Starting phenix.real_space_refine on Sun Feb 18 11:45:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iaw_4440/02_2024/6iaw_4440.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iaw_4440/02_2024/6iaw_4440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iaw_4440/02_2024/6iaw_4440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iaw_4440/02_2024/6iaw_4440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iaw_4440/02_2024/6iaw_4440.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iaw_4440/02_2024/6iaw_4440.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.660 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 73 5.16 5 C 13949 2.51 5 N 3640 2.21 5 O 4267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 220": "NH1" <-> "NH2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 23": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 220": "NH1" <-> "NH2" Residue "M PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 220": "NH1" <-> "NH2" Residue "O TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 23": "NH1" <-> "NH2" Residue "S ARG 8": "NH1" <-> "NH2" Residue "S PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21929 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3190 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 9, 'TRANS': 383} Chain: "B" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "C" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "J" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "I" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 237 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "H" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Chain: "M" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2738 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 8, 'TRANS': 329} Chain: "N" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "O" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "Q" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "S" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "L" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Chain: "X" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "Y" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 79 Classifications: {'peptide': 16} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 15} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 54 Classifications: {'peptide': 12} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 6} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 11.36, per 1000 atoms: 0.52 Number of scatterers: 21929 At special positions: 0 Unit cell: (189.214, 159.45, 120.119, 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 73 16.00 O 4267 8.00 N 3640 7.00 C 13949 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: 8.41 Conformation dependent library (CDL) restraints added in 4.0 seconds 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5322 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 33 sheets defined 26.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 17 through 21 removed outlier: 6.310A pdb=" N ALA A 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 removed outlier: 4.053A pdb=" N HIS A 27 " --> pdb=" O GLN A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.582A pdb=" N LEU A 107 " --> pdb=" O ASN A 104 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 108 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.556A pdb=" N ASN A 141 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.791A pdb=" N ALA A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 182 Processing helix chain 'A' and resid 195 through 205 removed outlier: 4.544A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.883A pdb=" N ARG A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 removed outlier: 5.608A pdb=" N ILE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.635A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 removed outlier: 4.153A pdb=" N HIS B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 104 through 110 removed outlier: 4.046A pdb=" N MET B 108 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.771A pdb=" N PHE B 142 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 182 removed outlier: 3.580A pdb=" N TYR B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.690A pdb=" N SER B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 4.269A pdb=" N ALA B 225 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 226 " --> pdb=" O GLY B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 226' Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.505A pdb=" N LYS B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.585A pdb=" N ALA B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 Processing helix chain 'C' and resid 22 through 27 removed outlier: 4.138A pdb=" N HIS C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.017A pdb=" N LEU C 107 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 145 through 180 removed outlier: 5.076A pdb=" N ILE C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 243 through 257 removed outlier: 5.655A pdb=" N ILE C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 268 removed outlier: 4.181A pdb=" N ASP C 268 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 290 through 299 Processing helix chain 'E' and resid 13 through 17 Processing helix chain 'H' and resid 38 through 53 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 104 through 110 removed outlier: 3.501A pdb=" N LEU M 107 " --> pdb=" O ASN M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 141 removed outlier: 3.890A pdb=" N ASN M 141 " --> pdb=" O ASP M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 182 removed outlier: 3.649A pdb=" N TYR M 156 " --> pdb=" O ALA M 152 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE M 163 " --> pdb=" O LYS M 159 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN M 164 " --> pdb=" O ILE M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 205 removed outlier: 3.513A pdb=" N ILE M 205 " --> pdb=" O VAL M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 221 Processing helix chain 'M' and resid 244 through 258 removed outlier: 5.831A pdb=" N ILE M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ALA M 256 " --> pdb=" O ASP M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 268 removed outlier: 4.138A pdb=" N ASP M 268 " --> pdb=" O ASP M 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 265 through 268' Processing helix chain 'M' and resid 290 through 299 removed outlier: 3.620A pdb=" N ALA M 299 " --> pdb=" O ASP M 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 76 Processing helix chain 'N' and resid 104 through 110 removed outlier: 3.630A pdb=" N LEU N 107 " --> pdb=" O ASN N 104 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS N 110 " --> pdb=" O LEU N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 142 removed outlier: 3.798A pdb=" N PHE N 142 " --> pdb=" O ARG N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 182 removed outlier: 3.969A pdb=" N TYR N 156 " --> pdb=" O ALA N 152 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE N 163 " --> pdb=" O LYS N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 209 removed outlier: 3.700A pdb=" N SER N 199 " --> pdb=" O GLU N 195 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU N 206 " --> pdb=" O PHE N 202 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN N 209 " --> pdb=" O ILE N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 217 through 221 Processing helix chain 'N' and resid 243 through 253 Processing helix chain 'N' and resid 266 through 268 No H-bonds generated for 'chain 'N' and resid 266 through 268' Processing helix chain 'N' and resid 290 through 299 removed outlier: 3.560A pdb=" N ALA N 299 " --> pdb=" O ASP N 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 20 removed outlier: 3.870A pdb=" N LYS O 19 " --> pdb=" O LYS O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 27 removed outlier: 3.603A pdb=" N ASN O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS O 27 " --> pdb=" O GLN O 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 22 through 27' Processing helix chain 'O' and resid 72 through 76 Processing helix chain 'O' and resid 106 through 110 Processing helix chain 'O' and resid 137 through 141 Processing helix chain 'O' and resid 145 through 180 removed outlier: 3.633A pdb=" N THR O 149 " --> pdb=" O LEU O 145 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE O 163 " --> pdb=" O LYS O 159 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN O 164 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 205 Processing helix chain 'O' and resid 217 through 221 Processing helix chain 'O' and resid 244 through 253 Processing helix chain 'O' and resid 266 through 268 No H-bonds generated for 'chain 'O' and resid 266 through 268' Processing helix chain 'O' and resid 290 through 300 removed outlier: 3.704A pdb=" N TYR O 300 " --> pdb=" O PHE O 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 53 Processing helix chain 'X' and resid 121 through 129 removed outlier: 3.584A pdb=" N UNK X 125 " --> pdb=" O UNK X 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 53 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.664A pdb=" N GLU A 88 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N TYR A 85 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR C 61 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU A 87 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 355 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 355 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 190 removed outlier: 5.865A pdb=" N ARG A 189 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE A 271 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 240 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N PHE A 273 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 242 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 279 through 282 removed outlier: 4.807A pdb=" N VAL A 279 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.557A pdb=" N GLU O 87 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR B 61 " --> pdb=" O GLU O 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 78 removed outlier: 6.056A pdb=" N LYS B 77 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 91 Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.545A pdb=" N THR B 394 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE B 271 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 240 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 280 through 282 Processing sheet with id=AB3, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.841A pdb=" N PHE B 286 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 86 through 88 Processing sheet with id=AB5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'C' and resid 189 through 190 removed outlier: 3.612A pdb=" N ILE C 271 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 280 through 282 Processing sheet with id=AB8, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AB9, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AC1, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AC2, first strand: chain 'M' and resid 77 through 78 removed outlier: 3.587A pdb=" N LYS M 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 87 through 91 Processing sheet with id=AC4, first strand: chain 'M' and resid 188 through 190 removed outlier: 5.287A pdb=" N ARG M 189 " --> pdb=" O THR M 394 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TYR M 341 " --> pdb=" O THR M 243 