Starting phenix.real_space_refine on Sun Sep 13 07:42:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iaw_4440/09_2026/6iaw_4440.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iaw_4440/09_2026/6iaw_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 { model { file = "/net/cci-nas-00/data/ceres_data/6iaw_4440/09_2026/6iaw_4440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iaw_4440/09_2026/6iaw_4440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iaw_4440/09_2026/6iaw_4440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iaw_4440/09_2026/6iaw_4440.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 5.40, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 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: 1.76 Conformation dependent library (CDL) restraints added in 904.6 milliseconds 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: 0.53 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: 3.59 Time building geometry restraints manager: 2.42 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: 0.00 - 3.71: 29545 3.71 - 7.43: 536 7.43 - 11.14: 70 11.14 - 14.85: 8 14.85 - 18.57: 4 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 Time spend for trying shortcut: 0.00 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: 0.680 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.010 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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= 0.374 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.017 0.001 ARG A 354 TYR 0.023 0.003 TYR N 121 PHE 0.025 0.003 PHE N 343 TRP 0.024 0.002 TRP C 74 HIS 0.019 0.003 HIS S 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.37 (22334) covalent geometry : angle 1.26605 / 0.67 (30163) hydrogen bonds : bond 0.16314 / 9.98 ( 627) hydrogen bonds : angle 7.82229 / 5.37 ( 1665) *********************** 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 to be fit. rotamer outliers: 33 poor density : 832 time to evaluate : 0.773 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: 0.7471 (mmpt) cc_final: 0.7190 (mmmt) REVERT: A 127 LYS cc_start: 0.9568 (mptm) cc_final: 0.9206 (mmmm) REVERT: A 160 ILE cc_start: 0.9542 (pp) cc_final: 0.9315 (mp) REVERT: A 163 ILE cc_start: 0.9369 (pp) cc_final: 0.9108 (pt) REVERT: A 174 MET cc_start: 0.7074 (mmp) cc_final: 0.6646 (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: 0.8836 (t70) cc_final: 0.8526 (t0) REVERT: A 357 LYS cc_start: 0.9465 (mtpp) cc_final: 0.9063 (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: 0.7659 (tmm) REVERT: B 127 LYS cc_start: 0.9238 (mtpp) cc_final: 0.8629 (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: 0.8763 (pp20) REVERT: B 172 ARG cc_start: 0.8990 (ppt-90) cc_final: 0.8534 (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: 0.9225 (mp) REVERT: B 320 ASP cc_start: 0.8821 (t0) cc_final: 0.8493 (t0) REVERT: C 45 MET cc_start: 0.7919 (mpm) cc_final: 0.7572 (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: 0.8956 (p0) REVERT: C 170 GLU cc_start: 0.8600 (pp20) cc_final: 0.8230 (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: 0.8295 (t70) REVERT: C 370 ASP cc_start: 0.8891 (t0) cc_final: 0.8530 (t70) REVERT: C 371 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7784 (mt-10) 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: 0.7761 (tmm) REVERT: J 23 ARG cc_start: 0.8120 (mpp-170) cc_final: 0.7714 (mpt180) REVERT: J 29 ASN cc_start: 0.7988 (t0) cc_final: 0.7568 (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: 0.8728 (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: 0.8575 (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: 0.9102 (tppt) REVERT: M 234 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8487 (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: 0.8455 (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: 0.8666 (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: 0.8971 (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: 0.8325 (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: 0.8370 (t70) REVERT: N 304 GLN cc_start: 0.8394 (pp30) cc_final: 0.8084 (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: 