN P 176 " --> pdb=" O VAL P 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU P 161 " --> pdb=" O SER P 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER P 174 " --> pdb=" O LEU P 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL P 163 " --> pdb=" O LEU P 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 135 through 142 removed outlier: 4.512A pdb=" N LEU P 154 " --> pdb=" O LYS P 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER P 183 " --> pdb=" O GLN P 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR P 184 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU R 154 " --> pdb=" O LYS R 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER R 183 " --> pdb=" O GLN R 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR R 184 " --> pdb=" O SER R 208 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU Q 154 " --> pdb=" O LYS Q 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER Q 183 " --> pdb=" O GLN Q 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR Q 184 " --> pdb=" O SER Q 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU O 154 " --> pdb=" O LYS O 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER O 183 " --> pdb=" O GLN O 153 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR O 184 " --> pdb=" O SER O 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU N 154 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER N 183 " --> pdb=" O GLN N 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR N 184 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU M 154 " --> pdb=" O LYS M 135 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER M 183 " --> pdb=" O GLN M 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR M 184 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU L 154 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER L 183 " --> pdb=" O GLN L 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 184 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU K 154 " --> pdb=" O LYS K 135 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER K 183 " --> pdb=" O GLN K 153 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR K 184 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU J 154 " --> pdb=" O LYS J 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER J 183 " --> pdb=" O GLN J 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR J 184 " --> pdb=" O SER J 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE J 35 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL J 123 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER J 37 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY J 125 " --> pdb=" O SER J 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE J 34 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU J 81 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL J 36 " --> pdb=" O LEU J 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 42 through 43 removed outlier: 6.509A pdb=" N ALA J 158 " --> pdb=" O ILE J 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR J 130 " --> pdb=" O GLN J 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN J 156 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE J 157 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER J 178 " --> pdb=" O ILE J 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL J 159 " --> pdb=" O ASN J 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN J 176 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU J 161 " --> pdb=" O SER J 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER J 174 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL J 163 " --> pdb=" O LEU J 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE K 35 " --> pdb=" O ILE K 121 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL K 123 " --> pdb=" O PHE K 35 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER K 37 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY K 125 " --> pdb=" O SER K 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE K 34 " --> pdb=" O ILE K 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU K 81 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL K 36 " --> pdb=" O LEU K 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA K 158 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR K 130 " --> pdb=" O GLN K 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN K 156 " --> pdb=" O TYR K 130 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE K 157 " --> pdb=" O SER K 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER K 178 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL K 159 " --> pdb=" O ASN K 176 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN K 176 " --> pdb=" O VAL K 159 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU K 161 " --> pdb=" O SER K 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER K 174 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL K 163 " --> pdb=" O LEU K 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE L 35 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL L 123 " --> pdb=" O PHE L 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER L 37 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY L 125 " --> pdb=" O SER L 37 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE L 34 " --> pdb=" O ILE L 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU L 81 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL L 36 " --> pdb=" O LEU L 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA L 158 " --> pdb=" O ILE L 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR L 130 " --> pdb=" O GLN L 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN L 156 " --> pdb=" O TYR L 130 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE L 157 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER L 178 " --> pdb=" O ILE L 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL L 159 " --> pdb=" O ASN L 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN L 176 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU L 161 " --> pdb=" O SER L 174 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER L 174 " --> pdb=" O LEU L 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL L 163 " --> pdb=" O LEU L 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE M 35 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL M 123 " --> pdb=" O PHE M 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER M 37 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY M 125 " --> pdb=" O SER M 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE M 34 " --> pdb=" O ILE M 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU M 81 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL M 36 " --> pdb=" O LEU M 