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR M 243 " --> pdb=" O TYR M 341 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 279 through 282 removed outlier: 4.665A pdb=" N VAL M 279 " --> pdb=" O ILE M 334 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 86 through 91 removed outlier: 3.587A pdb=" N GLU N 88 " --> pdb=" O LYS N 119 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 188 through 190 removed outlier: 3.615A pdb=" N THR N 394 " --> pdb=" O ARG N 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 240 through 241 removed outlier: 6.687A pdb=" N ILE N 240 " --> pdb=" O ILE N 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'N' and resid 280 through 282 Processing sheet with id=AD1, first strand: chain 'N' and resid 286 through 287 removed outlier: 3.642A pdb=" N PHE N 286 " --> pdb=" O ILE N 311 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 77 through 78 removed outlier: 5.951A pdb=" N LYS O 77 " --> pdb=" O ARG O 354 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE O 131 " --> pdb=" O HIS O 374 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 189 through 190 removed outlier: 3.563A pdb=" N THR O 394 " --> pdb=" O ARG O 189 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE O 271 " --> pdb=" O ILE O 238 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE O 240 " --> pdb=" O ILE O 271 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE O 273 " --> pdb=" O ILE O 240 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR O 242 " --> pdb=" O PHE O 273 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 280 through 282 Processing sheet with id=AD5, first strand: chain 'L' and resid 21 through 23 Processing sheet with id=AD6, first strand: chain 'K' and resid 21 through 23 641 hydrogen bonds defined for protein. 1665 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: 6.32 Time building geometry restraints manager: 9.06 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: 6956 1.34 - 1.46: 4786 1.46 - 1.58: 10446 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 22334 Sorted by residual: bond pdb=" CG GLU M 168 " pdb=" CD GLU M 168 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.33e+00 bond pdb=" CA ASN A 348 " pdb=" CB ASN A 348 " ideal model delta sigma weight residual 1.532 1.565 -0.032 1.56e-02 4.11e+03 4.24e+00 bond pdb=" CA SER S 14 " pdb=" C SER S 14 " ideal model delta sigma weight residual 1.521 1.548 -0.027 1.38e-02 5.25e+03 3.94e+00 bond pdb=" CA ILE S 45 " pdb=" CB ILE S 45 " ideal model delta sigma weight residual 1.540 1.567 -0.027 1.36e-02 5.41e+03 3.84e+00 bond pdb=" CG1 ILE M 91 " pdb=" CD1 ILE M 91 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.82e+00 ... (remaining 22329 not shown) Histogram of bond angle deviations from ideal: 94.48 - 102.55: 99 102.55 - 110.63: 6493 110.63 - 118.71: 10986 118.71 - 126.79: 12365 126.79 - 134.87: 220 Bond angle restraints: 30163 Sorted by residual: angle pdb=" N SER E 40 " pdb=" CA SER E 40 " pdb=" C SER E 40 " ideal model delta sigma weight residual 107.23 120.29 -13.06 1.67e+00 3.59e-01 6.11e+01 angle pdb=" N GLU C 326 " pdb=" CA GLU C 326 " pdb=" C GLU C 326 " ideal model delta sigma weight residual 111.71 117.97 -6.26 1.15e+00 7.56e-01 2.96e+01 angle pdb=" CG1 ILE I 45 " pdb=" CB ILE I 45 " pdb=" CG2 ILE I 45 " ideal model delta sigma weight residual 110.70 94.48 16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" C GLN S 44 " pdb=" N ILE S 45 " pdb=" CA ILE S 45 " ideal model delta sigma weight residual 121.97 131.68 -9.71 1.80e+00 3.09e-01 2.91e+01 angle pdb=" CA LEU B 183 " pdb=" CB LEU B 183 " pdb=" CG LEU B 183 " ideal model delta sigma weight residual 116.30 134.87 -18.57 3.50e+00 8.16e-02 2.81e+01 ... (remaining 30158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.76: 11955 14.76 - 29.53: 1079 29.53 - 44.29: 349 44.29 - 59.05: 34 59.05 - 73.82: 11 Dihedral angle restraints: 13428 sinusoidal: 5201 harmonic: 8227 Sorted by residual: dihedral pdb=" CA GLN I 44 " pdb=" C GLN I 44 " pdb=" N ILE I 45 " pdb=" CA ILE I 45 " ideal model delta harmonic sigma weight residual 180.00 121.63 58.37 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA GLN S 44 " pdb=" C GLN S 44 " pdb=" N ILE S 45 " pdb=" CA ILE S 45 " ideal model delta harmonic sigma weight residual 180.00 133.29 46.71 0 5.00e+00 4.00e-02 8.73e+01 dihedral pdb=" CA LEU C 206 " pdb=" C LEU C 206 " pdb=" N ASN C 207 " pdb=" CA ASN C 207 " ideal model delta harmonic sigma weight residual 180.00 141.62 38.38 0 5.00e+00 4.00e-02 5.89e+01 ... (remaining 13425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2526 0.073 - 0.145: 715 0.145 - 0.218: 102 0.218 - 0.290: 23 0.290 - 0.363: 4 Chirality restraints: 3370 Sorted by residual: chirality pdb=" CB ILE E 45 " pdb=" CA ILE E 45 " pdb=" CG1 ILE E 45 " pdb=" CG2 ILE E 45 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB ILE D 32 " pdb=" CA ILE D 32 " pdb=" CG1 ILE D 32 " pdb=" CG2 ILE D 32 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE I 45 " pdb=" CA ILE I 45 " pdb=" CG1 ILE I 45 " pdb=" CG2 ILE I 45 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 3367 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN S 44 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C GLN S 44 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN S 44 " 0.028 2.00e-02 2.50e+03 pdb=" N ILE S 45 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 44 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C GLN I 44 " 0.068 2.00e-02 2.50e+03 pdb=" O GLN I 44 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE I 45 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU M 168 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" CD GLU M 168 " -0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU M 168 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU M 168 " 0.019 2.00e-02 2.50e+03 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 6 2.13 - 2.82: 7199 2.82 - 3.52: 30355 3.52 - 4.21: 51276 4.21 - 4.90: 84362 Nonbonded interactions: 173198 Sorted by model distance: nonbonded pdb=" OD2 ASP N 265 " pdb=" CD1 TYR Q 41 " model vdw 1.440 3.340 nonbonded pdb=" OD2 ASP M 265 " pdb=" CD1 TYR S 41 " model vdw 1.454 3.340 nonbonded pdb=" CG2 ILE B 261 " pdb=" OD1 ASP B 265 " model vdw 1.571 3.460 nonbonded pdb=" OD2 ASP B 265 " pdb=" CD1 TYR J 41 " model vdw 1.648 3.340 nonbonded pdb=" CG2 ILE A 261 " pdb=" OD1 ASP A 265 " model vdw 1.886 3.460 ... (remaining 173193 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' and resid 59 through 396) selection = (chain 'B' and resid 59 through 396) selection = (chain 'C' and resid 59 through 396) selection = chain 'M' selection = (chain 'N' and resid 59 through 396) selection = (chain 'O' and resid 59 through 396) } ncs_group { reference = chain 'E' selection = (chain 'I' and resid 1 through 54) selection = (chain 'J' and resid 1 through 54) selection = (chain 'Q' and resid 1 through 54) selection = (chain 'S' and resid 1 through 54) } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'X' and (resid 115 through 129 or (resid 130 and (name N or name CA or na \ me C or name O )))) selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.280 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 56.080 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.120 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.008 0.076 22334 Z= 0.498 Angle : 1.266 18.566 30163 Z= 0.667 Chirality : 0.067 0.363 3370 Planarity : 0.006 0.055 3876 Dihedral : 12.853 73.818 8106 Min Nonbonded Distance : 1.440 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.70 % Favored : 88.10 % Rotamer: Outliers : 1.42 % Allowed : 10.84 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -4.49 (0.13), residues: 2555 helix: -3.11 (0.16), residues: 519 sheet: -2.88 (0.20), residues: 455 loop : -3.10 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 74 HIS 0.019 0.003 HIS S 46 PHE 0.025 0.003 PHE N 343 TYR 0.023 0.003 TYR N 121 ARG 0.017 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 832 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8585 (pt0) cc_final: 0.7567 (mp10) REVERT: A 110 LYS cc_start: 0.7472 (mmpt) cc_final: 0.7188 (mmmt) REVERT: A 127 LYS cc_start: 0.9568 (mptm) cc_final: 0.9206 (mmmm) REVERT: A 163 ILE cc_start: 0.9369 (pp) cc_final: 0.9115 (pt) REVERT: A 174 MET cc_start: 0.7074 (mmp) cc_final: 0.6643 (mmm) REVERT: A 194 LYS cc_start: 0.9142 (tmmt) cc_final: 0.8752 (tptt) REVERT: A 203 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8853 (mt-10) REVERT: A 238 ILE cc_start: 0.9235 (pp) cc_final: 0.9003 (mp) REVERT: A 275 ASP cc_start: 0.8835 (t70) cc_final: 0.8525 (t0) REVERT: A 357 LYS cc_start: 0.9465 (mtpp) cc_final: 0.9062 (mtpp) REVERT: B 94 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8867 (p) REVERT: B 99 MET cc_start: 0.8223 (ppp) cc_final: 0.7656 (tmm) REVERT: B 127 LYS cc_start: 0.9238 (mtpp) cc_final: 0.8630 (mmmm) REVERT: B 139 ARG cc_start: 0.8526 (mmt90) cc_final: 0.8159 (mtp-110) REVERT: B 153 LEU cc_start: 0.8712 (tt) cc_final: 0.8419 (tt) REVERT: B 170 GLU cc_start: 0.9029 (pp20) cc_final: 0.8765 (pp20) REVERT: B 172 ARG cc_start: 0.8990 (ppt-90) cc_final: 0.8539 (ptt90) REVERT: B 220 ARG cc_start: 0.8499 (ttm110) cc_final: 0.8209 (mtm-85) REVERT: B 238 ILE cc_start: 0.9516 (pp) cc_final: 0.9252 (mp) REVERT: B 320 ASP cc_start: 0.8821 (t0) cc_final: 0.8482 (t0) REVERT: C 45 MET cc_start: 0.7919 (mpm) cc_final: 0.7570 (mpp) REVERT: C 94 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8377 (p) REVERT: C 99 MET cc_start: 0.8372 (pmm) cc_final: 0.8164 (pmm) REVERT: C 123 ASN cc_start: 0.9251 (p0) cc_final: 0.8957 (p0) REVERT: C 170 GLU cc_start: 0.8600 (pp20) cc_final: 0.8229 (pp20) REVERT: C 172 ARG cc_start: 0.9310 (ttp80) cc_final: 0.8545 (ptt90) REVERT: C 174 MET cc_start: 0.6788 (mmp) cc_final: 0.6270 (mmp) REVERT: C 244 ASP cc_start: 0.8646 (t70) cc_final: 0.8072 (t0) REVERT: C 320 ASP cc_start: 0.8587 (t70) cc_final: 0.8294 (t70) REVERT: C 370 ASP cc_start: 0.8891 (t0) cc_final: 0.8540 (t70) REVERT: C 391 ILE cc_start: 0.9732 (OUTLIER) cc_final: 0.9489 (mm) REVERT: J 1 MET cc_start: 0.8144 (ttp) cc_final: 0.7762 (tmm) REVERT: J 23 ARG cc_start: 0.8120 (mpp-170) cc_final: 0.7709 (mpt180) REVERT: J 29 ASN cc_start: 0.7988 (t0) cc_final: 0.7571 (t0) REVERT: J 36 LYS cc_start: 0.8989 (tmmm) cc_final: 0.8743 (pttt) REVERT: J 39 ASP cc_start: 0.9038 (p0) cc_final: 0.8730 (p0) REVERT: I 5 ASN cc_start: 0.8800 (t0) cc_final: 0.8498 (t0) REVERT: I 7 MET cc_start: 0.7053 (mmm) cc_final: 0.6712 (mmm) REVERT: E 17 ASP cc_start: 0.8973 (m-30) cc_final: 0.8683 (m-30) REVERT: E 29 ASN cc_start: 0.8829 (m110) cc_final: 0.8574 (m-40) REVERT: M 63 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8899 (tm) REVERT: M 109 LEU cc_start: 0.9428 (mt) cc_final: 0.9141 (tt) REVERT: M 129 GLN cc_start: 0.8330 (tp40) cc_final: 0.7593 (tp-100) REVERT: M 159 LYS cc_start: 0.9527 (ttmp) cc_final: 0.9103 (tppt) REVERT: M 234 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8485 (mmmt) REVERT: M 236 LYS cc_start: 0.9130 (mtmp) cc_final: 0.8909 (mtmm) REVERT: M 268 ASP cc_start: 0.8399 (t0) cc_final: 0.8132 (t70) REVERT: M 289 GLN cc_start: 0.8831 (mp10) cc_final: 0.8456 (mp-120) REVERT: M 291 GLN cc_start: 0.9554 (tp-100) cc_final: 0.9015 (tp-100) REVERT: M 295 ASP cc_start: 0.9303 (p0) cc_final: 0.9005 (p0) REVERT: M 353 LYS cc_start: 0.9209 (mtpp) cc_final: 0.8821 (mtpp) REVERT: M 356 THR cc_start: 0.9267 (p) cc_final: 0.8917 (t) REVERT: M 357 LYS cc_start: 0.8898 (mptt) cc_final: 0.8665 (mmmm) REVERT: M 364 PHE cc_start: 0.9515 (t80) cc_final: 