0.8222 (mm110) REVERT: O 97 ILE cc_start: 0.9375 (pp) cc_final: 0.8849 (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: 0.8917 (ptpt) REVERT: O 238 ILE cc_start: 0.9114 (pp) cc_final: 0.8898 (mp) REVERT: O 261 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.4734 (pp) REVERT: Q 20 LEU cc_start: 0.9085 (tt) cc_final: 0.8537 (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: 0.8002 (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: 0.8050 (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: 0.1767 time to fit residues: 222.0936 Evaluate side-chains 594 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 587 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.5263 > 50:) chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 C 182 GLN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN C 260 GLN ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 5 ASN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 ASN N 374 HIS ** O 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN S 5 ASN S 46 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074800 restraints weight = 71259.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.077060 restraints weight = 38246.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.078583 restraints weight = 24587.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079624 restraints weight = 17590.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.080413 restraints weight = 13661.885| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22334 Z= 0.198 Angle : 0.878 11.934 30163 Z= 0.449 Chirality : 0.049 0.346 3370 Planarity : 0.004 0.063 3876 Dihedral : 7.656 43.909 2984 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.19 % Favored : 88.73 % Rotamer: Outliers : 4.30 % Allowed : 17.04 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.15), residues: 2555 helix: -1.81 (0.20), residues: 514 sheet: -2.63 (0.21), residues: 463 loop : -2.80 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 23 TYR 0.032 0.002 TYR Q 41 PHE 0.022 0.001 PHE A 131 TRP 0.017 0.002 TRP B 74 HIS 0.007 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (22334) covalent geometry : angle 0.87805 / 0.45 (30163) hydrogen bonds : bond 0.04990 / 3.20 ( 627) hydrogen bonds : angle 6.27256 / 4.32 ( 1665) *********************** 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 730 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 630 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9097 (ptm160) cc_final: 0.8768 (ptm160) REVERT: A 84 GLN cc_start: 0.8523 (pt0) cc_final: 0.7412 (mp10) REVERT: A 127 LYS cc_start: 0.9529 (mptm) cc_final: 0.9134 (mmmm) REVERT: A 160 ILE cc_start: 0.9441 (pp) cc_final: 0.9204 (mp) REVERT: A 163 ILE cc_start: 0.9307 (pp) cc_final: 0.8837 (pt) REVERT: A 167 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: A 168 GLU cc_start: 0.9266 (tt0) cc_final: 0.8920 (tt0) REVERT: A 275 ASP cc_start: 0.8692 (t70) cc_final: 0.8389 (t0) REVERT: A 347 ILE cc_start: 0.8946 (tp) cc_final: 0.8492 (pt) REVERT: A 357 LYS cc_start: 0.9447 (mtpp) cc_final: 0.9083 (mtpp) REVERT: A 361 LYS cc_start: 0.9401 (mmmt) cc_final: 0.9060 (mmtp) REVERT: A 375 TRP cc_start: 0.8806 (m-90) cc_final: 0.8452 (m-10) REVERT: B 39 TRP cc_start: 0.9511 (t-100) cc_final: 0.9144 (t-100) REVERT: B 99 MET cc_start: 0.8115 (ppp) cc_final: 0.7411 (tmm) REVERT: B 127 LYS cc_start: 0.9306 (mtpp) cc_final: 0.8871 (mtpp) REVERT: B 139 ARG cc_start: 0.8609 (mmt90) cc_final: 0.8252 (mtp-110) REVERT: B 167 GLU cc_start: 0.8861 (tp30) cc_final: 0.8491 (tp30) REVERT: B 168 GLU cc_start: 0.8495 (tt0) cc_final: 0.8010 (tt0) REVERT: B 170 GLU cc_start: 0.8864 (pp20) cc_final: 0.8639 (pp20) REVERT: B 220 ARG cc_start: 0.8353 (ttm110) cc_final: 0.7834 (mtt180) REVERT: B 236 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8698 (tppt) REVERT: B 320 ASP cc_start: 0.8753 (t0) cc_final: 0.8520 (t70) REVERT: C 45 MET cc_start: 0.7906 (mpm) cc_final: 0.7540 (mpp) REVERT: C 77 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8724 (mptt) REVERT: C 79 GLN cc_start: 0.8827 (pm20) cc_final: 0.8067 (pm20) REVERT: C 108 MET cc_start: 0.8674 (mmm) cc_final: 0.8356 (mmt) REVERT: C 123 ASN cc_start: 0.9230 (p0) cc_final: 0.8972 (p0) REVERT: C 167 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8544 (tp30) REVERT: C 170 GLU cc_start: 0.8689 (pp20) cc_final: 0.8367 (pp20) REVERT: C 172 ARG cc_start: 0.9243 (ttp80) cc_final: 0.8420 (ptt90) REVERT: C 237 ASP cc_start: 0.7714 (p0) cc_final: 0.7155 (p0) REVERT: C 285 GLU cc_start: 0.8205 (tm-30) cc_final: 0.8005 (tm-30) REVERT: C 346 ASP cc_start: 0.7579 (t0) cc_final: 0.7202 (t0) REVERT: C 370 ASP cc_start: 0.8796 (t0) cc_final: 0.8377 (t70) REVERT: J 1 MET cc_start: 0.8175 (ttp) cc_final: 0.7855 (tmm) REVERT: J 10 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6992 (mmm) REVERT: J 23 ARG cc_start: 0.8072 (mpp-170) cc_final: 0.7646 (mpt180) REVERT: J 29 ASN cc_start: 0.7714 (t0) cc_final: 0.7416 (t0) REVERT: J 36 LYS cc_start: 0.8930 (tmmm) cc_final: 0.8678 (pttt) REVERT: I 10 MET cc_start: 0.8539 (mpp) cc_final: 0.7746 (mpp) REVERT: I 15 TYR cc_start: 0.7236 (t80) cc_final: 0.7013 (t80) REVERT: I 30 MET cc_start: 0.8235 (tmm) cc_final: 0.7940 (tmm) REVERT: I 41 TYR cc_start: 0.7501 (t80) cc_final: 0.7066 (t80) REVERT: D 45 ILE cc_start: 0.6757 (tp) cc_final: 0.6539 (mp) REVERT: E 17 ASP cc_start: 0.8782 (m-30) cc_final: 0.8502 (m-30) REVERT: E 30 MET cc_start: 0.8410 (tpp) cc_final: 0.8208 (tpp) REVERT: M 88 GLU cc_start: 0.8329 (pp20) cc_final: 0.8088 (pp20) REVERT: M 99 MET cc_start: 0.7398 (mmm) cc_final: 0.7015 (mmm) REVERT: M 109 LEU cc_start: 0.9383 (mt) cc_final: 0.9100 (tt) REVERT: M 129 GLN cc_start: 0.8124 (tp40) cc_final: 0.7840 (tp-100) REVERT: M 289 GLN cc_start: 0.8790 (mp10) cc_final: 0.8401 (mp-120) REVERT: M 291 GLN cc_start: 0.9284 (tp-100) cc_final: 0.8699 (tp-100) REVERT: M 295 ASP cc_start: 0.9123 (p0) cc_final: 0.8771 (p0) REVERT: M 356 THR cc_start: 0.9306 (p) cc_final: 0.9029 (t) REVERT: M 375 TRP cc_start: 0.6230 (m-10) cc_final: 0.6004 (m-10) REVERT: M 378 TYR cc_start: 0.9389 (p90) cc_final: 0.9001 (p90) REVERT: N 28 ASP cc_start: 0.8631 (p0) cc_final: 0.8415 (p0) REVERT: N 45 MET cc_start: 0.8387 (pmm) cc_final: 0.7961 (mpp) REVERT: N 51 ASN cc_start: 0.9237 (m110) cc_final: 0.8848 (t0) REVERT: N 92 MET cc_start: 0.9239 (mmm) cc_final: 0.8920 (mmm) REVERT: N 94 THR cc_start: 0.9151 (p) cc_final: 0.8881 (p) REVERT: N 115 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8247 (mtm180) REVERT: N 126 VAL cc_start: 0.9448 (p) cc_final: 0.9154 (p) REVERT: N 128 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8830 (mmmt) REVERT: N 129 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7986 (mm-40) REVERT: N 139 ARG cc_start: 0.8357 (mmt90) cc_final: 0.7970 (mtp-110) REVERT: N 147 ASP cc_start: 0.8763 (p0) cc_final: 0.8371 (p0) REVERT: N 156 TYR cc_start: 0.9177 (t80) cc_final: 0.8772 (t80) REVERT: N 168 GLU cc_start: 0.9347 (pp20) cc_final: 0.9128 (pt0) REVERT: N 170 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8524 (tm-30) REVERT: N 171 MET cc_start: 0.9082 (ppp) cc_final: 0.8774 (ppp) REVERT: N 202 PHE cc_start: 0.9079 (t80) cc_final: 0.8796 (t80) REVERT: N 203 GLU cc_start: 0.8920 (pp20) cc_final: 0.8597 (tm-30) REVERT: N 217 GLU cc_start: 0.7674 (tp30) cc_final: 0.7273 (tp30) REVERT: N 234 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8685 (mmmt) REVERT: N 237 ASP cc_start: 0.8361 (p0) cc_final: 0.7561 (p0) REVERT: N 284 LYS cc_start: 0.9258 (mtmt) cc_final: 0.8916 (mtmm) REVERT: N 298 ARG cc_start: 0.9204 (mmt-90) cc_final: 0.8867 (mmp80) REVERT: N 302 ASP cc_start: 0.8516 (t0) cc_final: 0.7776 (t70) REVERT: N 346 ASP cc_start: 0.8623 (p0) cc_final: 0.7998 (p0) REVERT: N 377 HIS cc_start: 0.9142 (m90) cc_final: 0.8851 (m-70) REVERT: O 39 TRP cc_start: 0.9345 (t-100) cc_final: 0.8994 (t-100) REVERT: O 40 ASP cc_start: 0.9217 (t0) cc_final: 0.8982 (t70) REVERT: O 79 GLN cc_start: 0.8582 (mm110) cc_final: 0.8227 (mm110) REVERT: O 97 ILE cc_start: 0.9549 (pp) cc_final: 0.9330 (mp) REVERT: O 99 MET cc_start: 0.7302 (ppp) cc_final: 0.7046 (ppp) REVERT: O 108 MET cc_start: 0.8412 (ptm) cc_final: 0.7939 (mtt) REVERT: O 110 LYS cc_start: 0.9325 (mmtm) cc_final: 0.8948 (mmtm) REVERT: O 153 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8453 (mm) REVERT: O 370 ASP