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA M 158 " --> pdb=" O ILE M 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR M 130 " --> pdb=" O GLN M 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN M 156 " --> pdb=" O TYR M 130 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE M 157 " --> pdb=" O SER M 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER M 178 " --> pdb=" O ILE M 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL M 159 " --> pdb=" O ASN M 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN M 176 " --> pdb=" O VAL M 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU M 161 " --> pdb=" O SER M 174 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER M 174 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL M 163 " --> pdb=" O LEU M 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE N 35 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL N 123 " --> pdb=" O PHE N 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER N 37 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY N 125 " --> pdb=" O SER N 37 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE N 34 " --> pdb=" O ILE N 79 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU N 81 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL N 36 " --> pdb=" O LEU N 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA N 158 " --> pdb=" O ILE N 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR N 130 " --> pdb=" O GLN N 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN N 156 " --> pdb=" O TYR N 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE N 157 " --> pdb=" O SER N 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER N 178 " --> pdb=" O ILE N 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL N 159 " --> pdb=" O ASN N 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN N 176 " --> pdb=" O VAL N 159 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU N 161 " --> pdb=" O SER N 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER N 174 " --> pdb=" O LEU N 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL N 163 " --> pdb=" O LEU N 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE O 35 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL O 123 " --> pdb=" O PHE O 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER O 37 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY O 125 " --> pdb=" O SER O 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE O 34 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU O 81 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL O 36 " --> pdb=" O LEU O 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 42 through 43 removed outlier: 6.508A pdb=" N ALA O 158 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR O 130 " --> pdb=" O GLN O 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN O 156 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE O 157 " --> pdb=" O SER O 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER O 178 " --> pdb=" O ILE O 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL O 159 " --> pdb=" O ASN O 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN O 176 " --> pdb=" O VAL O 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU O 161 " --> pdb=" O SER O 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER O 174 " --> pdb=" O LEU O 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL O 163 " --> pdb=" O LEU O 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 42 through 43 removed outlier: 6.404A pdb=" N PHE Q 35 " --> pdb=" O ILE Q 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL Q 123 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER Q 37 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY Q 125 " --> pdb=" O SER Q 37 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE Q 34 " --> pdb=" O ILE Q 79 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU Q 81 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL Q 36 " --> pdb=" O LEU Q 81 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 42 through 43 removed outlier: 6.509A pdb=" N ALA Q 158 " --> pdb=" O ILE Q 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR Q 130 " --> pdb=" O GLN Q 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN Q 156 " --> pdb=" O TYR Q 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE Q 157 " --> pdb=" O SER Q 178 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER Q 178 " --> pdb=" O ILE Q 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL Q 159 " --> pdb=" O ASN Q 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN Q 176 " --> pdb=" O VAL Q 159 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU Q 161 " --> pdb=" O SER Q 174 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER Q 174 " --> pdb=" O LEU Q 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL Q 163 " --> pdb=" O LEU Q 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 42 through 43 removed outlier: 6.403A pdb=" N PHE R 35 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL R 123 " --> pdb=" O PHE R 35 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N SER R 37 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLY R 125 " --> pdb=" O SER R 37 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE R 34 " --> pdb=" O ILE R 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU R 81 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL R 36 " --> pdb=" O LEU R 81 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 42 through 43 removed outlier: 6.509A pdb=" N ALA R 158 " --> pdb=" O ILE R 128 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR R 130 " --> pdb=" O GLN R 156 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN R 156 " --> pdb=" O TYR R 130 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE R 157 " --> pdb=" O SER R 178 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER R 178 " --> pdb=" O ILE R 157 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL R 159 " --> pdb=" O ASN R 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN R 176 " --> pdb=" O VAL R 159 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU R 161 " --> pdb=" O SER R 174 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER R 174 " --> pdb=" O LEU R 161 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL R 163 " --> pdb=" O LEU R 172 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2241 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: 5.63 Time building geometry restraints manager: 7.