0.9224 (t80) REVERT: M 387 PHE cc_start: 0.9198 (m-80) cc_final: 0.8970 (m-80) REVERT: N 28 ASP cc_start: 0.8774 (p0) cc_final: 0.8563 (p0) REVERT: N 31 LYS cc_start: 0.9002 (tptt) cc_final: 0.8780 (mmtm) REVERT: N 45 MET cc_start: 0.8384 (pmm) cc_final: 0.8001 (mpp) REVERT: N 51 ASN cc_start: 0.9313 (m110) cc_final: 0.8938 (t0) REVERT: N 92 MET cc_start: 0.9290 (mmm) cc_final: 0.8916 (mmm) REVERT: N 94 THR cc_start: 0.9145 (p) cc_final: 0.8386 (p) REVERT: N 97 ILE cc_start: 0.9647 (tt) cc_final: 0.9276 (tp) REVERT: N 126 VAL cc_start: 0.9651 (p) cc_final: 0.9274 (p) REVERT: N 128 LYS cc_start: 0.9498 (mmmt) cc_final: 0.9294 (mmmt) REVERT: N 139 ARG cc_start: 0.8475 (mmt90) cc_final: 0.8078 (mtp-110) REVERT: N 147 ASP cc_start: 0.8920 (p0) cc_final: 0.8437 (p0) REVERT: N 156 TYR cc_start: 0.9244 (t80) cc_final: 0.8713 (t80) REVERT: N 159 LYS cc_start: 0.9215 (ptpt) cc_final: 0.8855 (ttpt) REVERT: N 172 ARG cc_start: 0.9159 (ppt-90) cc_final: 0.8953 (ptt-90) REVERT: N 217 GLU cc_start: 0.7691 (tp30) cc_final: 0.7463 (tp30) REVERT: N 228 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8552 (tm-30) REVERT: N 234 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8787 (mmmt) REVERT: N 237 ASP cc_start: 0.8643 (p0) cc_final: 0.7746 (p0) REVERT: N 281 LYS cc_start: 0.9239 (tptp) cc_final: 0.8760 (tptp) REVERT: N 291 GLN cc_start: 0.9176 (tp40) cc_final: 0.8326 (tm-30) REVERT: N 295 ASP cc_start: 0.9435 (p0) cc_final: 0.8679 (p0) REVERT: N 302 ASP cc_start: 0.8739 (t0) cc_final: 0.8369 (t70) REVERT: N 304 GLN cc_start: 0.8394 (pp30) cc_final: 0.8083 (pp30) REVERT: N 309 ASP cc_start: 0.7553 (m-30) cc_final: 0.7276 (m-30) REVERT: N 346 ASP cc_start: 0.8882 (p0) cc_final: 0.8506 (p0) REVERT: N 387 PHE cc_start: 0.8971 (m-10) cc_final: 0.8547 (m-10) REVERT: O 39 TRP cc_start: 0.9345 (t-100) cc_final: 0.9129 (t-100) REVERT: O 79 GLN cc_start: 0.8556 (mm110) cc_final: 0.8223 (mm110) REVERT: O 97 ILE cc_start: 0.9375 (pp) cc_final: 0.8851 (pp) REVERT: O 108 MET cc_start: 0.8542 (ptm) cc_final: 0.8043 (mtt) REVERT: O 167 GLU cc_start: 0.8475 (tp30) cc_final: 0.7966 (tp30) REVERT: O 203 GLU cc_start: 0.8792 (pp20) cc_final: 0.8471 (pp20) REVERT: O 236 LYS cc_start: 0.9145 (pttp) cc_final: 0.8915 (ptpt) REVERT: O 261 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.4733 (pp) REVERT: Q 20 LEU cc_start: 0.9085 (tt) cc_final: 0.8538 (tt) REVERT: Q 21 ASN cc_start: 0.8282 (t0) cc_final: 0.8026 (t0) REVERT: Q 23 ARG cc_start: 0.8263 (pmm150) cc_final: 0.8003 (pmt170) REVERT: Q 33 ASP cc_start: 0.8282 (t70) cc_final: 0.7945 (t70) REVERT: S 10 MET cc_start: 0.8315 (mpt) cc_final: 0.7812 (mmm) REVERT: S 14 SER cc_start: 0.6663 (m) cc_final: 0.5382 (m) REVERT: S 39 ASP cc_start: 0.8295 (p0) cc_final: 0.8051 (p0) REVERT: S 49 SER cc_start: 0.8937 (t) cc_final: 0.8655 (p) outliers start: 33 outliers final: 2 residues processed: 849 average time/residue: 0.3959 time to fit residues: 486.7912 Evaluate side-chains 594 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 587 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain O residue 261 ILE Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 0.0770 chunk 204 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS A 377 HIS B 70 ASN C 27 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN C 260 GLN I 46 HIS D 46 HIS E 5 ASN M 135 ASN N 219 HIS N 374 HIS O 389 ASN ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 5 ASN S 46 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22334 Z= 0.279 Angle : 0.862 11.769 30163 Z= 0.441 Chirality : 0.048 0.353 3370 Planarity : 0.004 0.064 3876 Dihedral : 7.742 45.376 2984 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.12 % Favored : 88.81 % Rotamer: Outliers : 4.65 % Allowed : 17.94 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.71 (0.15), residues: 2555 helix: -1.68 (0.20), residues: 512 sheet: -2.59 (0.21), residues: 457 loop : -2.82 (0.14), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 74 HIS 0.009 0.001 HIS E 46 PHE 0.021 0.001 PHE A 131 TYR 0.030 0.002 TYR B 249 ARG 0.010 0.001 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 619 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9162 (ptm160) cc_final: 0.8872 (ptm160) REVERT: A 84 GLN cc_start: 0.8649 (pt0) cc_final: 0.7499 (mp10) REVERT: A 110 LYS cc_start: 0.7786 (mmpt) cc_final: 0.7501 (mmmt) REVERT: A 127 LYS cc_start: 0.9541 (mptm) cc_final: 0.9167 (mmmm) REVERT: A 163 ILE cc_start: 0.9298 (pp) cc_final: 0.8864 (pt) REVERT: A 167 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: A 168 GLU cc_start: 0.9291 (tt0) cc_final: 0.8696 (tt0) REVERT: A 275 ASP cc_start: 0.8731 (t70) cc_final: 0.8423 (t0) REVERT: A 357 LYS cc_start: 0.9453 (mtpp) cc_final: 0.8653 (ttmm) REVERT: A 361 LYS cc_start: 0.9304 (mmmt) cc_final: 0.9041 (mmtp) REVERT: A 375 TRP cc_start: 0.8807 (m-90) cc_final: 0.8465 (m-10) REVERT: B 39 TRP cc_start: 0.9496 (t-100) cc_final: 0.9089 (t-100) REVERT: B 92 MET cc_start: 0.9265 (mmm) cc_final: 0.8884 (mmm) REVERT: B 99 MET cc_start: 0.8099 (ppp) cc_final: 0.7386 (tmm) REVERT: B 127 LYS cc_start: 0.9330 (mtpp) cc_final: 0.9008 (mmmm) REVERT: B 139 ARG cc_start: 0.8766 (mmt90) cc_final: 0.8296 (mtp-110) REVERT: B 170 GLU cc_start: 0.8881 (pp20) cc_final: 0.8642 (pp20) REVERT: B 220 ARG cc_start: 0.8483 (ttm110) cc_final: 0.7904 (mtt180) REVERT: B 320 ASP cc_start: 0.8877 (t0) cc_final: 0.8606 (t70) REVERT: B 346 ASP cc_start: 0.8752 (p0) cc_final: 0.8493 (p0) REVERT: C 45 MET cc_start: 0.7904 (mpm) cc_final: 0.7531 (mpp) REVERT: C 75 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8497 (mm) REVERT: C 77 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8703 (mptt) REVERT: C 79 GLN cc_start: 0.8870 (pm20) cc_final: 0.8326 (pm20) REVERT: C 92 MET cc_start: 0.8729 (mmm) cc_final: 0.8435 (mmm) REVERT: C 99 MET cc_start: 0.8433 (pmm) cc_final: 0.8168 (pmm) REVERT: C 110 LYS cc_start: 0.9505 (mtmm) cc_final: 0.9159 (mtmm) REVERT: C 123 ASN cc_start: 0.9296 (p0) cc_final: 0.8981 (p0) REVERT: C 167 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8436 (tp30) REVERT: C 170 GLU cc_start: 0.8747 (pp20) cc_final: 0.8406 (pp20) REVERT: C 174 MET cc_start: 0.6530 (mmp) cc_final: 0.5842 (tpp) REVERT: C 244 ASP cc_start: 0.8531 (t70) cc_final: 0.7745 (t0) REVERT: C 285 GLU cc_start: 0.8264 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 320 ASP cc_start: 0.8504 (t70) cc_final: 0.8302 (t70) REVERT: C 351 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8781 (ptpp) REVERT: C 371 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7996 (mp0) REVERT: J 1 MET cc_start: 0.8099 (ttp) cc_final: 0.7721 (tmm) REVERT: J 10 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7223 (mmm) REVERT: J 23 ARG cc_start: 0.8163 (mpp-170) cc_final: 0.7678 (mpt180) REVERT: J 29 ASN cc_start: 0.7703 (t0) cc_final: 0.7280 (t0) REVERT: J 36 LYS cc_start: 0.9055 (tmmm) cc_final: 0.8706 (pttt) REVERT: I 10 MET cc_start: 0.8553 (mpp) cc_final: 0.8264 (mpp) REVERT: I 41 TYR cc_start: 0.6618 (t80) cc_final: 0.6219 (t80) REVERT: E 8 ARG cc_start: 0.6098 (tmt170) cc_final: 0.5891 (tmt170) REVERT: E 17 ASP cc_start: 0.8880 (m-30) cc_final: 0.8587 (m-30) REVERT: E 36 LYS cc_start: 0.8075 (pttm) cc_final: 0.7717 (pttm) REVERT: M 88 GLU cc_start: 0.8482 (pp20) cc_final: 0.8260 (pp20) REVERT: M 99 MET cc_start: 0.7462 (mmm) cc_final: 0.7182 (mmm) REVERT: M 109 LEU cc_start: 0.9409 (mt) cc_final: 0.9156 (tt) REVERT: M 129 GLN cc_start: 0.8146 (tp40) cc_final: 0.7864 (tp-100) REVERT: M 261 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7727 (pt) REVERT: M 356 THR cc_start: 0.9289 (p) cc_final: 0.8993 (t) REVERT: M 359 MET cc_start: 0.7765 (tmm) cc_final: 0.7549 (tmm) REVERT: M 378 TYR cc_start: 0.9370 (p90) cc_final: 0.8999 (p90) REVERT: N 28 ASP cc_start: 0.8779 (p0) cc_final: 0.8557 (p0) REVERT: N 45 MET cc_start: 0.8445 (pmm) cc_final: 0.8073 (mpp) REVERT: N 51 ASN cc_start: 0.9298 (m110) cc_final: 0.8931 (t0) REVERT: N 92 MET cc_start: 0.9302 (mmm) cc_final: 0.8933 (mmm) REVERT: N 94 THR cc_start: 0.9184 (p) cc_final: 0.8860 (p) REVERT: N 110 LYS cc_start: 0.9289 (tppt) cc_final: 0.9012 (mmtt) REVERT: N 115 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8186 (mtm180) REVERT: N 119 LYS cc_start: 0.8378 (tptt) cc_final: 0.8169 (tppt) REVERT: N 126 VAL cc_start: 0.9436 (p) cc_final: 0.9171 (p) REVERT: N 128 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8904 (mmmt) REVERT: N 129 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7409 (mm-40) REVERT: N 139 ARG cc_start: 0.8493 (mmt90) cc_final: 0.8068 (mtp-110) REVERT: N 147 ASP cc_start: 0.8949 (p0) cc_final: 0.8611 (p0) REVERT: N 156 TYR cc_start: 0.9193 (t80) cc_final: 0.8783 (t80) REVERT: N 168 GLU cc_start: 0.9366 (pp20) cc_final: 0.8908 (pp20) REVERT: N 171 MET cc_start: 0.9097 (ppp) cc_final: 0.8832 (ppp) REVERT: N 202 PHE cc_start: 0.9036 (t80) cc_final: 0.8772 (t80) REVERT: N 203 GLU cc_start: 0.8956 (pp20) cc_final: 0.8652 (tm-30) REVERT: N 217 GLU cc_start: 0.7905 (tp30) cc_final: 0.7468 (tp30) REVERT: N 234 LYS cc_start: 0.9151 (mtpp) cc_final: 0.8704 (mmmt) REVERT: N 237 ASP cc_start: 0.8534 (p0) cc_final: 0.7582 (p0) REVERT: N 284 LYS cc_start: 0.9255 (mtmt) cc_final: 0.8925 (mtmm) REVERT: N 298 ARG cc_start: 0.9125 (mmt-90) cc_final: 0.8871 (mmt-90) REVERT: N 302 ASP cc_start: 0.8533 (t0) cc_final: 0.8333 (t0) REVERT: N 346 ASP cc_start: 0.8716 (p0) cc_final: 0.8057 (p0) REVERT: N 377 HIS cc_start: 0.9130 (m90) cc_final: 0.8861 (m-70) REVERT: O 39 TRP cc_start: 0.9373 (t-100) cc_final: 0.9011 (t-100) REVERT: O 60 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8126 (mm-30) REVERT: O 79 GLN cc_start: 0.8557 (mm110) cc_final: 0.8203 (mm110) REVERT: O 97 ILE cc_start: 0.9543 (pp) cc_final: 0.9134 (mp) REVERT: O 99 MET cc_start: 0.7402 (ppp) cc_final: 0.7096 (ppp) REVERT: O 108 MET cc_start: 0.8478 (ptm) cc_final: 0.7981 (mtt) REVERT: O 110 LYS cc_start: 0.9394 (mmtm) cc_final: 0.8959 (mmtm) REVERT: O 153 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8466 (mm) REVERT: O 203 GLU cc_start: 0.8668 (pp20) cc_final: 0.8344 (pp20) REVERT: O 370 ASP cc_start: 0.8314 (t70) cc_final: 0.8072 (t0) REVERT: Q 21 ASN cc_start: 0.8350 (t0) cc_final: 0.8075 (t0) REVERT: Q 23 ARG cc_start: 0.8281 (pmm150) cc_final: 0.7576 (pmm150) REVERT: Q 33 ASP cc_start: 0.8195 (t70) cc_final: 0.7714 (t70) REVERT: Q 39 ASP cc_start: 0.8303 (t70) cc_final: 0.8063 (t70) REVERT: S 7 MET cc_start: 0.7945 (mmm) cc_final: 0.7683 (mmm) REVERT: S 10 MET cc_start: 0.8317 (mpt) cc_final: 0.7878 (mmt) REVERT: S 49 SER cc_start: 0.8987 (t) cc_final: 0.8734 (p) outliers start: 108 outliers final: 48 residues processed: 681 average time/residue: 0.3939 time to fit residues: 394.5285 Evaluate side-chains 594 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 540 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 351 LYS Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain I residue 6 ASN Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 6 ASN Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 140 PHE Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 237 ASP Chi-restraints excluded: chain M residue 261 ILE Chi-restraints excluded: chain M residue 274 ASP Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 257 ASN Chi-restraints excluded: chain N residue 323 LYS Chi-restraints excluded: chain N residue 325 LYS Chi-restraints excluded: chain N residue 337 LYS Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 268 ASP Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain Q residue 5 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 