cc_start: 0.8260 (t70) cc_final: 0.7987 (t0) REVERT: Q 21 ASN cc_start: 0.8384 (t0) cc_final: 0.8154 (t0) REVERT: Q 23 ARG cc_start: 0.8246 (pmm150) cc_final: 0.7511 (pmm150) REVERT: Q 33 ASP cc_start: 0.8271 (t70) cc_final: 0.7801 (t70) REVERT: S 10 MET cc_start: 0.8422 (mpt) cc_final: 0.8026 (mmt) REVERT: S 14 SER cc_start: 0.9576 (m) cc_final: 0.9289 (p) REVERT: S 49 SER cc_start: 0.8973 (t) cc_final: 0.8724 (p) outliers start: 100 outliers final: 42 residues processed: 689 average time/residue: 0.1791 time to fit residues: 184.3027 Evaluate side-chains 595 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 550 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain B residue 359 MET 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 359 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 43 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 52 SER 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 208 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain N residue 252 ASP Chi-restraints excluded: chain N residue 323 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 205 ILE Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 237 ASP Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 263 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 207 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN B 269 HIS ** 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 I 29 ASN ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 5 ASN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 ASN N 129 GLN N 181 ASN N 228 GLN O 27 HIS S 46 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073991 restraints weight = 71361.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076266 restraints weight = 38390.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077804 restraints weight = 24788.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078848 restraints weight = 17826.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.079618 restraints weight = 13822.706| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22334 Z= 0.209 Angle : 0.831 11.136 30163 Z= 0.426 Chirality : 0.049 0.293 3370 Planarity : 0.004 0.047 3876 Dihedral : 7.035 42.818 2975 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 4.86 % Allowed : 18.42 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.15), residues: 2555 helix: -1.23 (0.21), residues: 515 sheet: -2.38 (0.21), residues: 453 loop : -2.63 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 23 TYR 0.021 0.002 TYR O 229 PHE 0.017 0.001 PHE M 364 TRP 0.017 0.002 TRP M 74 HIS 0.007 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (22334) covalent geometry : angle 0.83099 / 0.43 (30163) hydrogen bonds : bond 0.04504 / 2.90 ( 627) hydrogen bonds : angle 5.99894 / 4.12 ( 1665) *********************** 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 698 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 585 time to evaluate : 0.842 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: 0.8551 (pt0) cc_final: 0.7448 (mp10) REVERT: A 127 LYS cc_start: 0.9549 (mptm) cc_final: 0.9089 (mmmm) REVERT: A 160 ILE cc_start: 0.9475 (pp) cc_final: 0.9098 (mp) REVERT: A 168 GLU cc_start: 0.9281 (tt0) cc_final: 0.8931 (tt0) REVERT: A 194 LYS cc_start: 0.9360 (tttp) cc_final: 0.8940 (tptt) REVERT: A 241 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9205 (pt) REVERT: A 275 ASP cc_start: 0.8751 (t70) cc_final: 0.8470 (t0) REVERT: A 357 LYS cc_start: 0.9500 (mtpp) cc_final: 0.9298 (mtpp) REVERT: A 361 LYS cc_start: 0.9451 (mmmt) cc_final: 0.9139 (mmmt) REVERT: A 375 TRP cc_start: 0.8846 (m-90) cc_final: 0.8442 (m-10) REVERT: A 378 TYR cc_start: 0.9461 (p90) cc_final: 0.9205 (p90) REVERT: B 39 TRP cc_start: 0.9533 (t-100) cc_final: 0.9247 (t-100) REVERT: B 66 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9275 (pp) REVERT: B 79 GLN cc_start: 0.8350 (pp30) cc_final: 0.7914 (pp30) REVERT: B 92 MET cc_start: 0.8934 (mmm) cc_final: 0.8582 (mmm) REVERT: B 99 MET cc_start: 0.8217 (ppp) cc_final: 0.7604 (tmm) REVERT: B 127 LYS cc_start: 0.9265 (mtpp) cc_final: 0.9003 (mmmm) REVERT: B 139 ARG cc_start: 0.8746 (mmt90) cc_final: 0.8248 (mtp-110) REVERT: B 170 GLU cc_start: 0.8895 (pp20) cc_final: 0.8637 (pp20) REVERT: B 220 ARG cc_start: 0.8454 (ttm110) cc_final: 0.7862 (mtt180) REVERT: B 236 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8744 (tppt) REVERT: B 375 TRP cc_start: 0.9135 (m-90) cc_final: 0.8614 (m-10) REVERT: C 45 MET cc_start: 0.7912 (mpm) cc_final: 0.7524 (mpp) REVERT: C 77 LYS cc_start: 0.9330 (mmmm) cc_final: 0.8839 (mmmm) REVERT: C 79 GLN cc_start: 0.8936 (pm20) cc_final: 0.8173 (pm20) REVERT: C 108 MET cc_start: 0.8676 (mmm) cc_final: 0.8385 (mmt) REVERT: C 123 ASN cc_start: 0.9247 (p0) cc_final: 0.8938 (p0) REVERT: C 167 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8728 (tp30) REVERT: C 170 GLU cc_start: 0.8646 (pp20) cc_final: 0.8423 (pp20) REVERT: C 171 MET cc_start: 0.9218 (tpp) cc_final: 0.9002 (tpp) REVERT: C 172 ARG cc_start: 0.9274 (ttp80) cc_final: 0.8459 (ptt90) REVERT: C 174 MET cc_start: 0.6653 (mmp) cc_final: 0.6014 (tpt) REVERT: C 237 ASP cc_start: 0.7641 (p0) cc_final: 0.7117 (p0) REVERT: C 254 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9263 (mmtt) REVERT: C 285 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8087 (tm-30) REVERT: C 346 ASP cc_start: 0.7556 (t0) cc_final: 0.6991 (t0) REVERT: C 370 ASP cc_start: 0.8782 (t0) cc_final: 0.8254 (t70) REVERT: J 1 MET cc_start: 0.8137 (ttp) cc_final: 0.7842 (tmm) REVERT: J 10 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7209 (mmm) REVERT: J 21 ASN cc_start: 0.8826 (t0) cc_final: 0.8538 (t0) REVERT: J 29 ASN cc_start: 0.7638 (t0) cc_final: 0.7384 (t0) REVERT: J 36 LYS cc_start: 0.8929 (tmmm) cc_final: 0.8529 (pttt) REVERT: I 10 MET cc_start: 0.8516 (mpp) cc_final: 0.7780 (mpp) REVERT: D 45 ILE cc_start: 0.6750 (tp) cc_final: 0.6502 (mp) REVERT: E 8 ARG cc_start: 0.6198 (tmt170) cc_final: 0.5923 (tmt170) REVERT: E 17 ASP cc_start: 0.8823 (m-30) cc_final: 0.8553 (m-30) REVERT: E 36 LYS cc_start: 0.8029 (pttm) cc_final: 0.7788 (pttm) REVERT: M 92 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7551 (mtp) REVERT: M 129 GLN cc_start: 0.8267 (tp40) cc_final: 0.7990 (tp-100) REVERT: M 203 GLU cc_start: 0.9077 (tp30) cc_final: 0.8374 (tp30) REVERT: M 289 GLN cc_start: 0.8777 (mp10) cc_final: 0.8431 (mp-120) REVERT: M 291 GLN cc_start: 0.9296 (tp-100) cc_final: 0.8722 (tp-100) REVERT: M 295 ASP cc_start: 0.9070 (p0) cc_final: 0.8623 (p0) REVERT: M 359 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7807 (tmm) REVERT: M 378 TYR cc_start: 0.9428 (p90) cc_final: 0.9168 (p90) REVERT: N 28 ASP cc_start: 0.8630 (p0) cc_final: 0.8407 (p0) REVERT: N 45 MET cc_start: 0.8450 (pmm) cc_final: 0.8078 (mpp) REVERT: N 51 ASN cc_start: 0.9195 (m110) cc_final: 0.8735 (t0) REVERT: N 88 GLU cc_start: 0.7376 (pm20) cc_final: 0.7149 (pm20) REVERT: N 92 MET cc_start: 0.9291 (mmm) cc_final: 0.8906 (mmm) REVERT: N 115 ARG cc_start: 0.8654 (mtp85) cc_final: 0.8415 (mtm180) REVERT: N 139 ARG cc_start: 0.8424 (mmt90) cc_final: 0.7972 (mtp-110) REVERT: N 144 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.9032 (p) REVERT: N 156 TYR cc_start: 0.9174 (t80) cc_final: 0.8869 (t80) REVERT: N 168 GLU cc_start: 0.9363 (pp20) cc_final: 0.8919 (pp20) REVERT: N 171 MET cc_start: 0.9114 (ppp) cc_final: 0.8740 (ppp) REVERT: N 203 GLU cc_start: 0.8924 (pp20) cc_final: 0.8683 (tm-30) REVERT: N 209 GLN cc_start: 0.9267 (pt0) cc_final: 0.9057 (pt0) REVERT: N 220 ARG cc_start: 0.8878 (mtt180) cc_final: 0.8673 (ttp-170) REVERT: N 234 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8660 (mmmt) REVERT: N 237 ASP cc_start: 0.8384 (p0) cc_final: 0.7593 (p0) REVERT: N 284 LYS cc_start: 0.9271 (mtmt) cc_final: 0.8932 (mtmm) REVERT: N 298 ARG cc_start: 0.9242 (mmt-90) cc_final: 0.8899 (mmp80) REVERT: N 346 ASP cc_start: 0.8592 (p0) cc_final: 0.8091 (p0) REVERT: N 353 LYS cc_start: 0.9299 (mtpp) cc_final: 0.9094 (mtpp) REVERT: N 382 LYS cc_start: 0.8923 (mttp) cc_final: 0.8597 (mttm) REVERT: O 39 TRP cc_start: 0.9344 (t-100) cc_final: 0.9029 (t-100) REVERT: O 79 GLN cc_start: 0.8659 (mm110) cc_final: 0.8341 (mm110) REVERT: O 92 MET cc_start: 0.8974 (mpp) cc_final: 0.8541 (mpp) REVERT: O 97 ILE cc_start: 0.9539 (pp) cc_final: 0.9137 (mp) REVERT: O 153 