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6397 1.34 - 1.45: 2857 1.45 - 1.57: 10456 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 19845 Sorted by residual: bond pdb=" CA THR E 2 " pdb=" C THR E 2 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.35e-02 5.49e+03 2.12e+00 bond pdb=" CA THR D 2 " pdb=" C THR D 2 " ideal model delta sigma weight residual 1.526 1.506 0.020 1.35e-02 5.49e+03 2.10e+00 bond pdb=" CA THR F 2 " pdb=" C THR F 2 " ideal model delta sigma weight residual 1.526 1.506 0.019 1.35e-02 5.49e+03 2.08e+00 bond pdb=" CA THR A 2 " pdb=" C THR A 2 " ideal model delta sigma weight residual 1.526 1.506 0.019 1.35e-02 5.49e+03 2.08e+00 bond pdb=" CA THR B 2 " pdb=" C THR B 2 " ideal model delta sigma weight residual 1.526 1.506 0.019 1.35e-02 5.49e+03 2.07e+00 ... (remaining 19840 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.54: 747 106.54 - 113.39: 10472 113.39 - 120.24: 7190 120.24 - 127.09: 8377 127.09 - 133.94: 133 Bond angle restraints: 26919 Sorted by residual: angle pdb=" N THR D 2 " pdb=" CA THR D 2 " pdb=" C THR D 2 " ideal model delta sigma weight residual 111.30 106.28 5.02 1.36e+00 5.41e-01 1.36e+01 angle pdb=" N THR E 2 " pdb=" CA THR E 2 " pdb=" C THR E 2 " ideal model delta sigma weight residual 111.30 106.28 5.02 1.36e+00 5.41e-01 1.36e+01 angle pdb=" N THR F 2 " pdb=" CA THR F 2 " pdb=" C THR F 2 " ideal model delta sigma weight residual 111.30 106.29 5.01 1.36e+00 5.41e-01 1.36e+01 angle pdb=" N THR A 2 " pdb=" CA THR A 2 " pdb=" C THR A 2 " ideal model delta sigma weight residual 111.30 106.29 5.01 1.36e+00 5.41e-01 1.35e+01 angle pdb=" N THR G 2 " pdb=" CA THR G 2 " pdb=" C THR G 2 " ideal model delta sigma weight residual 111.30 106.30 5.00 1.36e+00 5.41e-01 1.35e+01 ... (remaining 26914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 10746 17.63 - 35.27: 990 35.27 - 52.90: 198 52.90 - 70.54: 18 70.54 - 88.17: 27 Dihedral angle restraints: 11979 sinusoidal: 4779 harmonic: 7200 Sorted by residual: dihedral pdb=" CA SER J 126 " pdb=" C SER J 126 " pdb=" N ILE J 127 " pdb=" CA ILE J 127 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA SER Q 126 " pdb=" C SER Q 126 " pdb=" N ILE Q 127 " pdb=" CA ILE Q 127 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA SER N 126 " pdb=" C SER N 126 " pdb=" N ILE N 127 " pdb=" CA ILE N 127 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 11976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1997 0.043 - 0.086: 747 0.086 - 0.129: 204 0.129 - 0.172: 49 0.172 - 0.215: 27 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA VAL R 163 " pdb=" N VAL R 163 " pdb=" C VAL R 163 " pdb=" CB VAL R 163 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA VAL N 163 " pdb=" N VAL N 163 " pdb=" C VAL N 163 " pdb=" CB VAL N 163 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL L 163 " pdb=" N VAL L 163 " pdb=" C VAL L 163 " pdb=" CB VAL L 163 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3021 not shown) Planarity restraints: 3546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY I 1 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C GLY I 1 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY I 1 " -0.017 2.00e-02 2.50e+03 pdb=" N THR I 2 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 1 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C GLY H 1 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY H 1 " -0.017 2.00e-02 2.50e+03 pdb=" N THR H 2 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 1 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C GLY E 1 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY E 1 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 2 " 0.016 2.00e-02 2.50e+03 ... (remaining 3543 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5288 2.79 - 3.32: 18123 3.32 - 3.85: 35588 3.85 - 4.37: 43344 4.37 - 4.90: 72627 Nonbonded interactions: 174970 Sorted by model distance: nonbonded pdb=" OH TYR K 130 " pdb=" OD2 ASP K 155 " model vdw 2.267 2.440 nonbonded pdb=" OH TYR Q 130 " pdb=" OD2 ASP Q 155 " model vdw 2.267 2.440 nonbonded pdb=" OH TYR J 130 " pdb=" OD2 ASP J 155 " model vdw 2.267 2.440 nonbonded pdb=" OH TYR N 130 " pdb=" OD2 ASP N 155 " model vdw 2.267 2.440 nonbonded pdb=" OH TYR P 130 " pdb=" OD2 ASP P 155 " model vdw 2.267 2.440 ... (remaining 174965 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 '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' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.460 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 49.590 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 0.036 19845 Z= 0.291 Angle : 0.792 6.231 26919 Z= 0.476 Chirality : 0.052 0.215 3024 Planarity : 0.006 0.054 3546 Dihedral : 14.712 88.171 7353 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.14), residues: 2448 helix: -4.32 (0.08), residues: 657 sheet: -2.79 (0.18), residues: 657 loop : -2.13 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 77 HIS 0.001 0.000 HIS Q 26 PHE 0.012 0.002 PHE C 21 TYR 0.011 0.001 TYR O 143 ARG 0.003 0.000 ARG Q 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 126 SER cc_start: 0.8480 (m) cc_final: 0.8257 (m) REVERT: J 153 GLN cc_start: 0.7913 (mt0) cc_final: 0.7627 (mt0) REVERT: J 256 MET cc_start: 0.6516 (mtt) cc_final: 0.6271 (mtp) REVERT: K 256 MET cc_start: 0.6591 (mtt) cc_final: 0.6302 (mtp) REVERT: L 153 GLN cc_start: 0.7989 (mt0) cc_final: 0.7701 (mt0) REVERT: L 256 MET cc_start: 0.6559 (mtt) cc_final: 0.6301 (mtp) REVERT: M 40 ASN cc_start: 0.7731 (t0) cc_final: 0.7488 (t0) REVERT: M 256 MET cc_start: 0.6519 (mtt) cc_final: 0.6244 (mtp) REVERT: N 44 GLU cc_start: 0.7176 (pt0) cc_final: 0.6880 (pt0) REVERT: N 67 MET cc_start: 0.8224 (mtt) cc_final: 0.7384 (mtp) REVERT: N 82 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7189 (tm-30) REVERT: N 126 SER cc_start: 0.8329 (m) cc_final: 0.7954 (m) REVERT: N 153 GLN cc_start: 0.7930 (mt0) cc_final: 0.7729 (mt0) REVERT: N 217 MET cc_start: 0.8052 (tpt) cc_final: 0.7148 (tpt) REVERT: N 256 MET cc_start: 0.6548 (mtt) cc_final: 0.6326 (mtp) REVERT: O 165 ASN cc_start: 0.7581 (t0) cc_final: 0.7295 (t0) REVERT: O 256 MET cc_start: 0.6544 (mtt) cc_final: 0.6248 (mtp) REVERT: Q 153 GLN cc_start: 0.7850 (mt0) cc_final: 0.7584 (mt0) REVERT: Q 256 MET cc_start: 0.6629 (mtt) cc_final: 0.6351 (mtp) REVERT: R 82 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7229 (tm-30) REVERT: R 165 ASN cc_start: 0.7602 (t0) cc_final: 0.7357 (t0) REVERT: R 256 MET cc_start: 0.6611 (mtt) cc_final: 0.6387 (mtm) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.3649 time to fit residues: 279.1647 Evaluate side-chains 336 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 220 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN ** P 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN J 133 ASN J 153 GLN J 156 GLN ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** D 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 ASN L 153 GLN L 156 GLN ** E 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 156 GLN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 ASN N 153 GLN N 156 GLN ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN G 29 GLN O 40 ASN O 88 ASN ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 ASN ** Q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 133 ASN Q 153 GLN Q 156 GLN ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN ** R 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 156 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19845 Z= 0.221 Angle : 0.559 8.719 26919 Z= 0.299 Chirality : 0.042 0.148 3024 Planarity : 0.005 0.038 3546 Dihedral : 5.124 18.452 2700 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.53 % Allowed : 15.07 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.15), residues: 2448 helix: -2.80 (0.13), residues: 702 sheet: -2.21 (0.21), residues: 594 loop : -1.89 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 77 HIS 0.001 0.000 HIS R 26 PHE 0.015 0.001 PHE K 191 TYR 0.024 0.001 TYR R 21 ARG 0.006 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 404 time to evaluate : 2.413 Fit side-chains revert: symmetry clash REVERT: P 164 VAL cc_start: 0.8726 (t) cc_final: 0.8471 (t) REVERT: P 217 MET cc_start: 0.8063 (tpp) cc_final: 0.7573 (tpt) REVERT: J 35 PHE cc_start: 0.8581 (m-80) cc_final: 0.8320 (m-80) REVERT: J 131 GLU cc_start: 0.6680 (tp30) cc_final: 0.6464 (tp30) REVERT: J 200 LEU cc_start: 0.7841 (tt) cc_final: 0.7426 (tp) REVERT: J 256 MET cc_start: 0.6644 (mtt) cc_final: 0.6319 (mtp) REVERT: K 152 TYR cc_start: 0.8665 (p90) cc_final: 0.8458 (p90) REVERT: K 217 MET cc_start: 0.8175 (tpt) cc_final: 0.7715 (tpt) REVERT: K 256 MET cc_start: 0.6649 (mtt) cc_final: 0.6321 (mtp) REVERT: D 33 LYS cc_start: 0.7852 (mppt) cc_final: 0.7594 (mmtm) REVERT: L 256 MET cc_start: 0.6501 (mtt) cc_final: 0.6210 (mtp) REVERT: M 82 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7239 (tm-30) REVERT: M 256 MET cc_start: 0.6630 (mtt) cc_final: 0.6326 (mtp) REVERT: N 256 MET cc_start: 0.6497 (mtt) cc_final: 0.6245 (mtp) REVERT: O 124 GLU cc_start: 0.7250 (tp30) cc_final: 0.7024 (tp30) REVERT: O 200 LEU cc_start: 0.7889 (tt) cc_final: 0.7561 (tp) REVERT: O 256 MET cc_start: 0.6626 (mtt) cc_final: 0.6323 (mtp) REVERT: Q 217 MET cc_start: 0.7953 (tpp) cc_final: 0.6866 (tpt) REVERT: Q 256 MET cc_start: 0.6596 (mtt) cc_final: 0.6312 (mtp) REVERT: R 82 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7204 (tm-30) REVERT: R 170 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7052 (mt-10) REVERT: R 200 LEU cc_start: 0.7909 (tt) cc_final: 0.7578 (tp) REVERT: R 217 MET cc_start: 0.8285 (tpt) cc_final: 0.7834 (tpt) REVERT: R 256 MET cc_start: 0.6682 (mtt) cc_final: 0.6349 (mtp) outliers start: 75 outliers final: 33 residues processed: 448 average time/residue: 0.3237 time to fit residues: 217.6982 Evaluate side-chains 370 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 337 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain R residue 44 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 183 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 221 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 219 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 153 GLN P 240 GLN ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 GLN ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19845 Z= 0.229 Angle : 0.539 8.598 26919 Z= 0.284 Chirality : 0.041 0.195 3024 Planarity : 0.004 0.041 3546 Dihedral : 4.917 17.588 2700 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.86 % Allowed : 17.80 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.15), residues: 2448 helix: -1.58 (0.16), residues: 711 sheet: -2.27 (0.20), residues: 594 loop : -1.58 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 237 HIS 0.001 0.000 HIS N 26 PHE 0.012 0.001 PHE R 144 TYR 0.019 0.001 TYR E 32 ARG 0.006 0.000 ARG H 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 375 time to evaluate : 2.285 Fit side-chains revert: symmetry clash REVERT: P 164 VAL cc_start: 0.8781 (t) cc_final: 0.8528 (t) REVERT: P 217 MET cc_start: 0.7958 (tpp) cc_final: 0.7745 (tpt) REVERT: J 35 PHE cc_start: 0.8580 (m-80) cc_final: 0.8266 (m-80) REVERT: J 200 LEU cc_start: 0.8154 (tt) cc_final: 0.7798 (tp) REVERT: J 256 MET cc_start: 0.6689 (mtt) cc_final: 0.6362 (mtp) REVERT: K 152 TYR cc_start: 0.8595 (p90) cc_final: 0.8394 (p90) REVERT: K 217 MET cc_start: 0.8106 (tpt) cc_final: 0.7727 (tpt) REVERT: K 256 MET cc_start: 0.6685 (mtt) cc_final: 0.6348 (mtp) REVERT: D 33 LYS cc_start: 0.7942 (mppt) cc_final: 0.7731 (mmtm) REVERT: L 234 ARG cc_start: 0.6795 (tpp80) cc_final: 0.6545 (tpp80) REVERT: L 256 MET cc_start: 0.6532 (mtt) cc_final: 0.6232 (mtp) REVERT: M 82 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7350 (tm-30) REVERT: M 170 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7084 (mt-10) REVERT: M 256 MET cc_start: 0.6663 (mtt) cc_final: 0.6339 (mtp) REVERT: N 143 TYR cc_start: 0.7958 (t80) cc_final: 0.7751 (t80) REVERT: N 256 MET cc_start: 0.6526 (mtt) cc_final: 0.6321 (mtp) REVERT: O 82 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7219 (tm-30) REVERT: O 217 MET cc_start: 0.8326 (tpt) cc_final: 0.7743 (tpt) REVERT: O 256 MET cc_start: 0.6739 (mtt) cc_final: 0.6461 (mtp) REVERT: H 16 PRO cc_start: 0.9229 (Cg_endo) cc_final: 0.9023 (Cg_exo) REVERT: Q 212 VAL cc_start: 0.9316 (p) cc_final: 0.9074 (t) REVERT: Q 234 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6311 (mtt90) REVERT: Q 256 MET cc_start: 0.6736 (mtt) cc_final: 0.6430 (mtp) REVERT: I 32 TYR cc_start: 0.8347 (m-80) cc_final: 0.7921 (m-80) REVERT: R 82 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7276 (tm-30) REVERT: R 200 LEU cc_start: 0.8093 (tt) cc_final: 0.7732 (tp) REVERT: R 217 MET cc_start: 0.8299 (tpt) cc_final: 0.7935 (tpt) REVERT: R 256 MET cc_start: 0.6644 (mtt) cc_final: 0.6303 (mtp) outliers start: 82 outliers final: 52 residues processed: 426 average time/residue: 0.3287 time to fit residues: 209.7164 Evaluate side-chains 401 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 348 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 234 ARG Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 115 optimal weight: 0.4980 chunk 210 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN M 47 GLN ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19845 Z= 0.323 Angle : 0.560 7.080 26919 Z= 0.298 Chirality : 0.042 0.145 3024 Planarity : 0.004 0.042 3546 Dihedral : 4.975 19.077 2700 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.18 % Allowed : 17.28 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.16), residues: 2448 helix: -0.99 (0.17), residues: 756 sheet: -2.36 (0.19), residues: 