50.0000 chunk 76 optimal weight: 7.9990 chunk 204 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 265 optimal weight: 40.0000 chunk 218 optimal weight: 8.9990 chunk 243 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN D 44 GLN D 46 HIS E 5 ASN E 29 ASN N 181 ASN N 187 ASN N 374 HIS O 27 HIS ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 22334 Z= 0.398 Angle : 0.858 12.425 30163 Z= 0.442 Chirality : 0.049 0.345 3370 Planarity : 0.004 0.050 3876 Dihedral : 7.153 42.498 2974 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.07 % Favored : 86.89 % Rotamer: Outliers : 5.98 % Allowed : 19.97 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.42 (0.15), residues: 2555 helix: -1.22 (0.21), residues: 536 sheet: -2.39 (0.22), residues: 441 loop : -2.74 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 74 HIS 0.007 0.002 HIS I 46 PHE 0.017 0.002 PHE O 55 TYR 0.020 0.002 TYR E 41 ARG 0.006 0.001 ARG S 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 550 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8742 (pm20) cc_final: 0.8496 (pm20) REVERT: A 71 ARG cc_start: 0.9177 (ptm160) cc_final: 0.8850 (ptm160) REVERT: A 127 LYS cc_start: 0.9553 (mptm) cc_final: 0.9127 (mmmt) REVERT: A 168 GLU cc_start: 0.9366 (tt0) cc_final: 0.9082 (tt0) REVERT: A 241 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9288 (pt) REVERT: A 275 ASP cc_start: 0.8763 (t70) cc_final: 0.8484 (t0) REVERT: A 357 LYS cc_start: 0.9417 (mtpp) cc_final: 0.9129 (mtpp) REVERT: A 361 LYS cc_start: 0.9421 (mmmt) cc_final: 0.9122 (mmmt) REVERT: A 375 TRP cc_start: 0.8977 (m-90) cc_final: 0.8502 (m-10) REVERT: A 391 ILE cc_start: 0.9696 (OUTLIER) cc_final: 0.9480 (mm) REVERT: B 39 TRP cc_start: 0.9537 (t-100) cc_final: 0.9233 (t-100) REVERT: B 79 GLN cc_start: 0.8248 (pp30) cc_final: 0.7933 (pp30) REVERT: B 92 MET cc_start: 0.9255 (mmm) cc_final: 0.8613 (mmm) REVERT: B 99 MET cc_start: 0.8240 (ppp) cc_final: 0.7629 (tmm) REVERT: B 115 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8607 (mtm-85) REVERT: B 139 ARG cc_start: 0.8754 (mmt90) cc_final: 0.8308 (mtp-110) REVERT: B 158 LYS cc_start: 0.9586 (tppt) cc_final: 0.9362 (tptp) REVERT: B 164 ASN cc_start: 0.9094 (m-40) cc_final: 0.8592 (t0) REVERT: B 170 GLU cc_start: 0.8940 (pp20) cc_final: 0.8698 (pp20) REVERT: B 236 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8766 (tppt) REVERT: B 320 ASP cc_start: 0.8766 (t0) cc_final: 0.8532 (t0) REVERT: C 45 MET cc_start: 0.7903 (mpm) cc_final: 0.7484 (mpp) REVERT: C 77 LYS cc_start: 0.9360 (mmmm) cc_final: 0.9055 (mmmm) REVERT: C 79 GLN cc_start: 0.9022 (pm20) cc_final: 0.8326 (pm20) REVERT: C 92 MET cc_start: 0.8720 (mmm) cc_final: 0.8351 (mmm) REVERT: C 123 ASN cc_start: 0.9317 (p0) cc_final: 0.8997 (p0) REVERT: C 167 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8769 (tp30) REVERT: C 170 GLU cc_start: 0.8685 (pp20) cc_final: 0.8450 (pp20) REVERT: C 171 MET cc_start: 0.9331 (tpp) cc_final: 0.9101 (tpp) REVERT: C 172 ARG cc_start: 0.9193 (ttp80) cc_final: 0.8401 (ptt90) REVERT: C 285 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8140 (tm-30) REVERT: J 1 MET cc_start: 0.8132 (ttp) cc_final: 0.7832 (tmm) REVERT: J 10 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7239 (mmm) REVERT: J 23 ARG cc_start: 0.8224 (mpp-170) cc_final: 0.7878 (mpt180) REVERT: J 29 ASN cc_start: 0.7846 (t0) cc_final: 0.7482 (t0) REVERT: J 30 MET cc_start: 0.8816 (tpp) cc_final: 0.8526 (tpp) REVERT: J 36 LYS cc_start: 0.9077 (tmmm) cc_final: 0.8509 (pttt) REVERT: I 10 MET cc_start: 0.8560 (mpp) cc_final: 0.7732 (mpp) REVERT: I 15 TYR cc_start: 0.7445 (t80) cc_final: 0.7229 (t80) REVERT: I 22 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8098 (pmtt) REVERT: D 36 LYS cc_start: 0.7959 (pmtt) cc_final: 0.7702 (pmtt) REVERT: D 46 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6566 (t70) REVERT: E 8 ARG cc_start: 0.6299 (tmt170) cc_final: 0.5904 (tmt170) REVERT: E 17 ASP cc_start: 0.8915 (m-30) cc_final: 0.8576 (m-30) REVERT: E 30 MET cc_start: 0.8456 (tpp) cc_final: 0.8215 (mmm) REVERT: E 36 LYS cc_start: 0.8070 (pttm) cc_final: 0.7696 (pttm) REVERT: M 129 GLN cc_start: 0.8281 (tp40) cc_final: 0.8046 (tp-100) REVERT: M 289 GLN cc_start: 0.8852 (mp10) cc_final: 0.8631 (mp-120) REVERT: M 291 GLN cc_start: 0.9295 (tp-100) cc_final: 0.8871 (tp-100) REVERT: M 295 ASP cc_start: 0.9235 (p0) cc_final: 0.8938 (p0) REVERT: M 354 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8135 (ptt180) REVERT: N 45 MET cc_start: 0.8616 (pmm) cc_final: 0.8165 (mpp) REVERT: N 51 ASN cc_start: 0.9282 (m110) cc_final: 0.8868 (t0) REVERT: N 92 MET cc_start: 0.9363 (mmm) cc_final: 0.8782 (mmm) REVERT: N 115 ARG cc_start: 0.8670 (mtp85) cc_final: 0.8431 (mtm180) REVERT: N 128 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8745 (mmmm) REVERT: N 139 ARG cc_start: 0.8446 (mmt90) cc_final: 0.8085 (mtp-110) REVERT: N 147 ASP cc_start: 0.8929 (p0) cc_final: 0.8706 (p0) REVERT: N 156 TYR cc_start: 0.9259 (t80) cc_final: 0.8903 (t80) REVERT: N 168 GLU cc_start: 0.9436 (pp20) cc_final: 0.9001 (pp20) REVERT: N 171 MET cc_start: 0.9163 (ppp) cc_final: 0.8767 (ppp) REVERT: N 217 GLU cc_start: 0.7823 (tp30) cc_final: 0.7348 (tp30) REVERT: N 234 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8678 (mmmt) REVERT: N 237 ASP cc_start: 0.8582 (p0) cc_final: 0.7557 (p0) REVERT: N 284 LYS cc_start: 0.9289 (mtmt) cc_final: 0.8950 (mtmm) REVERT: N 298 ARG cc_start: 0.8981 (mmt-90) cc_final: 0.8643 (mmt-90) REVERT: N 346 ASP cc_start: 0.8671 (p0) cc_final: 0.8073 (p0) REVERT: O 93 ASP cc_start: 0.8821 (m-30) cc_final: 0.8167 (p0) REVERT: O 99 MET cc_start: 0.7589 (ppp) cc_final: 0.7160 (ppp) REVERT: O 108 MET cc_start: 0.7798 (ptm) cc_final: 0.7469 (mtt) REVERT: O 153 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8675 (mm) REVERT: O 236 LYS cc_start: 0.9257 (pttp) cc_final: 0.9038 (ptpt) REVERT: Q 21 ASN cc_start: 0.8530 (t0) cc_final: 0.8039 (t0) REVERT: Q 23 ARG cc_start: 0.8431 (pmm150) cc_final: 0.7692 (pmm150) REVERT: Q 33 ASP cc_start: 0.8274 (t70) cc_final: 0.7795 (t70) REVERT: Q 39 ASP cc_start: 0.8355 (t70) cc_final: 0.8143 (t70) REVERT: S 10 MET cc_start: 0.7966 (mpt) cc_final: 0.7627 (mmp) REVERT: S 45 ILE cc_start: 0.7419 (mm) cc_final: 0.7176 (mm) outliers start: 139 outliers final: 74 residues processed: 634 average time/residue: 0.3746 time to fit residues: 352.0871 Evaluate side-chains 591 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 510 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 36 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 6 ASN Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 237 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 265 ASP Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 354 ARG Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 177 ASP Chi-restraints excluded: chain N residue 181 ASN Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 231 THR Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 257 ASN Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 309 ASP Chi-restraints excluded: chain N residue 323 LYS Chi-restraints excluded: chain N residue 325 LYS Chi-restraints excluded: chain N residue 337 LYS Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 268 ASP Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 117 optimal weight: 0.0170 chunk 164 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 260 optimal weight: 40.0000 chunk 128 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN B 182 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN D 46 HIS N 219 HIS N 374 HIS O 23 GLN ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22334 Z= 0.205 Angle : 0.789 11.206 30163 Z= 0.396 Chirality : 0.048 0.287 3370 Planarity : 0.003 0.041 3876 Dihedral : 6.704 39.706 2974 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 5.72 % Allowed : 20.87 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.01 (0.15), residues: 2555 helix: -0.83 (0.22), residues: 511 sheet: -2.20 (0.22), residues: 420 loop : -2.46 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 74 HIS 0.013 0.001 HIS D 46 PHE 0.022 0.001 PHE I 53 TYR 0.020 0.002 TYR N 29 ARG 0.016 0.001 ARG O 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 582 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8568 (pt0) cc_final: 0.7676 (mp10) REVERT: A 127 LYS cc_start: 0.9543 (mptm) cc_final: 0.9240 (mmmt) REVERT: A 168 GLU cc_start: 0.9296 (tt0) cc_final: 0.8961 (tt0) REVERT: A 211 ASN cc_start: 0.8973 (m-40) cc_final: 0.8767 (m110) REVERT: A 234 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8643 (mmtt) REVERT: A 275 ASP cc_start: 0.8758 (t70) cc_final: 0.8511 (t0) REVERT: A 357 LYS cc_start: 0.9445 (mtpp) cc_final: 0.9106 (mtpp) REVERT: A 359 MET cc_start: 0.8439 (ttp) cc_final: 0.7812 (ptm) REVERT: A 361 LYS cc_start: 0.9383 (mmmt) cc_final: 0.9069 (mmmt) REVERT: A 375 TRP cc_start: 0.8796 (m-90) cc_final: 0.8395 (m-10) REVERT: A 391 ILE cc_start: 0.9673 (OUTLIER) cc_final: 0.9434 (mm) REVERT: B 31 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7926 (mmtm) REVERT: B 39 TRP cc_start: 0.9521 (t-100) cc_final: 0.9241 (t-100) REVERT: B 79 GLN cc_start: 0.8293 (pp30) cc_final: 0.7891 (pp30) REVERT: B 92 MET cc_start: 0.9188 (mmm) cc_final: 0.8837 (mmm) REVERT: B 99 MET cc_start: 0.8145 (ppp) cc_final: 0.7422 (tmm) REVERT: B 139 ARG cc_start: 0.8764 (mmt90) cc_final: 0.8308 (mtp-110) REVERT: B 158 LYS cc_start: 0.9492 (tppt) cc_final: 0.9205 (tptp) REVERT: B 168 GLU cc_start: 0.8562 (tt0) cc_final: 0.8219 (tt0) REVERT: B 170 GLU cc_start: 0.8929 (pp20) cc_final: 0.8635 (pp20) REVERT: B 236 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8745 (tppt) REVERT: B 320 ASP cc_start: 0.8876 (t0) cc_final: 0.8625 (t0) REVERT: B 346 ASP cc_start: 0.8611 (p0) cc_final: 0.8343 (p0) REVERT: B 360 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8941 (mm) REVERT: B 375 TRP cc_start: 0.8950 (m-90) cc_final: 0.8469 (m-10) REVERT: C 45 MET cc_start: 0.7881 (mpm) cc_final: 0.7440 (mpp) REVERT: C 77 LYS cc_start: 0.9401 (mmmm) cc_final: 0.9054 (mmmm) REVERT: C 79 GLN cc_start: 0.8910 (pm20) cc_final: 0.8230 (pm20) REVERT: C 92 MET cc_start: 0.8660 (mmm) cc_final: 0.8289 (mmm) REVERT: C 108 MET cc_start: 0.8609 (mmm) cc_final: 0.8209 (mmt) REVERT: C 110 LYS cc_start: 0.9525 (mtmt) cc_final: 0.9268 (mtmm) REVERT: C 123 ASN cc_start: 0.9275 (p0) cc_final: 0.9053 (p0) REVERT: C 158 LYS cc_start: 0.9165 (ttpp) cc_final: 0.8845 (ttpp) REVERT: C 167 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8753 (tp30) REVERT: C 168 GLU cc_start: 0.9470 (pp20) cc_final: 0.9030 (pp20) REVERT: C 170 GLU cc_start: 0.8837 (pp20) cc_final: 0.8461 (pp20) REVERT: C 171 MET cc_start: 0.9402 (tpp) cc_final: 0.9154 (tpp) REVERT: C 172 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8465 (ptt90) REVERT: C 285 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8109 (tm-30) REVERT: J 1 MET cc_start: 0.8143 (ttp) cc_final: 0.7876 (tmm) REVERT: J 10 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7018 (mmm) REVERT: J 29 ASN cc_start: 0.7643 (t0) cc_final: 0.7283 (t0) REVERT: J 30 MET cc_start: 0.8692 (tpp) cc_final: 0.8412 (tpp) REVERT: J 36 LYS cc_start: 0.9016 (tmmm) cc_final: 0.8508 (pttt) REVERT: I 10 MET cc_start: 0.8370 (mpp) cc_final: 0.7613 (mpp) REVERT: D 36 LYS cc_start: 0.7804 (pmtt) cc_final: 0.7574 (pmtt) REVERT: E 17 ASP cc_start: 0.8841 (m-30) cc_final: 0.8519 (m-30) REVERT: E 29 ASN cc_start: 0.8506 (m110) cc_final: 0.8296 (m-40) REVERT: M 177 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8861 (p0) REVERT: M 203 