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8660 (mm) REVERT: O 203 GLU cc_start: 0.8739 (pp20) cc_final: 0.8446 (pp20) REVERT: O 236 LYS cc_start: 0.9248 (pttp) cc_final: 0.8962 (ptpt) REVERT: Q 23 ARG cc_start: 0.8316 (pmm150) cc_final: 0.7531 (pmm150) REVERT: Q 33 ASP cc_start: 0.8234 (t70) cc_final: 0.7812 (t70) REVERT: Q 39 ASP cc_start: 0.8069 (t70) cc_final: 0.7860 (t70) REVERT: S 10 MET cc_start: 0.8361 (mpt) cc_final: 0.7862 (mmp) REVERT: S 14 SER cc_start: 0.9595 (m) cc_final: 0.9351 (p) REVERT: S 21 ASN cc_start: 0.8003 (p0) cc_final: 0.7798 (p0) REVERT: S 45 ILE cc_start: 0.7079 (mm) cc_final: 0.6814 (mm) REVERT: S 49 SER cc_start: 0.9005 (t) cc_final: 0.8791 (p) outliers start: 113 outliers final: 60 residues processed: 652 average time/residue: 0.1678 time to fit residues: 166.1996 Evaluate side-chains 594 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 526 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLN 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 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 340 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 116 MET 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 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 133 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 254 LYS 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 18 SER Chi-restraints excluded: chain J residue 24 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 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 92 MET Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 181 ASN Chi-restraints excluded: chain N residue 208 LEU Chi-restraints excluded: chain N residue 219 HIS Chi-restraints excluded: chain N residue 231 THR Chi-restraints excluded: chain N residue 276 LEU Chi-restraints excluded: chain N residue 297 LEU 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 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 287 LYS Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 47 SER 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 128 optimal weight: 0.4980 chunk 75 optimal weight: 8.9990 chunk 22 optimal weight: 0.0170 chunk 214 optimal weight: 8.9990 chunk 33 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 115 optimal weight: 0.0870 chunk 138 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 GLN N 211 ASN O 23 GLN S 46 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.074250 restraints weight = 70803.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.076518 restraints weight = 37787.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.078053 restraints weight = 24249.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079108 restraints weight = 17374.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079879 restraints weight = 13470.363| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22334 Z= 0.140 Angle : 0.803 11.405 30163 Z= 0.402 Chirality : 0.048 0.258 3370 Planarity : 0.004 0.038 3876 Dihedral : 6.636 39.872 2975 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 4.99 % Allowed : 19.62 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.15), residues: 2555 helix: -0.99 (0.22), residues: 511 sheet: -2.19 (0.22), residues: 441 loop : -2.47 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 115 TYR 0.018 0.001 TYR N 378 PHE 0.021 0.001 PHE A 202 TRP 0.023 0.001 TRP M 74 HIS 0.017 0.001 HIS N 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (22334) covalent geometry : angle 0.80256 / 0.40 (30163) hydrogen bonds : bond 0.04292 / 2.76 ( 627) hydrogen bonds : angle 5.86316 / 4.02 ( 1665) *********************** 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 716 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 600 time to evaluate : 0.874 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: A 71 ARG cc_start: 0.9159 (ptm160) cc_final: 0.8754 (ptm160) REVERT: A 84 GLN cc_start: 0.8426 (pt0) cc_final: 0.7369 (mp10) REVERT: A 127 LYS cc_start: 0.9540 (mptm) cc_final: 0.9070 (mmmm) REVERT: A 160 ILE cc_start: 0.9437 (pp) cc_final: 0.9124 (mt) REVERT: A 168 GLU cc_start: 0.9232 (tt0) cc_final: 0.8964 (tt0) REVERT: A 194 LYS cc_start: 0.9386 (tttp) cc_final: 