594 loop : -1.35 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 237 HIS 0.002 0.001 HIS M 26 PHE 0.017 0.002 PHE O 191 TYR 0.020 0.001 TYR E 32 ARG 0.007 0.001 ARG G 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 413 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: P 131 GLU cc_start: 0.7315 (tp30) cc_final: 0.7090 (tp30) REVERT: P 217 MET cc_start: 0.7996 (tpp) cc_final: 0.7290 (tpt) REVERT: K 82 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7203 (tm-30) REVERT: K 256 MET cc_start: 0.6861 (mtt) cc_final: 0.6514 (mtp) REVERT: D 33 LYS cc_start: 0.8038 (mppt) cc_final: 0.7801 (mmtm) REVERT: L 82 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7237 (tm-30) REVERT: L 234 ARG cc_start: 0.7190 (tpp80) cc_final: 0.6929 (tpp80) REVERT: L 256 MET cc_start: 0.6590 (mtt) cc_final: 0.6271 (mtp) REVERT: E 33 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7981 (mppt) REVERT: M 82 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7457 (tm-30) REVERT: M 131 GLU cc_start: 0.7146 (tp30) cc_final: 0.6929 (tp30) REVERT: M 199 LEU cc_start: 0.8654 (tp) cc_final: 0.8443 (tp) REVERT: M 217 MET cc_start: 0.8203 (tpt) cc_final: 0.7817 (tpt) REVERT: M 256 MET cc_start: 0.6752 (mtt) cc_final: 0.6414 (mtp) REVERT: N 82 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7294 (tm-30) REVERT: N 210 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7709 (mt-10) REVERT: N 256 MET cc_start: 0.6834 (mtt) cc_final: 0.6494 (mtp) REVERT: O 82 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7254 (tm-30) REVERT: O 131 GLU cc_start: 0.6824 (tp30) cc_final: 0.6452 (tp30) REVERT: H 29 GLN cc_start: 0.9134 (pt0) cc_final: 0.8677 (pt0) REVERT: Q 217 MET cc_start: 0.8377 (tpt) cc_final: 0.8042 (tpt) REVERT: Q 234 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6580 (mtt90) REVERT: Q 256 MET cc_start: 0.6779 (mtt) cc_final: 0.6407 (mtp) REVERT: R 82 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7197 (tm-30) REVERT: R 131 GLU cc_start: 0.7192 (tp30) cc_final: 0.6990 (tp30) REVERT: R 170 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7132 (mt-10) REVERT: R 200 LEU cc_start: 0.8468 (tt) cc_final: 0.8202 (tp) REVERT: R 217 MET cc_start: 0.8264 (tpt) cc_final: 0.7843 (tpt) REVERT: R 256 MET cc_start: 0.6801 (mtt) cc_final: 0.6356 (mtp) outliers start: 110 outliers final: 74 residues processed: 492 average time/residue: 0.3301 time to fit residues: 242.0369 Evaluate side-chains 460 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 385 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 153 GLN Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 234 ARG Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 174 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 162 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 ASN ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 153 GLN ** L 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN E 24 ASN ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 153 GLN ** R 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19845 Z= 0.190 Angle : 0.513 6.774 26919 Z= 0.274 Chirality : 0.041 0.152 3024 Planarity : 0.004 0.046 3546 Dihedral : 4.812 18.388 2700 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.38 % Allowed : 19.68 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2448 helix: -0.45 (0.18), residues: 756 sheet: -2.24 (0.19), residues: 594 loop : -1.20 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 237 HIS 0.001 0.000 HIS N 26 PHE 0.027 0.001 PHE O 191 TYR 0.021 0.001 TYR E 32 ARG 0.007 0.000 ARG G 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 412 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 164 VAL cc_start: 0.8743 (t) cc_final: 0.8536 (t) REVERT: B 33 LYS cc_start: 0.8058 (mppt) cc_final: 0.7746 (mmtm) REVERT: J 35 PHE cc_start: 0.8513 (m-80) cc_final: 0.8251 (m-80) REVERT: J 210 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7542 (mt-10) REVERT: J 217 MET cc_start: 0.8271 (tpt) cc_final: 0.7759 (tpt) REVERT: K 82 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7205 (tm-30) REVERT: K 217 MET cc_start: 0.8041 (tpt) cc_final: 0.7136 (tpt) REVERT: K 221 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: K 256 MET cc_start: 0.6809 (mtt) cc_final: 0.6468 (mtp) REVERT: L 234 ARG cc_start: 0.7158 (tpp80) cc_final: 0.6955 (tpp80) REVERT: L 256 MET cc_start: 0.6753 (mtt) cc_final: 0.6433 (mtp) REVERT: M 49 LYS cc_start: 0.9011 (mttm) cc_final: 0.8803 (mttp) REVERT: M 82 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7362 (tm-30) REVERT: M 217 MET cc_start: 0.8162 (tpt) cc_final: 0.7805 (tpt) REVERT: M 256 MET cc_start: 0.6743 (mtt) cc_final: 0.6415 (mtp) REVERT: N 210 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7610 (mt-10) REVERT: N 256 MET cc_start: 0.6800 (mtt) cc_final: 0.6522 (mtp) REVERT: O 82 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7220 (tm-30) REVERT: Q 124 GLU cc_start: 0.7116 (tp30) cc_final: 0.6833 (tp30) REVERT: Q 199 LEU cc_start: 0.8367 (tt) cc_final: 0.8139 (tt) REVERT: Q 217 MET cc_start: 0.8363 (tpt) cc_final: 0.7886 (tpt) REVERT: Q 234 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6466 (mtt90) REVERT: Q 256 MET cc_start: 0.6819 (mtt) cc_final: 0.6493 (mtp) REVERT: R 67 MET cc_start: 0.7992 (mtm) cc_final: 0.7694 (mtm) REVERT: R 82 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7217 (tm-30) REVERT: R 131 GLU cc_start: 0.6983 (tp30) cc_final: 0.6768 (tp30) REVERT: R 170 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7114 (mt-10) REVERT: R 200 LEU cc_start: 0.8332 (tt) cc_final: 0.7993 (tp) REVERT: R 217 MET cc_start: 0.8267 (tpt) cc_final: 0.7724 (tpt) REVERT: R 256 MET cc_start: 0.6769 (mtt) cc_final: 0.6377 (mtp) outliers start: 93 outliers final: 60 residues processed: 470 average time/residue: 0.3670 time to fit residues: 254.3053 Evaluate side-chains 439 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 377 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 217 MET Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 234 ARG Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 235 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 153 GLN B 27 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 ASN ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN ** L 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 153 GLN ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 133 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19845 Z= 0.290 Angle : 0.551 7.344 26919 Z= 0.292 Chirality : 0.042 0.187 3024 Planarity : 0.004 0.044 3546 Dihedral : 4.889 18.782 2700 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 5.18 % Allowed : 19.30 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2448 helix: -0.22 (0.18), residues: 756 sheet: -2.26 (0.19), residues: 594 loop : -1.05 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 77 HIS 0.001 0.000 HIS R 26 PHE 0.027 0.002 PHE L 191 TYR 0.022 0.001 TYR E 32 ARG 0.008 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 417 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: P 124 GLU cc_start: 0.7431 (tp30) cc_final: 0.7023 (tp30) REVERT: P 133 ASN cc_start: 0.8034 (m-40) cc_final: 0.7687 (m-40) REVERT: P 153 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: P 199 LEU cc_start: 0.8490 (tt) cc_final: 0.8132 (tp) REVERT: P 217 MET cc_start: 0.8307 (tpt) cc_final: 0.7915 (tpt) REVERT: B 33 LYS cc_start: 0.8043 (mppt) cc_final: 0.7770 (mmtm) REVERT: J 35 PHE cc_start: 0.8538 (m-80) cc_final: 0.8289 (m-80) REVERT: J 49 LYS cc_start: 0.9077 (mttm) cc_final: 0.8802 (mttp) REVERT: J 82 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7239 (tp30) REVERT: J 122 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7868 (ptm) REVERT: K 35 PHE cc_start: 0.8525 (m-80) cc_final: 0.8253 (m-80) REVERT: K 82 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7247 (tm-30) REVERT: K 217 MET cc_start: 0.8002 (tpt) cc_final: 0.7093 (tpt) REVERT: K 221 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: K 256 MET cc_start: 0.6928 (mtt) cc_final: 0.6551 (mtp) REVERT: L 234 ARG cc_start: 0.7336 (tpp80) cc_final: 0.7127 (tpp80) REVERT: L 256 MET cc_start: 0.6843 (mtt) cc_final: 0.6501 (mtp) REVERT: M 49 LYS cc_start: 0.9037 (mttm) cc_final: 0.8820 (mttp) REVERT: M 82 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7388 (tm-30) REVERT: M 217 MET cc_start: 0.8201 (tpt) cc_final: 0.7881 (tpt) REVERT: M 256 MET cc_start: 0.6742 (mtt) cc_final: 0.6403 (mtp) REVERT: N 82 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7127 (tm-30) REVERT: N 256 MET cc_start: 0.6876 (mtt) cc_final: 0.6526 (mtp) REVERT: O 82 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7213 (tm-30) REVERT: O 135 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7405 (ttmt) REVERT: O 144 PHE cc_start: 0.8123 (t80) cc_final: 0.7777 (t80) REVERT: Q 124 GLU cc_start: 0.7196 (tp30) cc_final: 0.6930 (tp30) REVERT: Q 217 MET cc_start: 0.8395 (tpt) cc_final: 0.7826 (tpt) REVERT: Q 256 MET cc_start: 0.6921 (mtt) cc_final: 0.6558 (mtp) REVERT: R 82 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7202 (tm-30) REVERT: R 131 GLU cc_start: 0.7167 (tp30) cc_final: 0.6897 (tp30) REVERT: R 170 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7129 (mt-10) REVERT: R 217 MET cc_start: 0.8253 (tpt) cc_final: 0.7871 (tpt) REVERT: R 256 MET cc_start: 0.6772 (mtt) cc_final: 0.6335 (mtp) outliers start: 110 outliers final: 82 residues processed: 481 average time/residue: 0.3608 time to fit residues: 254.1123 Evaluate side-chains 467 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 381 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 LYS Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 142 optimal weight: 0.0870 chunk 108 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 153 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 153 GLN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19845 Z= 0.213 Angle : 0.539 9.060 26919 Z= 0.282 Chirality : 0.041 0.177 3024 Planarity : 0.004 0.047 3546 Dihedral : 4.845 18.356 2700 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.90 % Allowed : 20.48 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2448 helix: 0.02 (0.19), residues: 738 sheet: -2.23 (0.19), residues: 594 loop : -0.98 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 237 HIS 0.001 0.000 HIS R 26 PHE 0.026 0.001 PHE L 191 TYR 0.023 0.001 TYR E 32 ARG 0.008 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 401 time to evaluate : 2.221 Fit side-chains REVERT: P 124 GLU cc_start: 0.7390 (tp30) cc_final: 0.7004 (tp30) REVERT: P 210 GLU cc_start: 0.7965 (tt0) cc_final: 0.7709 (tt0) REVERT: P 217 MET cc_start: 0.8301 (tpt) cc_final: 0.7907 (tpt) REVERT: B 33 LYS cc_start: 0.8008 (mppt) cc_final: 0.7731 (mmtm) REVERT: J 35 PHE cc_start: 0.8567 (m-80) cc_final: 0.8339 (m-80) REVERT: J 49 LYS cc_start: 0.9058 (mttm) cc_final: 0.8782 (mttp) REVERT: J 122 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7862 (ptm) REVERT: J 127 ILE cc_start: 0.9056 (mt) cc_final: 0.8779 (mt) REVERT: K 35 PHE cc_start: 0.8528 (m-80) cc_final: 0.8254 (m-80) REVERT: K 82 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7235 (tm-30) REVERT: K 217 MET cc_start: 0.7908 (tpt) cc_final: 0.7015 (tpt) REVERT: K 221 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: K 256 MET cc_start: 0.6930 (mtt) cc_final: 0.6571 (mtp) REVERT: L 67 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7102 (mtp) REVERT: L 142 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7403 (ttt180) REVERT: L 256 MET cc_start: 0.6847 (mtt) cc_final: 0.6512 (mtp) REVERT: M 67 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7168 (ttm) REVERT: M 82 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7316 (tm-30) REVERT: M 217 MET cc_start: 0.8242 (tpt) cc_final: 0.7450 (tpt) REVERT: M 256 MET cc_start: 0.6776 (mtt) cc_final: 0.6494 (mtp) REVERT: N 210 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7487 (mt-10) REVERT: N 256 MET cc_start: 0.6813 (mtt) cc_final: 0.6479 (mtp) REVERT: G 29 GLN cc_start: 0.9082 (pt0) cc_final: 0.8525 (pt0) REVERT: O 82 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7192 (tm-30) REVERT: O 135 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7387 (ttmt) REVERT: Q 124 GLU cc_start: 0.7160 (tp30) cc_final: 0.6748 (tp30) REVERT: Q 256 MET cc_start: 0.6930 (mtt) cc_final: 0.6578 (mtp) REVERT: R 82 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7277 (tp30) REVERT: R 131 GLU cc_start: 0.7053 (tp30) cc_final: 0.6785 (tp30) REVERT: R 200 LEU cc_start: 0.8627 (tt) cc_final: 0.8200 (tp) REVERT: R 217 MET cc_start: 0.8279 (tpt) cc_final: 0.7939 (tpt) REVERT: R 256 MET cc_start: 0.6786 (mtt) cc_final: 0.6356 (mtp) outliers start: 104 outliers final: 83 residues processed: 461 average time/residue: 0.3493 time to fit residues: 236.8980 Evaluate side-chains 466 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 378 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 153 GLN Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 207 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 126 SER Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 208 SER Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 135 LYS Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain O residue 208 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 153 GLN Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 201 GLU Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 153 