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8786 (tm-30) REVERT: M 289 GLN cc_start: 0.8857 (mp10) cc_final: 0.8609 (mp-120) REVERT: M 291 GLN cc_start: 0.9224 (tp-100) cc_final: 0.8706 (tp-100) REVERT: M 295 ASP cc_start: 0.9152 (p0) cc_final: 0.8760 (p0) REVERT: M 378 TYR cc_start: 0.9402 (p90) cc_final: 0.9089 (p90) REVERT: N 45 MET cc_start: 0.8566 (pmm) cc_final: 0.8065 (mpp) REVERT: N 51 ASN cc_start: 0.9236 (m110) cc_final: 0.8804 (t0) REVERT: N 88 GLU cc_start: 0.7297 (pm20) cc_final: 0.7057 (pm20) REVERT: N 92 MET cc_start: 0.9333 (mmm) cc_final: 0.8808 (mmm) REVERT: N 110 LYS cc_start: 0.9297 (tppt) cc_final: 0.8863 (mmtt) REVERT: N 115 ARG cc_start: 0.8642 (mtp85) cc_final: 0.8401 (mtm180) REVERT: N 139 ARG cc_start: 0.8356 (mmt90) cc_final: 0.8042 (mtp-110) REVERT: N 147 ASP cc_start: 0.8883 (p0) cc_final: 0.8663 (p0) REVERT: N 156 TYR cc_start: 0.9152 (t80) cc_final: 0.8893 (t80) REVERT: N 168 GLU cc_start: 0.9421 (pp20) cc_final: 0.8994 (pp20) REVERT: N 171 MET cc_start: 0.9232 (ppp) cc_final: 0.8856 (ppp) REVERT: N 203 GLU cc_start: 0.8860 (pp20) cc_final: 0.8624 (tm-30) REVERT: N 217 GLU cc_start: 0.7905 (tp30) cc_final: 0.7702 (tp30) REVERT: N 220 ARG cc_start: 0.8860 (mtt180) cc_final: 0.8630 (ttm170) REVERT: N 234 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8446 (mmmt) REVERT: N 237 ASP cc_start: 0.8472 (p0) cc_final: 0.7382 (p0) REVERT: N 284 LYS cc_start: 0.9270 (mtmt) cc_final: 0.8902 (mtmm) REVERT: N 346 ASP cc_start: 0.8686 (p0) cc_final: 0.8018 (p0) REVERT: O 99 MET cc_start: 0.7500 (ppp) cc_final: 0.7134 (ppp) REVERT: O 236 LYS cc_start: 0.9192 (pttp) cc_final: 0.8947 (ptpt) REVERT: O 351 LYS cc_start: 0.9204 (ttmm) cc_final: 0.8989 (ttmm) REVERT: O 370 ASP cc_start: 0.8346 (t0) cc_final: 0.8091 (t0) REVERT: Q 23 ARG cc_start: 0.8456 (pmm150) cc_final: 0.7776 (pmm150) REVERT: Q 33 ASP cc_start: 0.8127 (t70) cc_final: 0.7584 (t70) REVERT: Q 39 ASP cc_start: 0.8297 (t70) cc_final: 0.8002 (t70) REVERT: S 10 MET cc_start: 0.7534 (mpt) cc_final: 0.5699 (ptm) outliers start: 133 outliers final: 74 residues processed: 653 average time/residue: 0.3709 time to fit residues: 359.8755 Evaluate side-chains 612 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 533 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 140 PHE Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 177 ASP Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 237 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 265 ASP Chi-restraints excluded: chain M residue 351 LYS Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 104 ASN Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 231 THR Chi-restraints excluded: chain N residue 241 LEU Chi-restraints excluded: chain N residue 257 ASN Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 309 ASP Chi-restraints excluded: chain N residue 323 LYS Chi-restraints excluded: chain N residue 325 LYS Chi-restraints excluded: chain N residue 337 LYS Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 268 ASP Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 194 optimal weight: 0.0030 chunk 107 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 50.0000 chunk 234 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN D 46 HIS E 29 ASN N 187 ASN O 182 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22334 Z= 0.180 Angle : 0.789 12.930 30163 Z= 0.389 Chirality : 0.047 0.239 3370 Planarity : 0.003 0.038 3876 Dihedral : 6.314 34.284 2974 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 5.34 % Allowed : 22.50 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.80 (0.16), residues: 2555 helix: -0.70 (0.23), residues: 509 sheet: -1.94 (0.23), residues: 408 loop : -2.34 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 74 HIS 0.008 0.001 HIS N 377 PHE 0.020 0.001 PHE I 53 TYR 0.026 0.001 TYR O 178 ARG 0.016 0.001 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 588 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9101 (ptm160) cc_final: 0.8600 (ptm160) REVERT: A 84 GLN cc_start: 0.8460 (pt0) cc_final: 0.7607 (mp10) REVERT: A 85 TYR cc_start: 0.8930 (m-80) cc_final: 0.8612 (m-80) REVERT: A 110 LYS cc_start: 0.9033 (mppt) cc_final: 0.8788 (mppt) REVERT: A 127 LYS cc_start: 0.9527 (mptm) cc_final: 0.9078 (mmmm) REVERT: A 160 ILE cc_start: 0.9354 (pp) cc_final: 0.9136 (mt) REVERT: A 168 GLU cc_start: 0.9190 (tt0) cc_final: 0.8960 (tt0) REVERT: A 275 ASP cc_start: 0.8787 (t70) cc_final: 0.8523 (t0) REVERT: A 357 LYS cc_start: 0.9495 (mtpp) cc_final: 0.9098 (mtpp) REVERT: A 359 MET cc_start: 0.7949 (ttp) cc_final: 0.7644 (ptm) REVERT: A 361 LYS cc_start: 0.9440 (mmmt) cc_final: 0.9149 (mmmt) REVERT: A 375 TRP cc_start: 0.8773 (m-90) cc_final: 0.8423 (m-10) REVERT: B 39 TRP cc_start: 0.9524 (t-100) cc_final: 0.9288 (t-100) REVERT: B 79 GLN cc_start: 0.8327 (pp30) cc_final: 0.7970 (pp30) REVERT: B 92 MET cc_start: 0.9142 (mmm) cc_final: 0.8839 (mmm) REVERT: B 99 MET cc_start: 0.8083 (ppp) cc_final: 0.7133 (tmm) REVERT: B 139 ARG cc_start: 0.8744 (mmt90) cc_final: 0.8248 (mtp-110) REVERT: B 158 LYS cc_start: 0.9460 (tppt) cc_final: 0.9163 (tptp) REVERT: B 236 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8744 (tppt) REVERT: B 320 ASP cc_start: 0.8814 (t0) cc_final: 0.8588 (t70) REVERT: B 360 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8902 (mm) REVERT: B 375 TRP cc_start: 0.8820 (m-90) cc_final: 0.8426 (m-10) REVERT: C 45 MET cc_start: 0.7810 (mpm) cc_final: 0.7345 (mpp) REVERT: C 77 LYS cc_start: 0.9430 (mmmm) cc_final: 0.9081 (mmmm) REVERT: C 79 GLN cc_start: 0.8895 (pm20) cc_final: 0.8285 (pm20) REVERT: C 92 MET cc_start: 0.8663 (mmm) cc_final: 0.8275 (mmm) REVERT: C 99 MET cc_start: 0.8584 (pmm) cc_final: 0.8084 (pmm) REVERT: C 108 MET cc_start: 0.8583 (mmm) cc_final: 0.8340 (mmt) REVERT: C 123 ASN cc_start: 0.9254 (p0) cc_final: 0.9046 (p0) REVERT: C 158 LYS cc_start: 0.9085 (ttpp) cc_final: 0.8815 (ttpp) REVERT: C 167 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8744 (tp30) REVERT: C 168 GLU cc_start: 0.9508 (pp20) cc_final: 0.9112 (pp20) REVERT: C 170 GLU cc_start: 0.8859 (pp20) cc_final: 0.8326 (pp20) REVERT: C 171 MET cc_start: 0.9405 (tpp) cc_final: 0.9184 (tpp) REVERT: C 172 ARG cc_start: 0.9184 (ttp80) cc_final: 0.8455 (ptt90) REVERT: C 174 MET cc_start: 0.6613 (tpt) cc_final: 0.6092 (mmp) REVERT: C 285 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8093 (tm-30) REVERT: C 369 PHE cc_start: 0.8485 (m-80) cc_final: 0.8048 (t80) REVERT: C 371 GLU cc_start: 0.8026 (mp0) cc_final: 0.7512 (mp0) REVERT: J 1 MET cc_start: 0.8034 (ttp) cc_final: 0.7798 (tmm) REVERT: J 10 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6776 (mmm) REVERT: J 21 ASN cc_start: 0.9090 (t0) cc_final: 0.8276 (t0) REVERT: J 36 LYS cc_start: 0.8909 (tmmm) cc_final: 0.8564 (pttt) REVERT: I 10 MET cc_start: 0.8098 (mpp) cc_final: 0.7801 (mpp) REVERT: E 36 LYS cc_start: 0.7647 (pttm) cc_final: 0.7396 (pttp) REVERT: M 177 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8850 (p0) REVERT: M 289 GLN cc_start: 0.8850 (mp10) cc_final: 0.8570 (mp-120) REVERT: M 291 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8760 (tp-100) REVERT: M 295 ASP cc_start: 0.9105 (p0) cc_final: 0.8778 (p0) REVERT: M 351 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8862 (mmtt) REVERT: M 378 TYR cc_start: 0.9368 (p90) cc_final: 0.9136 (p90) REVERT: N 45 MET cc_start: 0.8506 (pmm) cc_final: 0.8082 (mpp) REVERT: N 51 ASN cc_start: 0.9189 (m110) cc_final: 0.8706 (t0) REVERT: N 92 MET cc_start: 0.9342 (mmm) cc_final: 0.8470 (mmm) REVERT: N 110 LYS cc_start: 0.9312 (tppt) cc_final: 0.8839 (mmtt) REVERT: N 115 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8308 (mtm180) REVERT: N 139 ARG cc_start: 0.8340 (mmt90) cc_final: 0.7975 (mtp-110) REVERT: N 147 ASP cc_start: 0.8939 (p0) cc_final: 0.8629 (p0) REVERT: N 168 GLU cc_start: 0.9438 (pp20) cc_final: 0.9153 (pt0) REVERT: N 171 MET cc_start: 0.9232 (ppp) cc_final: 0.8820 (ppp) REVERT: N 203 GLU cc_start: 0.8856 (pp20) cc_final: 0.8604 (tm-30) REVERT: N 220 ARG cc_start: 0.8883 (mtt180) cc_final: 0.8668 (ttm170) REVERT: N 234 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8300 (mmmt) REVERT: N 237 ASP cc_start: 0.8329 (p0) cc_final: 0.7258 (p0) REVERT: N 284 LYS cc_start: 0.9223 (mtmt) cc_final: 0.8867 (mtmm) REVERT: N 346 ASP cc_start: 0.8734 (p0) cc_final: 0.8090 (p0) REVERT: N 364 PHE cc_start: 0.8741 (t80) cc_final: 0.8498 (t80) REVERT: O 99 MET cc_start: 0.7517 (ppp) cc_final: 0.7146 (ppp) REVERT: O 197 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9075 (tp) REVERT: O 236 LYS cc_start: 0.9177 (pttp) cc_final: 0.8926 (ptpt) REVERT: O 370 ASP cc_start: 0.8253 (t0) cc_final: 0.7971 (t0) REVERT: Q 16 GLU cc_start: 0.8772 (mp0) cc_final: 0.8202 (pm20) REVERT: Q 23 ARG cc_start: 0.8305 (pmm150) cc_final: 0.7762 (pmm150) REVERT: Q 33 ASP cc_start: 0.8259 (t70) cc_final: 0.7757 (t70) REVERT: Q 39 ASP cc_start: 0.8261 (t70) cc_final: 0.7920 (t70) REVERT: S 10 MET cc_start: 0.7284 (mpt) cc_final: 0.5319 (ptm) REVERT: S 39 ASP cc_start: 0.8455 (p0) cc_final: 0.8214 (p0) outliers start: 124 outliers final: 74 residues processed: 655 average time/residue: 0.3831 time to fit residues: 376.1911 Evaluate side-chains 607 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 528 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 140 PHE Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 177 ASP Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 237 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 351 LYS Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 104 ASN Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 177 ASP Chi-restraints excluded: chain N residue 181 ASN Chi-restraints excluded: chain N residue 231 THR Chi-restraints excluded: chain N residue 257 ASN Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 309 ASP Chi-restraints excluded: chain N residue 323 LYS Chi-restraints excluded: chain N residue 337 LYS Chi-restraints excluded: chain N residue 350 ILE Chi-restraints excluded: chain O residue 64 ILE Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 268 ASP Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 5.9990 chunk 235 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 153 optimal weight: 7.9990 chunk 64 optimal weight: 0.0010 chunk 261 optimal weight: 40.0000 chunk 216 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 137 optimal weight: 40.0000 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 304 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 269 HIS N 164 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22334 Z= 0.178 Angle : 0.792 13.284 30163 Z= 0.389 Chirality : 0.047 0.239 3370 Planarity : 0.003 0.045 3876 Dihedral : 6.064 31.185 2974 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 5.08 % Allowed : 23.24 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.16), residues: 2555 helix: -0.68 (0.23), residues: 521 sheet: -1.73 (0.24), residues: 404 loop : -2.29 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 74 HIS 0.027 0.002 HIS D 46 PHE 0.022 0.001 PHE A 202 TYR 0.025 0.001 TYR O 178 ARG 0.007 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 570 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9057 (ptm160) cc_final: 0.8777 (ptm160) REVERT: A 84 GLN cc_start: 0.8475 (pt0) cc_final: 0.7645 (mp10) REVERT: A 85 TYR cc_start: 0.8913 (m-80) cc_final: 0.8628 (m-80) REVERT: A 127 LYS cc_start: 0.9530 (mptm) cc_final: 0.9224 (mmmt) REVERT: A 160 ILE cc_start: 0.9365 (pp) cc_final: 0.9120 (mt) REVERT: A 238 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 