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN ** K 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 153 GLN E 11 ASN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19845 Z= 0.245 Angle : 0.545 8.350 26919 Z= 0.287 Chirality : 0.042 0.203 3024 Planarity : 0.004 0.047 3546 Dihedral : 4.874 17.978 2700 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 5.13 % Allowed : 20.53 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.17), residues: 2448 helix: 0.11 (0.19), residues: 729 sheet: -2.21 (0.19), residues: 594 loop : -0.83 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 77 HIS 0.001 0.000 HIS K 26 PHE 0.023 0.001 PHE L 191 TYR 0.022 0.001 TYR E 32 ARG 0.009 0.001 ARG I 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 406 time to evaluate : 2.134 Fit side-chains REVERT: P 124 GLU cc_start: 0.7403 (tp30) cc_final: 0.7049 (tp30) REVERT: P 217 MET cc_start: 0.8317 (tpt) cc_final: 0.7975 (tpt) REVERT: B 33 LYS cc_start: 0.8000 (mppt) cc_final: 0.7736 (mmtm) REVERT: J 35 PHE cc_start: 0.8599 (m-80) cc_final: 0.8374 (m-80) REVERT: J 49 LYS cc_start: 0.9069 (mttm) cc_final: 0.8795 (mttp) REVERT: J 122 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7876 (ptm) REVERT: J 127 ILE cc_start: 0.9080 (mt) cc_final: 0.8816 (mt) REVERT: K 35 PHE cc_start: 0.8505 (m-80) cc_final: 0.8228 (m-80) REVERT: K 82 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7249 (tm-30) REVERT: K 217 MET cc_start: 0.7972 (tpt) cc_final: 0.7093 (tpt) REVERT: K 221 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: K 256 MET cc_start: 0.6984 (mtt) cc_final: 0.6619 (mtp) REVERT: L 82 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7270 (tp30) REVERT: L 256 MET cc_start: 0.6848 (mtt) cc_final: 0.6413 (mtp) REVERT: M 17 ARG cc_start: 0.7608 (mmm-85) cc_final: 0.7324 (mmt-90) REVERT: M 67 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.6956 (ttm) REVERT: M 82 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7295 (tm-30) REVERT: M 217 MET cc_start: 0.8259 (tpt) cc_final: 0.7356 (tpt) REVERT: M 256 MET cc_start: 0.6828 (mtt) cc_final: 0.6517 (mtp) REVERT: N 210 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7553 (mt-10) REVERT: N 217 MET cc_start: 0.7614 (tpp) cc_final: 0.7230 (tpp) REVERT: N 256 MET cc_start: 0.6732 (mtt) cc_final: 0.6394 (mtp) REVERT: G 29 GLN cc_start: 0.9097 (pt0) cc_final: 0.8512 (pt0) REVERT: O 33 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8599 (mtmm) REVERT: O 82 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7231 (tm-30) REVERT: O 135 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7401 (ttmt) REVERT: O 144 PHE cc_start: 0.8132 (t80) cc_final: 0.7835 (t80) REVERT: Q 124 GLU cc_start: 0.7175 (tp30) cc_final: 0.6730 (tp30) REVERT: Q 256 MET cc_start: 0.6949 (mtt) cc_final: 0.6595 (mtp) REVERT: R 82 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7228 (tp30) REVERT: R 131 GLU cc_start: 0.7116 (tp30) cc_final: 0.6840 (tp30) REVERT: R 217 MET cc_start: 0.8239 (tpt) cc_final: 0.7949 (tpt) REVERT: R 256 MET cc_start: 0.6802 (mtt) cc_final: 0.6356 (mtp) outliers start: 109 outliers final: 88 residues processed: 467 average time/residue: 0.3444 time to fit residues: 236.0012 Evaluate side-chains 483 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 390 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 208 SER Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 LYS Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain O residue 208 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 153 GLN Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 201 GLU Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.9990 chunk 204 optimal weight: 0.2980 chunk 218 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 197 optimal weight: 0.5980 chunk 206 optimal weight: 0.7980 chunk 217 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19845 Z= 0.206 Angle : 0.541 9.288 26919 Z= 0.283 Chirality : 0.042 0.240 3024 Planarity : 0.004 0.048 3546 Dihedral : 4.860 18.638 2700 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.43 % Allowed : 21.23 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2448 helix: 0.19 (0.19), residues: 729 sheet: -2.11 (0.20), residues: 594 loop : -0.81 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 237 HIS 0.000 0.000 HIS K 26 PHE 0.020 0.001 PHE L 191 TYR 0.022 0.001 TYR E 32 ARG 0.007 0.000 ARG H 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 399 time to evaluate : 2.247 Fit side-chains revert: symmetry clash REVERT: P 124 GLU cc_start: 0.7368 (tp30) cc_final: 0.7101 (tp30) REVERT: P 217 MET cc_start: 0.8308 (tpt) cc_final: 0.7453 (tpt) REVERT: B 33 LYS cc_start: 0.7991 (mppt) cc_final: 0.7728 (mmtm) REVERT: J 49 LYS cc_start: 0.9069 (mttm) cc_final: 0.8815 (mttp) REVERT: J 82 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6675 (tm-30) REVERT: J 122 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7859 (ptm) REVERT: K 35 PHE cc_start: 0.8497 (m-80) cc_final: 0.8253 (m-80) REVERT: K 217 MET cc_start: 0.7979 (tpt) cc_final: 0.7094 (tpt) REVERT: K 221 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: K 256 MET cc_start: 0.6980 (mtt) cc_final: 0.6609 (mtp) REVERT: L 82 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7135 (tp30) REVERT: L 142 ARG cc_start: 0.7582 (ttm-80) cc_final: 0.7323 (ttt180) REVERT: L 256 MET cc_start: 0.6851 (mtt) cc_final: 0.6551 (mtp) REVERT: M 17 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7318 (mmt-90) REVERT: M 67 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7098 (ttm) REVERT: M 82 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7292 (tm-30) REVERT: M 170 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6991 (mt-10) REVERT: M 217 MET cc_start: 0.8266 (tpt) cc_final: 0.7552 (tpt) REVERT: M 256 MET cc_start: 0.6827 (mtt) cc_final: 0.6527 (mtp) REVERT: N 210 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7651 (mt-10) REVERT: N 218 SER cc_start: 0.8916 (t) cc_final: 0.8605 (m) REVERT: N 256 MET cc_start: 0.6700 (mtt) cc_final: 0.6377 (mtp) REVERT: G 29 GLN cc_start: 0.9086 (pt0) cc_final: 0.8476 (pt0) REVERT: O 33 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8575 (mtmm) REVERT: O 82 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7184 (tm-30) REVERT: O 135 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7373 (ttmt) REVERT: O 144 PHE cc_start: 0.8074 (t80) cc_final: 0.7837 (t80) REVERT: Q 124 GLU cc_start: 0.7166 (tp30) cc_final: 0.6749 (tp30) REVERT: Q 256 MET cc_start: 0.6993 (mtt) cc_final: 0.6677 (mtp) REVERT: I 32 TYR cc_start: 0.8342 (m-80) cc_final: 0.8008 (m-80) REVERT: R 82 GLU cc_start: 0.7296 (tm-30) cc_final: 0.7047 (tp30) REVERT: R 217 MET cc_start: 0.8238 (tpt) cc_final: 0.7944 (tpt) REVERT: R 256 