275 ASP cc_start: 0.8801 (t70) cc_final: 0.8512 (t0) REVERT: A 357 LYS cc_start: 0.9470 (mtpp) cc_final: 0.9022 (mtpp) REVERT: A 361 LYS cc_start: 0.9444 (mmmt) cc_final: 0.9140 (mmmt) REVERT: A 375 TRP cc_start: 0.8771 (m-90) cc_final: 0.8405 (m-10) REVERT: B 31 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8145 (mmtm) REVERT: B 78 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7751 (mm-30) REVERT: B 79 GLN cc_start: 0.8350 (pp30) cc_final: 0.8043 (pp30) REVERT: B 92 MET cc_start: 0.9118 (mmm) cc_final: 0.8862 (mmm) REVERT: B 99 MET cc_start: 0.8106 (ppp) cc_final: 0.7333 (tmm) REVERT: B 139 ARG cc_start: 0.8737 (mmt90) cc_final: 0.8258 (mtp-110) REVERT: B 158 LYS cc_start: 0.9451 (tppt) cc_final: 0.9141 (tptp) REVERT: B 236 LYS cc_start: 0.9089 (mmmt) cc_final: 0.8776 (tppt) REVERT: B 238 ILE cc_start: 0.9389 (pp) cc_final: 0.8888 (mp) REVERT: B 320 ASP cc_start: 0.8814 (t0) cc_final: 0.8544 (t0) REVERT: B 346 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8311 (p0) REVERT: B 360 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8832 (mm) REVERT: B 375 TRP cc_start: 0.8843 (m-90) cc_final: 0.8338 (m-10) REVERT: C 45 MET cc_start: 0.7839 (mpm) cc_final: 0.7362 (mpp) REVERT: C 77 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9018 (mmmm) REVERT: C 79 GLN cc_start: 0.8926 (pm20) cc_final: 0.8305 (pm20) REVERT: C 92 MET cc_start: 0.8605 (mmm) cc_final: 0.8239 (mmm) REVERT: C 99 MET cc_start: 0.8576 (pmm) cc_final: 0.7955 (pmm) REVERT: C 108 MET cc_start: 0.8586 (mmm) cc_final: 0.8341 (mmt) REVERT: C 123 ASN cc_start: 0.9260 (p0) cc_final: 0.9055 (p0) REVERT: C 158 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8843 (ttpp) REVERT: C 167 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8786 (tp30) REVERT: C 168 GLU cc_start: 0.9504 (pp20) cc_final: 0.9102 (pp20) REVERT: C 170 GLU cc_start: 0.8851 (pp20) cc_final: 0.8452 (pp20) REVERT: C 171 MET cc_start: 0.9408 (tpp) cc_final: 0.9184 (tpp) REVERT: C 172 ARG cc_start: 0.9201 (ttp80) cc_final: 0.8495 (ptt90) REVERT: C 237 ASP cc_start: 0.7634 (p0) cc_final: 0.7331 (p0) REVERT: C 285 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8062 (tm-30) REVERT: C 369 PHE cc_start: 0.8501 (m-80) cc_final: 0.8124 (t80) REVERT: C 371 GLU cc_start: 0.8071 (mp0) cc_final: 0.7728 (mp0) REVERT: J 1 MET cc_start: 0.8007 (ttp) cc_final: 0.7780 (tmm) REVERT: J 10 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6687 (mmm) REVERT: J 36 LYS cc_start: 0.8857 (tmmm) cc_final: 0.8509 (pttt) REVERT: I 10 MET cc_start: 0.8092 (mpp) cc_final: 0.7545 (mpp) REVERT: D 35 ASN cc_start: 0.8689 (t0) cc_final: 0.8302 (t0) REVERT: M 99 MET cc_start: 0.7288 (tpp) cc_final: 0.7032 (mmm) REVERT: M 177 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8879 (p0) REVERT: M 289 GLN cc_start: 0.8808 (mp10) cc_final: 0.8533 (mp-120) REVERT: M 291 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8813 (tp-100) REVERT: M 295 ASP cc_start: 0.9095 (p0) cc_final: 0.8849 (p0) REVERT: M 351 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8917 (mmtt) REVERT: N 45 MET cc_start: 0.8503 (pmm) cc_final: 0.8097 (mpp) REVERT: N 51 ASN cc_start: 0.9165 (m110) cc_final: 0.8706 (t0) REVERT: N 92 MET cc_start: 0.9317 (mmm) cc_final: 0.8820 (mmm) REVERT: N 110 LYS cc_start: 0.9304 (tppt) cc_final: 0.8842 (mmtt) REVERT: N 115 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8324 (mtm180) REVERT: N 139 ARG cc_start: 0.8330 (mmt90) cc_final: 0.7975 (mtp-110) REVERT: N 147 ASP cc_start: 0.8966 (p0) cc_final: 0.8545 (p0) REVERT: N 168 GLU cc_start: 0.9447 (pp20) cc_final: 0.9025 (pp20) REVERT: N 171 MET cc_start: 0.9232 (ppp) cc_final: 0.8820 (ppp) REVERT: N 220 ARG cc_start: 0.8934 (mtt180) cc_final: 0.8731 (ttm170) REVERT: N 234 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8225 (mmmt) REVERT: N 237 ASP cc_start: 0.8360 (p0) cc_final: 0.7339 (p0) REVERT: N 284 LYS cc_start: 0.9213 (mtmt) cc_final: 0.8847 (mtmm) REVERT: N 298 ARG cc_start: 0.9200 (tpp80) cc_final: 0.8709 (mmt180) REVERT: N 346 ASP cc_start: 0.8744 (p0) cc_final: 0.8132 (p0) REVERT: N 364 PHE cc_start: 0.8732 (t80) cc_final: 0.8465 (t80) REVERT: O 99 MET cc_start: 0.7527 (ppp) cc_final: 0.7204 (ppp) REVERT: O 197 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9047 (tp) REVERT: O 236 LYS cc_start: 0.9179 (pttp) cc_final: 0.8906 (ptpt) REVERT: O 370 ASP cc_start: 0.8310 (t0) cc_final: 0.7977 (t0) REVERT: Q 16 GLU cc_start: 0.8745 (mp0) cc_final: 0.8194 (pm20) REVERT: Q 23 ARG cc_start: 0.8249 (pmm150) cc_final: 0.7872 (pmt170) REVERT: Q 33 ASP cc_start: 0.8253 (t70) cc_final: 0.7622 (t70) REVERT: Q 39 ASP cc_start: 0.8223 (t70) cc_final: 0.7844 (t70) REVERT: S 10 MET cc_start: 0.7271 (mpt) cc_final: 0.5268 (ptm) outliers start: 118 outliers final: 70 residues processed: 634 average time/residue: 0.3794 time to fit residues: 361.3225 Evaluate side-chains 611 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 533 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 140 PHE Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 177 ASP Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 351 LYS Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 104 ASN Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 177 ASP Chi-restraints excluded: chain N residue 181 ASN Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 231 THR Chi-restraints excluded: chain N residue 241 LEU Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 257 ASN Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 285 GLU Chi-restraints excluded: chain N residue 350 ILE Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 207 ASN Chi-restraints excluded: chain O residue 268 ASP Chi-restraints excluded: chain O residue 345 LEU Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 148 optimal weight: 0.0970 chunk 190 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 260 optimal weight: 40.0000 chunk 162 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 HIS N 164 ASN S 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22334 Z= 0.249 Angle : 0.795 12.890 30163 Z= 0.396 Chirality : 0.048 0.267 3370 Planarity : 0.003 0.037 3876 Dihedral : 6.016 34.103 2974 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 5.16 % Allowed : 23.71 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.61 (0.16), residues: 2555 helix: -0.63 (0.23), residues: 528 sheet: -1.79 (0.23), residues: 436 loop : -2.20 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 74 HIS 0.021 0.002 HIS D 46 PHE 0.016 0.001 PHE I 53 TYR 0.027 0.002 TYR B 341 ARG 0.005 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 552 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8622 (pt0) cc_final: 0.7744 (mp10) REVERT: A 85 TYR cc_start: 0.9025 (m-80) cc_final: 0.8727 (m-80) REVERT: A 127 LYS cc_start: 0.9516 (mptm) cc_final: 0.9048 (mmmt) REVERT: A 160 ILE cc_start: 0.9425 (pp) cc_final: 0.9114 (mt) REVERT: A 211 ASN cc_start: 0.8603 (m-40) cc_final: 0.8362 (m-40) REVERT: A 238 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8733 (mp) REVERT: A 275 ASP cc_start: 0.8843 (t70) cc_final: 0.8557 (t0) REVERT: A 357 LYS cc_start: 0.9495 (mtpp) cc_final: 0.9098 (mtpp) REVERT: A 361 LYS cc_start: 0.9472 (mmmt) cc_final: 0.9216 (mmmt) REVERT: A 375 TRP cc_start: 0.8831 (m-90) cc_final: 0.8453 (m-10) REVERT: B 79 GLN cc_start: 0.8344 (pp30) cc_final: 0.8024 (pp30) REVERT: B 92 MET cc_start: 0.9171 (mmm) cc_final: 0.8922 (mmm) REVERT: B 99 MET cc_start: 0.8172 (ppp) cc_final: 0.7365 (tmm) REVERT: B 158 LYS cc_start: 0.9480 (tppt) cc_final: 0.9134 (tptp) REVERT: B 187 ASN cc_start: 0.9124 (m110) cc_final: 0.8737 (m-40) REVERT: B 236 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8733 (mmmt) REVERT: B 238 ILE cc_start: 0.9407 (pp) cc_final: 0.8963 (mp) REVERT: B 320 ASP cc_start: 0.8850 (t0) cc_final: 0.8593 (t0) REVERT: B 346 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8323 (p0) REVERT: B 360 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8843 (mm) REVERT: B 375 TRP cc_start: 0.8891 (m-90) cc_final: 0.8489 (m-10) REVERT: C 45 MET cc_start: 0.7814 (mpm) cc_final: 0.7320 (mpp) REVERT: C 77 LYS cc_start: 0.9474 (mmmm) cc_final: 0.9071 (mmmm) REVERT: C 79 GLN cc_start: 0.9000 (pm20) cc_final: 0.8349 (pm20) REVERT: C 92 MET cc_start: 0.8550 (mmm) cc_final: 0.8148 (mmm) REVERT: C 99 MET cc_start: 0.8509 (pmm) cc_final: 0.7879 (ppp) REVERT: C 108 MET cc_start: 0.8591 (mmm) cc_final: 0.8336 (mmt) REVERT: C 123 ASN cc_start: 0.9257 (p0) cc_final: 0.9042 (p0) REVERT: C 158 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8850 (ttpp) REVERT: C 167 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8732 (tp30) REVERT: C 168 GLU cc_start: 0.9507 (pp20) cc_final: 0.9093 (pp20) REVERT: C 170 GLU cc_start: 0.8893 (pp20) cc_final: 0.8450 (pp20) REVERT: C 171 MET cc_start: 0.9437 (tpp) cc_final: 0.9164 (tpp) REVERT: C 172 ARG cc_start: 0.9241 (ttp80) cc_final: 0.8480 (ptt90) REVERT: C 285 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 346 ASP cc_start: 0.7731 (t0) cc_final: 0.7419 (t0) REVERT: C 369 PHE cc_start: 0.8512 (m-80) cc_final: 0.8188 (t80) REVERT: J 1 MET cc_start: 0.7986 (ttp) cc_final: 0.7327 (tmm) REVERT: J 10 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6944 (mmm) REVERT: I 10 MET cc_start: 0.8174 (mpp) cc_final: 0.7550 (mpp) REVERT: I 36 LYS cc_start: 0.8532 (pttm) cc_final: 0.8316 (pttm) REVERT: D 35 ASN cc_start: 0.8646 (t0) cc_final: 0.8433 (t0) REVERT: M 88 GLU cc_start: 0.8561 (pp20) cc_final: 0.8316 (pp20) REVERT: M 89 TYR cc_start: 0.9105 (p90) cc_final: 0.8749 (p90) REVERT: M 99 MET cc_start: 0.7411 (tpp) cc_final: 0.7041 (mmm) REVERT: M 229 TYR cc_start: 0.9038 (t80) cc_final: 0.8773 (t80) REVERT: M 289 GLN cc_start: 0.8861 (mp10) cc_final: 0.8604 (mp-120) REVERT: M 291 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8606 (tp-100) REVERT: M 295 ASP cc_start: 0.9099 (p0) cc_final: 0.8643 (p0) REVERT: M 351 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8907 (mmtt) REVERT: N 45 MET cc_start: 0.8625 (pmm) cc_final: 0.8197 (mpp) REVERT: N 51 ASN cc_start: 0.9165 (m110) cc_final: 0.8765 (t0) REVERT: N 92 MET cc_start: 0.9362 (mmm) cc_final: 0.8802 (mmm) REVERT: N 110 LYS cc_start: 0.9291 (tppt) cc_final: 0.8823 (mmtt) REVERT: N 115 ARG cc_start: 0.8568 (mtp85) cc_final: 0.8244 (mtm180) REVERT: N 139 ARG cc_start: 0.8367 (mmt90) cc_final: 0.7866 (mtp-110) REVERT: N 147 ASP cc_start: 0.9003 (p0) cc_final: 0.8612 (p0) REVERT: N 168 GLU cc_start: 0.9480 (pp20) cc_final: 0.9056 (pp20) REVERT: N 171 MET cc_start: 0.9241 (ppp) cc_final: 0.8845 (ppp) REVERT: N 203 GLU cc_start: 0.8847 (pp20) cc_final: 0.8583 (pp20) REVERT: N 234 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8326 (mmmt) REVERT: N 237 ASP cc_start: 0.8501 (p0) cc_final: 0.7567 (p0) REVERT: N 284 LYS cc_start: 0.9282 (mtmt) cc_final: 0.8918 (mtmm) REVERT: N 298 ARG cc_start: 0.9233 (tpp80) cc_final: 0.8713 (mmt-90) REVERT: N 346 ASP cc_start: 0.8768 (p0) cc_final: 0.8264 (p0) REVERT: O 99 MET cc_start: 0.7647 (ppp) cc_final: 0.7292 (ppp) REVERT: O 197 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9108 (tp) REVERT: O 202 PHE cc_start: 0.9392 (t80) cc_final: 0.9170 (t80) REVERT: O 229 TYR cc_start: 0.9025 (t80) cc_final: 0.8795 (t80) REVERT: O 236 LYS cc_start: 0.9198 (pttp) cc_final: 0.8927 (ptpt) REVERT: O 370 ASP cc_start: 0.8487 (t0) cc_final: 0.8176 (t0) REVERT: Q 23 ARG cc_start: 0.8267 (pmm150) cc_final: 0.7901 (pmt170) REVERT: Q 33 ASP cc_start: 0.8347 (t70) cc_final: 0.7735 (t70) REVERT: Q 39 ASP cc_start: 0.8213 (t70) cc_final: 0.7838 (t70) REVERT: S 10 MET cc_start: 0.7391 (mpt) cc_final: 0.5482 (ptm) outliers start: 120 outliers final: 85 residues processed: 614 average time/residue: 0.3539 time to fit residues: 326.2859 Evaluate side-chains 615 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 524 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 237 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 351 LYS Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 104 ASN Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 169 LYS Chi-restraints excluded: chain N residue 177 ASP Chi-restraints excluded: chain N residue 181 ASN Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 231 THR Chi-restraints excluded: chain N residue 241 LEU Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 257 ASN Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 309 ASP Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 207 ASN Chi-restraints excluded: chain O residue 268 ASP Chi-restraints excluded: chain O residue 345 LEU Chi-restraints excluded: chain O residue 350 ILE Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 49 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 7.9990 chunk 103 optimal weight: 0.4980 chunk 155 optimal weight: 7.9990 chunk 78 optimal weight: 0.1980 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 ASN ** N 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22334 Z= 0.257 Angle : 0.813 12.776 30163 Z= 0.407 Chirality : 0.048 0.254 3370 Planarity : 0.003 0.039 3876 Dihedral : 6.022 38.431 2974 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 5.16 % Allowed : 24.23 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.61 (0.16), residues: 2555 helix: -0.70 (0.22), residues: 534 sheet: -1.72 (0.23), residues: 436 loop : -2.21 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 74 HIS 0.027 0.002 HIS D 46 PHE 0.019 0.001 PHE A 202 TYR 0.030 0.002 TYR O 178 ARG 0.007 0.001 ARG M 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 530 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.0166 (OUTLIER) cc_final: -0.1417 (t0) REVERT: A 127 LYS cc_start: 0.9518 (mptm) cc_final: 0.9027 (mmmt) REVERT: A 160 ILE cc_start: 0.9434 (pp) cc_final: 0.9108 (mt) REVERT: A 168 GLU cc_start: 0.9363 (tt0) cc_final: 0.9082 (tt0) REVERT: A 275 ASP cc_start: 0.8868 (t70) cc_final: 0.8590 (t0) REVERT: A 357 LYS cc_start: 0.9484 (mtpp) cc_final: 0.8908 (mtpp) REVERT: A 361 LYS cc_start: 0.9509 (mmmt) cc_final: 0.9236 (mmmt) REVERT: A 375 TRP cc_start: 0.8788 (m-90) cc_final: 0.8293 (m-10) REVERT: A 391 ILE cc_start: 0.9781 (mt) cc_final: 0.9557 (mp) REVERT: B 78 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7924 (tp30) REVERT: B 79 GLN cc_start: 0.8354 (pp30) cc_final: 0.8025 (pp30) REVERT: B 92 MET cc_start: 0.9172 (mmm) cc_final: 0.8901 (mmm) REVERT: B 99 MET cc_start: 0.8223 (ppp) cc_final: 0.7707 (ppp) REVERT: B 158 LYS cc_start: 0.9482 (tppt) cc_final: 0.9223 (tptp) REVERT: B 187 ASN cc_start: 0.9134 (m110) cc_final: 0.8735 (m-40) REVERT: B 236 LYS cc_start: 0.9099 (mmmt) cc_final: 0.8742 (mmmt) REVERT: B 238 ILE cc_start: 0.9400 (pp) cc_final: 0.8958 (mp) REVERT: B 320 ASP cc_start: 0.8795 (t0) cc_final: 0.8511 (t0) REVERT: B 346 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8292 (p0) REVERT: B 360 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8864 (mm) REVERT: B 375 TRP cc_start: 0.8893 (m-90) cc_final: 0.8497 (m-10) REVERT: C 45 MET cc_start: 0.7815 (mpm) cc_final: 0.7327 (mpp) REVERT: C 77 LYS cc_start: 0.9475 (mmmm) cc_final: 0.9088 (mmmm) REVERT: C 79 GLN cc_start: 0.8995 (pm20) cc_final: 0.8362 (pm20) REVERT: C 99 MET cc_start: 0.8496 (pmm) cc_final: 0.7863 (ppp) REVERT: C 108 MET cc_start: 0.8599 (mmm) cc_final: 0.8340 (mmt) REVERT: C 158 LYS cc_start: 0.9089 (ttpp) cc_final: 0.8874 (ttpp) REVERT: C 167 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8780 (tp30) REVERT: C 168 GLU cc_start: 0.9503 (pp20) cc_final: 0.9103 (pp20) REVERT: C 170 GLU cc_start: 0.8903 (pp20) cc_final: 0.8456 (pp20) REVERT: C 171 MET cc_start: 0.9438 (tpp) cc_final: 0.9173 (tpp) REVERT: C 172 ARG cc_start: 0.9238 (ttp80) cc_final: 0.8461 (ptt90) REVERT: C 285 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 369 PHE cc_start: 0.8524 (m-80) cc_final: 0.8198 (t80) REVERT: J 1 MET cc_start: 0.7981 (ttp) cc_final: 0.7319 (tmm) REVERT: J 10 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7049 (mmm) REVERT: J 19 ARG cc_start: 0.7668 (tmm160) cc_final: 0.7456 (tmm160) REVERT: J 21 ASN cc_start: 0.9060 (t0) cc_final: 0.8798 (t0) REVERT: I 10 MET cc_start: 0.8145 (mpp) cc_final: 0.7483 (mpp) REVERT: E 30 MET cc_start: 0.8266 (tpp) cc_final: 0.7921 (tpp) REVERT: M 88 GLU cc_start: 0.8595 (pp20) cc_final: 0.8381 (pp20) REVERT: M 89 TYR cc_start: 0.9016 (p90) cc_final: 0.8765 (p90) REVERT: M 99 MET cc_start: 0.7336 (tpp) cc_final: 0.6937 (mmm) REVERT: M 289 GLN cc_start: 0.8862 (mp10) cc_final: 0.8603 (mp-120) REVERT: M 291 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8815 (tp-100) REVERT: M 295 ASP cc_start: 0.9095 (p0) cc_final: 0.8825 (p0) REVERT: M 351 LYS cc_start: 0.9318 (ptpp) cc_final: 0.8908 (mmtt) REVERT: N 45 MET cc_start: 0.8629 (pmm) cc_final: 0.8225 (mpp) REVERT: N 51 ASN cc_start: 0.9138 (m110) cc_final: 0.8725 (t0) REVERT: N 92 MET cc_start: 0.9335 (mmm) cc_final: 0.8677 (mmm) REVERT: N 110 LYS cc_start: 0.9287 (tppt) cc_final: 0.8817 (mmtt) REVERT: N 119 LYS cc_start: 0.8875 (tppt) cc_final: 0.8669 (tppt) REVERT: N 139 ARG cc_start: 0.8382 (mmt90) cc_final: 0.7866 (mtp-110) REVERT: N 147 ASP cc_start: 0.9025 (p0) cc_final: 0.8590 (p0) REVERT: N 168 GLU cc_start: 0.9467 (pp20) cc_final: 0.9025 (pp20) REVERT: N 171 MET cc_start: 0.9257 (ppp) cc_final: 0.8855 (ppp) REVERT: N 203 GLU cc_start: 0.8864 (pp20) cc_final: 0.8597 (pp20) REVERT: N 220 ARG cc_start: 0.9161 (ttm170) cc_final: 0.8930 (mtm180) REVERT: N 234 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8371 (mmmt) REVERT: N 237 ASP cc_start: 0.8540 (p0) cc_final: 0.7603 (p0) REVERT: N 274 ASP cc_start: 0.8719 (p0) cc_final: 0.8496 (p0) REVERT: N 284 LYS cc_start: 0.9125 (mtmt) cc_final: 0.8751 (mtmm) REVERT: N 298 ARG cc_start: 0.9239 (tpp80) cc_final: 0.8693 (mmt-90) REVERT: N 346 ASP cc_start: 0.8772 (p0) cc_final: 0.8302 (p0) REVERT: O 93 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8298 (p0) REVERT: O 99 MET cc_start: 0.7730 (ppp) cc_final: 0.7384 (ppp) REVERT: O 167 GLU cc_start: 0.8209 (tp30) cc_final: 0.7734 (tp30) REVERT: O 197 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9093 (tp) REVERT: O 202 PHE cc_start: 0.9406 (t80) cc_final: 0.9190 (t80) REVERT: O 229 TYR cc_start: 0.9062 (t80) cc_final: 0.8763 (t80) REVERT: O 236 LYS cc_start: 0.9202 (pttp) cc_final: 0.8953 (ptpt) REVERT: Q 23 ARG cc_start: 0.8256 (pmm150) cc_final: 0.7886 (pmt170) REVERT: Q 33 ASP cc_start: 0.8351 (t70) cc_final: 0.7591 (t0) REVERT: Q 39 ASP cc_start: 0.8193 (t70) cc_final: 0.7849 (t70) REVERT: S 10 MET cc_start: 0.7464 (mpt) cc_final: 0.5624 (ptm) outliers start: 120 outliers final: 87 residues processed: 596 average time/residue: 0.3619 time to fit residues: 322.7051 Evaluate side-chains 608 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 515 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 237 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 104 ASN Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 169 LYS Chi-restraints excluded: chain N residue 177 ASP Chi-restraints excluded: chain N residue 181 ASN Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 231 THR Chi-restraints excluded: chain N residue 238 ILE Chi-restraints excluded: chain N residue 241 LEU Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 257 ASN Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 309 ASP Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 207 ASN Chi-restraints excluded: chain O residue 268 ASP Chi-restraints excluded: chain O residue 274 ASP Chi-restraints excluded: chain O residue 345 LEU Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 4.9990 chunk 249 optimal weight: 8.9990 chunk 227 optimal weight: 0.5980 chunk 242 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 229 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 ASN ** N 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22334 Z= 0.191 Angle : 0.815 13.183 30163 Z= 0.401 Chirality : 0.048 0.254 3370 Planarity : 0.003 0.039 3876 Dihedral : 5.896 35.245 2974 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 3.92 % Allowed : 25.99 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.16), residues: 2555 helix: -0.64 (0.22), residues: 530 sheet: -1.56 (0.24), residues: 426 loop : -2.16 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 375 HIS 0.007 0.001 HIS N 219 PHE 0.015 0.001 PHE M 387 TYR 0.033 0.001 TYR N 341 ARG 0.008 0.000 ARG M 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 558 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8569 (pt0) cc_final: 0.7714 (mp10) REVERT: A 85 TYR cc_start: 0.8964 (m-80) cc_final: 0.8597 (m-80) REVERT: A 127 LYS cc_start: 0.9507 (mptm) cc_final: 0.9037 (mmmt) REVERT: A 160 ILE cc_start: 0.9401 (pp) cc_final: 0.9087 (mt) REVERT: A 168 GLU cc_start: 0.9323 (tt0) cc_final: 0.9067 (tt0) REVERT: A 194 LYS cc_start: 0.9330 (tttm) cc_final: 0.9083 (tptt) REVERT: A 203 GLU cc_start: 0.8696 (pt0) cc_final: 0.8474 (pm20) REVERT: A 275 ASP cc_start: 0.8843 (t70) cc_final: 0.8562 (t0) REVERT: A 357 LYS cc_start: 0.9415 (mtpp) cc_final: 0.8795 (mtpp) REVERT: A 361 LYS cc_start: 0.9504 (mmmt) cc_final: 0.9245 (mmmt) REVERT: A 375 TRP cc_start: 0.8783 (m-90) cc_final: 0.8363 (m-10) REVERT: B 79 GLN cc_start: 0.8338 (pp30) cc_final: 0.8062 (pp30) REVERT: B 92 MET cc_start: 0.9114 (mmm) cc_final: 0.8865 (mmm) REVERT: B 99 MET cc_start: 0.8208 (ppp) cc_final: 0.7740 (ppp) REVERT: B 139 ARG cc_start: 0.8527 (mmt90) cc_final: 0.8255 (mtp-110) REVERT: B 158 LYS cc_start: 0.9427 (tppt) cc_final: 0.9067 (tptp) REVERT: B 168 GLU cc_start: 0.8620 (tt0) cc_final: 0.8407 (tt0) REVERT: B 187 ASN cc_start: 0.9144 (m110) cc_final: 0.8707 (m-40) REVERT: B 236 LYS cc_start: 0.9082 (mmmt) cc_final: 0.8767 (tppt) REVERT: B 238 ILE cc_start: 0.9347 (pp) cc_final: 0.8915 (mp) REVERT: B 320 ASP cc_start: 0.8806 (t0) cc_final: 0.8521 (t0) REVERT: B 346 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8250 (p0) REVERT: B 360 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8804 (mm) REVERT: B 375 TRP cc_start: 0.8787 (m-90) cc_final: 0.8398 (m-10) REVERT: C 45 MET cc_start: 0.7831 (mpm) cc_final: 0.7321 (mpp) REVERT: C 77 LYS cc_start: 0.9456 (mmmm) cc_final: 0.9080 (mmmm) REVERT: C 79 GLN cc_start: 0.8936 (pm20) cc_final: 0.8342 (pm20) REVERT: C 92 MET cc_start: 0.8717 (mmm) cc_final: 0.8472 (mmm) REVERT: C 99 MET cc_start: 0.8458 (pmm) cc_final: 0.7791 (ppp) REVERT: C 108 MET cc_start: 0.8586 (mmm) cc_final: 0.8342 (mmt) REVERT: C 127 LYS cc_start: 0.9527 (tppp) cc_final: 0.9244 (mmmt) REVERT: C 167 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8642 (tp30) REVERT: C 168 GLU cc_start: 0.9490 (pp20) cc_final: 0.9079 (pp20) REVERT: C 170 GLU cc_start: 0.8901 (pp20) cc_final: 0.8339 (pp20) REVERT: C 171 MET cc_start: 0.9431 (tpp) cc_final: 0.9206 (tpp) REVERT: C 172 ARG cc_start: 0.9234 (ttp80) cc_final: 0.8422 (ptt90) REVERT: C 174 MET cc_start: 0.6680 (tpt) cc_final: 0.6245 (mmp) REVERT: C 285 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 369 PHE cc_start: 0.8487 (m-80) cc_final: 0.8169 (t80) REVERT: C 370 ASP cc_start: 0.8826 (t0) cc_final: 0.8420 (t70) REVERT: J 1 MET cc_start: 0.7933 (ttp) cc_final: 0.7338 (tmm) REVERT: J 10 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6798 (mmm) REVERT: J 21 ASN cc_start: 0.9098 (t0) cc_final: 0.8893 (t0) REVERT: J 36 LYS cc_start: 0.8923 (tmmm) cc_final: 0.8549 (pttt) REVERT: I 10 MET cc_start: 0.7967 (mpp) cc_final: 0.7536 (mmp) REVERT: E 30 MET cc_start: 0.8188 (tpp) cc_final: 0.7868 (tpp) REVERT: M 89 TYR cc_start: 0.8980 (p90) cc_final: 0.8672 (p90) REVERT: M 99 MET cc_start: 0.6680 (tpp) cc_final: 0.6424 (mmm) REVERT: M 229 TYR cc_start: 0.9071 (t80) cc_final: 0.8659 (t80) REVERT: M 234 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8338 (tptp) REVERT: M 289 GLN cc_start: 0.8860 (mp10) cc_final: 0.8622 (mp-120) REVERT: M 291 GLN cc_start: 0.9168 (tp-100) cc_final: 0.8797 (tp-100) REVERT: M 295 ASP cc_start: 0.9076 (p0) cc_final: 0.8804 (p0) REVERT: M 298 ARG cc_start: 0.9497 (tpp-160) cc_final: 0.9098 (tpp80) REVERT: M 351 LYS cc_start: 0.9281 (ptpp) cc_final: 0.9011 (mmtt) REVERT: N 45 MET cc_start: 0.8562 (pmm) cc_final: 0.8163 (mpp) REVERT: N 51 ASN cc_start: 0.9085 (m110) cc_final: 0.8744 (t0) REVERT: N 92 MET cc_start: 0.9309 (mmm) cc_final: 0.8672 (mmm) REVERT: N 139 ARG cc_start: 0.8303 (mmt90) cc_final: 0.7839 (mtp-110) REVERT: N 147 ASP cc_start: 0.9018 (p0) cc_final: 0.8573 (p0) REVERT: N 168 GLU cc_start: 0.9464 (pp20) cc_final: 0.9047 (pp20) REVERT: N 171 MET cc_start: 0.9290 (ppp) cc_final: 0.8867 (ppp) REVERT: N 220 ARG cc_start: 0.9130 (ttm170) cc_final: 0.8876 (mtm180) REVERT: N 234 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8262 (mmmt) REVERT: N 237 ASP cc_start: 0.8447 (p0) cc_final: 0.7535 (p0) REVERT: N 274 ASP cc_start: 0.8630 (p0) cc_final: 0.8394 (p0) REVERT: N 284 LYS cc_start: 0.9094 (mtmt) cc_final: 0.8727 (mtmm) REVERT: N 298 ARG cc_start: 0.9234 (tpp80) cc_final: 0.8659 (mmt-90) REVERT: N 346 ASP cc_start: 0.8750 (p0) cc_final: 0.8338 (p0) REVERT: O 51 ASN cc_start: 0.8655 (m-40) cc_final: 0.8441 (m110) REVERT: O 99 MET cc_start: 0.7761 (ppp) cc_final: 0.7443 (ppp) REVERT: O 197 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8925 (tp) REVERT: O 236 LYS cc_start: 0.9176 (pttp) cc_final: 0.8931 (ptpt) REVERT: Q 23 ARG cc_start: 0.8271 (pmm150) cc_final: 0.7866 (pmt170) REVERT: Q 33 ASP cc_start: 0.8312 (t70) cc_final: 0.7514 (t0) REVERT: S 10 MET cc_start: 0.6704 (mpt) cc_final: 0.6281 (mmp) outliers start: 91 outliers final: 72 residues processed: 609 average time/residue: 0.3689 time to fit residues: 336.0847 Evaluate side-chains 607 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 531 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 237 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 104 ASN Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 177 ASP Chi-restraints excluded: chain N residue 181 ASN Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 231 THR Chi-restraints excluded: chain N residue 238 ILE Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 257 ASN Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 207 ASN Chi-restraints excluded: chain O residue 268 ASP Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 345 LEU Chi-restraints excluded: chain S residue 5 ASN Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 0.0970 chunk 256 optimal weight: 0.0070 chunk 156 optimal weight: 5.9990 chunk 121 optimal weight: 0.0670 chunk 178 optimal weight: 9.9990 chunk 268 optimal weight: 50.0000 chunk 247 optimal weight: 0.8980 chunk 214 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 131 optimal weight: 0.0570 overall best weight: 0.1852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 ASN N 207 ASN ** N 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN S 35 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22334 Z= 0.195 Angle : 0.836 13.420 30163 Z= 0.412 Chirality : 0.047 0.295 3370 Planarity : 0.003 0.045 3876 Dihedral : 5.769 40.019 2974 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 3.40 % Allowed : 27.15 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2555 helix: -0.65 (0.23), residues: 524 sheet: -1.44 (0.24), residues: 416 loop : -2.08 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 375 HIS 0.007 0.001 HIS E 46 PHE 0.025 0.001 PHE A 202 TYR 0.029 0.001 TYR C 341 ARG 0.008 0.000 ARG M 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 562 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8392 (pt0) cc_final: 0.7698 (mp-120) REVERT: A 85 TYR cc_start: 0.8888 (m-80) cc_final: 0.8550 (m-80) REVERT: A 127 LYS cc_start: 0.9503 (mptm) cc_final: 0.9019 (mmmt) REVERT: A 160 ILE cc_start: 0.9373 (pp) cc_final: 0.9111 (mt) REVERT: A 194 LYS cc_start: 0.9325 (tttm) cc_final: 0.9099 (tptt) REVERT: A 203 GLU cc_start: 0.8603 (pt0) cc_final: 0.8371 (pm20) REVERT: A 275 ASP cc_start: 0.8826 (t70) cc_final: 0.8558 (t0) REVERT: A 357 LYS cc_start: 0.9512 (mtpp) cc_final: 0.9279 (mtpp) REVERT: A 375 TRP cc_start: 0.8613 (m-90) cc_final: 0.8296 (m-10) REVERT: B 92 MET cc_start: 0.9067 (mmm) cc_final: 0.8844 (mmm) REVERT: B 99 MET cc_start: 0.8184 (ppp) cc_final: 0.7797 (ppp) REVERT: B 139 ARG cc_start: 0.8497 (mmt90) cc_final: 0.8263 (mtp-110) REVERT: B 158 LYS cc_start: 0.9425 (tppt) cc_final: 0.9032 (tptp) REVERT: B 187 ASN cc_start: 0.9048 (m110) cc_final: 0.8639 (m-40) REVERT: B 195 GLU cc_start: 0.8941 (pp20) cc_final: 0.8686 (pp20) REVERT: B 236 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8718 (tppt) REVERT: B 238 ILE cc_start: 0.9338 (pp) cc_final: 0.8901 (mp) REVERT: B 254 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8661 (mmtm) REVERT: B 320 ASP cc_start: 0.8780 (t0) cc_final: 0.8495 (t0) REVERT: B 375 TRP cc_start: 0.8748 (m-90) cc_final: 0.8363 (m-10) REVERT: B 382 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6412 (tmtt) REVERT: C 45 MET cc_start: 0.7856 (mpm) cc_final: 0.7326 (mpp) REVERT: C 77 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9068 (mmmm) REVERT: C 79 GLN cc_start: 0.8943 (pm20) cc_final: 0.8293 (pm20) REVERT: C 92 MET cc_start: 0.8748 (mmm) cc_final: 0.8459 (mmm) REVERT: C 99 MET cc_start: 0.8348 (pmm) cc_final: 0.7766 (ppp) REVERT: C 108 MET cc_start: 0.8589 (mmm) cc_final: 0.8319 (mmt) REVERT: C 127 LYS cc_start: 0.9505 (tppp) cc_final: 0.9244 (mmmt) REVERT: C 167 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8763 (mm-30) REVERT: C 168 GLU cc_start: 0.9496 (pp20) cc_final: 0.9069 (pp20) REVERT: C 170 GLU cc_start: 0.8896 (pp20) cc_final: 0.8385 (pp20) REVERT: C 172 ARG cc_start: 0.9235 (ttp80) cc_final: 0.8542 (ptt90) REVERT: C 174 MET cc_start: 0.6640 (tpt) cc_final: 0.6154 (mmp) REVERT: C 285 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 369 PHE cc_start: 0.8459 (m-80) cc_final: 0.8033 (t80) REVERT: C 371 GLU cc_start: 0.8145 (mp0) cc_final: 0.7725 (mp0) REVERT: C 375 TRP cc_start: 0.8872 (m-90) cc_final: 0.7903 (m-10) REVERT: J 1 MET cc_start: 0.7988 (ttp) cc_final: 0.7754 (tmm) REVERT: J 36 LYS cc_start: 0.8877 (tmmm) cc_final: 0.8514 (pttt) REVERT: I 10 MET cc_start: 0.7815 (mpp) cc_final: 0.5288 (ppp) REVERT: E 30 MET cc_start: 0.8113 (tpp) cc_final: 0.7886 (tpp) REVERT: M 234 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8227 (tptp) REVERT: M 260 GLN cc_start: 0.9396 (mm-40) cc_final: 0.9033 (mm110) REVERT: M 289 GLN cc_start: 0.8850 (mp10) cc_final: 0.8591 (mp-120) REVERT: M 291 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8757 (tp-100) REVERT: M 295 ASP cc_start: 0.9076 (p0) cc_final: 0.8791 (p0) REVERT: M 298 ARG cc_start: 0.9490 (tpp-160) cc_final: 0.9092 (tpp80) REVERT: N 19 LYS cc_start: 0.6295 (pptt) cc_final: 0.5444 (pttp) REVERT: N 45 MET cc_start: 0.8505 (pmm) cc_final: 0.8138 (mpp) REVERT: N 51 ASN cc_start: 0.9047 (m110) cc_final: 0.8712 (t0) REVERT: N 92 MET cc_start: 0.9269 (mmm) cc_final: 0.8716 (mmm) REVERT: N 139 ARG cc_start: 0.8496 (mmt90) cc_final: 0.7914 (mtp-110) REVERT: N 147 ASP cc_start: 0.8983 (p0) cc_final: 0.8263 (p0) REVERT: N 168 GLU cc_start: 0.9473 (pp20) cc_final: 0.9032 (pp20) REVERT: N 171 MET cc_start: 0.9282 (ppp) cc_final: 0.8865 (ppp) REVERT: N 220 ARG cc_start: 0.9093 (ttm170) cc_final: 0.8863 (mtm180) REVERT: N 234 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8227 (mtpp) REVERT: N 237 ASP cc_start: 0.8394 (p0) cc_final: 0.7491 (p0) REVERT: N 274 ASP cc_start: 0.8612 (p0) cc_final: 0.8371 (p0) REVERT: N 284 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8737 (mtmm) REVERT: N 298 ARG cc_start: 0.9231 (tpp80) cc_final: 0.8630 (mmt-90) REVERT: N 346 ASP cc_start: 0.8747 (p0) cc_final: 0.8365 (p0) REVERT: N 375 TRP cc_start: 0.9319 (m-90) cc_final: 0.9080 (m-90) REVERT: O 39 TRP cc_start: 0.9053 (t-100) cc_final: 0.8683 (t-100) REVERT: O 51 ASN cc_start: 0.8616 (m-40) cc_final: 0.8385 (m110) REVERT: O 99 MET cc_start: 0.7874 (ppp) cc_final: 0.7546 (ppp) REVERT: O 167 GLU cc_start: 0.8133 (tp30) cc_final: 0.7743 (tp30) REVERT: O 189 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8293 (mtt180) REVERT: O 197 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8805 (tp) REVERT: O 236 LYS cc_start: 0.9171 (pttp) cc_final: 0.8917 (ptpt) REVERT: Q 23 ARG cc_start: 0.8235 (pmm150) cc_final: 0.7889 (pmt170) REVERT: Q 33 ASP cc_start: 0.8175 (t70) cc_final: 0.7269 (t0) REVERT: Q 36 LYS cc_start: 0.9068 (ptmm) cc_final: 0.8839 (ptmm) REVERT: S 10 MET cc_start: 0.6454 (mpt) cc_final: 0.4689 (ttp) outliers start: 79 outliers final: 66 residues processed: 608 average time/residue: 0.3665 time to fit residues: 331.7552 Evaluate side-chains 612 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 544 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain N residue 24 ASP Chi-restraints excluded: chain N residue 104 ASN Chi-restraints excluded: chain N residue 153 LEU Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 177 ASP Chi-restraints excluded: chain N residue 181 ASN Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 231 THR Chi-restraints excluded: chain N residue 238 ILE Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 350 ILE Chi-restraints excluded: chain O residue 92 MET Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 136 ASN Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 207 ASN Chi-restraints excluded: chain O residue 268 ASP Chi-restraints excluded: chain O residue 274 ASP Chi-restraints excluded: chain O residue 345 LEU Chi-restraints excluded: chain S residue 34 THR Chi-restraints excluded: chain S residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 214 optimal weight: 0.0980 chunk 89 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 207 ASN ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN S 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.091570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077681 restraints weight = 71869.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.079981 restraints weight = 38898.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081568 restraints weight = 25378.492| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.288 22334 Z= 0.286 Angle : 1.055 59.199 30163 Z= 0.576 Chirality : 0.049 0.527 3370 Planarity : 0.003 0.043 3876 Dihedral : 5.766 41.091 2974 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.84 % Favored : 89.12 % Rotamer: Outliers : 3.36 % Allowed : 27.19 % Favored : 69.45 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.16), residues: 2555 helix: -0.68 (0.23), residues: 524 sheet: -1.43 (0.24), residues: 416 loop : -2.09 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 74 HIS 0.009 0.001 HIS E 46 PHE 0.022 0.001 PHE A 49 TYR 0.028 0.002 TYR N 89 ARG 0.008 0.001 ARG O 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6119.72 seconds wall clock time: 111 minutes 26.99 seconds (6686.99 seconds total)