MET cc_start: 0.6739 (mtt) cc_final: 0.6321 (mtp) outliers start: 94 outliers final: 72 residues processed: 451 average time/residue: 0.3465 time to fit residues: 229.4732 Evaluate side-chains 463 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 386 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 LYS Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain O residue 208 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 201 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 201 GLU Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 160 optimal weight: 0.0070 chunk 242 optimal weight: 0.9990 chunk 222 optimal weight: 0.3980 chunk 192 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN ** N 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 GLN R 40 ASN R 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19845 Z= 0.214 Angle : 0.557 11.046 26919 Z= 0.288 Chirality : 0.042 0.236 3024 Planarity : 0.004 0.048 3546 Dihedral : 4.874 18.970 2700 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.10 % Allowed : 21.94 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2448 helix: 0.24 (0.19), residues: 729 sheet: -2.04 (0.20), residues: 594 loop : -0.79 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 237 HIS 0.001 0.000 HIS Q 26 PHE 0.020 0.001 PHE L 191 TYR 0.023 0.001 TYR E 32 ARG 0.008 0.000 ARG F 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 394 time to evaluate : 1.972 Fit side-chains REVERT: P 124 GLU cc_start: 0.7361 (tp30) cc_final: 0.7089 (tp30) REVERT: P 142 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7446 (ttt180) REVERT: P 217 MET cc_start: 0.8127 (tpt) cc_final: 0.7618 (tpt) REVERT: B 33 LYS cc_start: 0.7901 (mppt) cc_final: 0.7667 (mmtm) REVERT: J 49 LYS cc_start: 0.9070 (mttm) cc_final: 0.8811 (mttp) REVERT: J 82 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6686 (tm-30) REVERT: J 122 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7826 (ptm) REVERT: K 35 PHE cc_start: 0.8510 (m-80) cc_final: 0.8267 (m-80) REVERT: K 89 LEU cc_start: 0.9192 (tt) cc_final: 0.8987 (tt) REVERT: K 217 MET cc_start: 0.7970 (tpt) cc_final: 0.7068 (tpt) REVERT: K 221 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: K 256 MET cc_start: 0.6964 (mtt) cc_final: 0.6588 (mtp) REVERT: L 82 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7001 (tp30) REVERT: L 142 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7345 (ttt180) REVERT: L 256 MET cc_start: 0.6898 (mtt) cc_final: 0.6604 (mtp) REVERT: M 17 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7326 (mmt-90) REVERT: M 67 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7078 (ttm) REVERT: M 82 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7279 (tm-30) REVERT: M 170 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6988 (mt-10) REVERT: M 217 MET cc_start: 0.8263 (tpt) cc_final: 0.7568 (tpt) REVERT: M 256 MET cc_start: 0.6780 (mtt) cc_final: 0.6472 (mtp) REVERT: N 210 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7591 (mt-10) REVERT: N 218 SER cc_start: 0.8936 (t) cc_final: 0.8736 (m) REVERT: N 256 MET cc_start: 0.6697 (mtt) cc_final: 0.6436 (mtp) REVERT: O 33 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8573 (mtmm) REVERT: O 82 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7181 (tm-30) REVERT: O 124 GLU cc_start: 0.7057 (tp30) cc_final: 0.6704 (tp30) REVERT: O 135 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7356 (ttmt) REVERT: O 144 PHE cc_start: 0.8072 (t80) cc_final: 0.7842 (t80) REVERT: Q 67 MET cc_start: 0.7725 (mtm) cc_final: 0.7404 (mtm) REVERT: Q 124 GLU cc_start: 0.7218 (tp30) cc_final: 0.6741 (tp30) REVERT: Q 142 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.7395 (ttt180) REVERT: Q 217 MET cc_start: 0.7511 (tmm) cc_final: 0.7188 (tpp) REVERT: Q 256 MET cc_start: 0.6997 (mtt) cc_final: 0.6687 (mtp) REVERT: I 32 TYR cc_start: 0.8309 (m-80) cc_final: 0.8026 (m-80) REVERT: R 82 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7015 (tp30) REVERT: R 217 MET cc_start: 0.8201 (tpt) cc_final: 0.7922 (tpt) REVERT: R 256 MET cc_start: 0.6730 (mtt) cc_final: 0.6310 (mtp) outliers start: 87 outliers final: 78 residues processed: 446 average time/residue: 0.3534 time to fit residues: 231.2237 Evaluate side-chains 470 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 387 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 117 THR Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 183 SER Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 183 SER Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 190 VAL Chi-restraints excluded: chain K residue 201 GLU Chi-restraints excluded: chain K residue 221 GLU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 67 MET Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 117 THR Chi-restraints excluded: chain N residue 132 SER Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 208 SER Chi-restraints excluded: chain O residue 33 LYS Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 69 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 135 LYS Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain O residue 208 SER Chi-restraints excluded: chain O residue 213 MET Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 57 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 153 GLN Chi-restraints excluded: chain Q residue 183 SER Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 201 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 183 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 201 GLU Chi-restraints excluded: chain R residue 204 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 177 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 193 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 198 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN M 156 GLN ** M 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.160657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141316 restraints weight = 25131.288| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.56 r_work: 0.3521 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19845 Z= 0.195 Angle : 0.554 9.599 26919 Z= 0.285 Chirality : 0.042 0.245 3024 Planarity : 0.004 0.049 3546 Dihedral : 4.838 18.671 2700 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.91 % Allowed : 22.22 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2448 helix: 0.29 (0.19), residues: 729 sheet: -1.98 (0.20), residues: 594 loop : -0.78 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 237 HIS 0.000 0.000 HIS K 26 PHE 0.019 0.001 PHE L 191 TYR 0.022 0.001 TYR E 32 ARG 0.006 0.000 ARG H 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5012.25 seconds wall clock time: 91 minutes 58.28 seconds (5518.28 seconds total)