0.8850 (tptt) REVERT: A 241 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9160 (pt) REVERT: A 275 ASP cc_start: 0.8733 (t70) cc_final: 0.8475 (t0) REVERT: A 357 LYS cc_start: 0.9495 (mtpp) cc_final: 0.9123 (mtpp) REVERT: A 359 MET cc_start: 0.8396 (ttp) cc_final: 0.7896 (ptm) REVERT: A 361 LYS cc_start: 0.9464 (mmmt) cc_final: 0.9155 (mmmt) REVERT: A 375 TRP cc_start: 0.8758 (m-90) cc_final: 0.8434 (m-10) REVERT: B 39 TRP cc_start: 0.9531 (t-100) cc_final: 0.9264 (t-100) REVERT: B 66 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9271 (pp) REVERT: B 79 GLN cc_start: 0.8337 (pp30) cc_final: 0.8023 (pp30) REVERT: B 92 MET cc_start: 0.8885 (mmm) cc_final: 0.8581 (mmm) REVERT: B 99 MET cc_start: 0.8201 (ppp) cc_final: 0.7522 (tmm) REVERT: B 139 ARG cc_start: 0.8555 (mmt90) cc_final: 0.8166 (mtp-110) REVERT: B 167 GLU cc_start: 0.8793 (tp30) cc_final: 0.8373 (tp30) REVERT: B 170 GLU cc_start: 0.8885 (pp20) cc_final: 0.8584 (pp20) REVERT: B 220 ARG cc_start: 0.8392 (ttm110) cc_final: 0.7785 (mtt180) REVERT: B 236 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8651 (tppt) REVERT: B 375 TRP cc_start: 0.8927 (m-90) cc_final: 0.8411 (m-10) REVERT: C 45 MET cc_start: 0.7897 (mpm) cc_final: 0.7512 (mpp) REVERT: C 77 LYS cc_start: 0.9388 (mmmm) cc_final: 0.8896 (mmmm) REVERT: C 79 GLN cc_start: 0.8867 (pm20) cc_final: 0.8120 (pm20) REVERT: C 99 MET cc_start: 0.8381 (pmm) cc_final: 0.8154 (pmm) REVERT: C 108 MET cc_start: 0.8610 (mmm) cc_final: 0.8151 (mmt) REVERT: C 110 LYS cc_start: 0.9495 (mtmm) cc_final: 0.9246 (mtmm) REVERT: C 123 ASN cc_start: 0.9248 (p0) cc_final: 0.8987 (p0) REVERT: C 167 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8734 (tp30) REVERT: C 168 GLU cc_start: 0.9406 (OUTLIER) cc_final: 0.9094 (pp20) REVERT: C 170 GLU cc_start: 0.8648 (pp20) cc_final: 0.8402 (pp20) REVERT: C 171 MET cc_start: 0.9269 (tpp) cc_final: 0.9039 (tpp) REVERT: C 172 ARG cc_start: 0.9249 (ttp80) cc_final: 0.8386 (ptt90) REVERT: C 174 MET cc_start: 0.6661 (mmp) cc_final: 0.5920 (tpt) REVERT: C 237 ASP cc_start: 0.7382 (p0) cc_final: 0.6680 (p0) REVERT: C 244 ASP cc_start: 0.8196 (m-30) cc_final: 0.7957 (m-30) REVERT: C 285 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8054 (tm-30) REVERT: C 346 ASP cc_start: 0.7469 (t0) cc_final: 0.6621 (t0) REVERT: J 10 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7276 (mmm) REVERT: J 13 THR cc_start: 0.9303 (t) cc_final: 0.8959 (t) REVERT: J 16 GLU cc_start: 0.8787 (mp0) cc_final: 0.8140 (pm20) REVERT: J 21 ASN cc_start: 0.8927 (t0) cc_final: 0.8541 (t0) REVERT: J 36 LYS cc_start: 0.8932 (tmmm) cc_final: 0.8534 (pttm) REVERT: I 10 MET cc_start: 0.8305 (mpp) cc_final: 0.7970 (mpp) REVERT: E 30 MET cc_start: 0.8396 (tpp) cc_final: 0.8111 (tpp) REVERT: E 36 LYS cc_start: 0.7949 (pttm) cc_final: 0.7696 (pttm) REVERT: M 65 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8560 (p0) REVERT: M 92 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7389 (mtp) REVERT: M 99 MET cc_start: 0.7284 (mmm) cc_final: 0.6729 (tpt) REVERT: M 203 GLU cc_start: 0.8980 (tp30) cc_final: 0.8689 (tp30) REVERT: M 234 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8227 (tptt) REVERT: M 291 GLN cc_start: 0.9259 (tp-100) cc_final: 0.8634 (tp-100) REVERT: M 295 ASP cc_start: 0.9027 (p0) cc_final: 0.8587 (p0) REVERT: N 28 ASP cc_start: 0.8641 (p0) cc_final: 0.8436 (p0) REVERT: N 45 MET cc_start: 0.8372 (pmm) cc_final: 0.7950 (mpp) REVERT: N 51 ASN cc_start: 0.9203 (m110) cc_final: 0.8719 (t0) REVERT: N 88 GLU cc_start: 0.7165 (pm20) cc_final: 0.6964 (pm20) REVERT: N 92 MET cc_start: 0.9298 (mmm) cc_final: 0.8924 (mmm) REVERT: N 110 LYS cc_start: 0.9384 (tppt) cc_final: 0.8976 (mmtt) REVERT: N 115 ARG cc_start: 0.8693 (mtp85) cc_final: 0.8437 (mtm180) REVERT: N 128 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8699 (mmmt) REVERT: N 139 ARG cc_start: 0.8453 (mmt90) cc_final: 0.7861 (mtp-110) REVERT: N 156 TYR cc_start: 0.9099 (t80) cc_final: 0.8878 (t80) REVERT: N 168 GLU cc_start: 0.9383 (pp20) cc_final: 0.9125 (pt0) REVERT: N 171 MET cc_start: 0.9184 (ppp) cc_final: 0.8768 (ppp) REVERT: N 203 GLU cc_start: 0.8924 (pp20) cc_final: 0.8662 (tm-30) REVERT: N 209 GLN cc_start: 0.9240 (pt0) cc_final: 0.9000 (pt0) REVERT: N 217 GLU cc_start: 0.7661 (tp30) cc_final: 0.7303 (tp30) REVERT: N 220 ARG cc_start: 0.8933 (mtt180) cc_final: 0.8624 (mtm180) REVERT: N 234 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8405 (mmmt) REVERT: N 237 ASP cc_start: 0.8301 (p0) cc_final: 0.7530 (p0) REVERT: N 284 LYS cc_start: 0.9235 (mtmt) cc_final: 0.8930 (mtmm) REVERT: N 346 ASP cc_start: 0.8607 (p0) cc_final: 0.8059 (p0) REVERT: N 375 TRP cc_start: 0.9340 (m-90) cc_final: 0.9012 (m-90) REVERT: O 39 TRP cc_start: 0.9316 (t-100) cc_final: 0.9037 (t-100) REVERT: O 40 ASP cc_start: 0.9175 (t0) cc_final: 0.8928 (t0) REVERT: O 92 MET cc_start: 0.8906 (mpp) cc_final: 0.8557 (mpp) REVERT: O 97 ILE cc_start: 0.9491 (pp) cc_final: 0.9129 (mp) REVERT: O 110 LYS cc_start: 0.9322 (mmtm) cc_final: 0.8932 (mmtm) REVERT: O 203 GLU cc_start: 0.8729 (pp20) cc_final: 0.8402 (pp20) REVERT: O 207 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8350 (m-40) REVERT: O 236 LYS cc_start: 0.9221 (pttp) cc_final: 0.8902 (ptpt) REVERT: Q 23 ARG cc_start: 0.8366 (pmm150) cc_final: 0.7950 (pmt170) REVERT: Q 33 ASP cc_start: 0.8191 (t70) cc_final: 0.7666 (t70) REVERT: S 10 MET cc_start: 0.8063 (mpt) cc_final: 0.7644 (mmp) REVERT: S 21 ASN cc_start: 0.8079 (p0) cc_final: 0.7763 (p0) REVERT: S 49 SER cc_start: 0.8959 (t) cc_final: 0.8745 (p) outliers start: 116 outliers final: 61 residues processed: 660 average time/residue: 0.1612 time to fit residues: 162.7338 Evaluate side-chains 603 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 535 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 63 LEU Chi-restraints excluded: chain A residue 95 VAL 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 235 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 GLU 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 360 LEU Chi-restraints excluded: chain J residue 10 MET 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 E residue 22 LYS Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 92 MET 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 208 LEU 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 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 276 LEU Chi-restraints excluded: chain N residue 297 LEU 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 N residue 350 ILE 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 145 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 207 ASN Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 287 LYS Chi-restraints excluded: chain O residue 360 LEU Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain S residue 31 SER 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 123 optimal weight: 5.9990 chunk 133 optimal weight: 50.0000 chunk 44 optimal weight: 10.0000 chunk 268 optimal weight: 50.0000 chunk 75 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 226 optimal weight: 0.0170 chunk 263 optimal weight: 30.0000 chunk 218 optimal weight: 0.0040 chunk 149 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 overall best weight: 1.7834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 269 HIS ** N 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.090370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076034 restraints weight = 70545.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.078357 restraints weight = 38188.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079946 restraints weight = 24794.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081054 restraints weight = 17926.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081809 restraints weight = 13971.768| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3567 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= 0.151 Angle : 0.805 12.190 30163 Z= 0.401 Chirality : 0.048 0.257 3370 Planarity : 0.004 0.053 3876 Dihedral : 6.378 37.208 2975 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 5.12 % Allowed : 21.73 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.15), residues: 2555 helix: -0.89 (0.22), residues: 518 sheet: -2.00 (0.22), residues: 457 loop : -2.36 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 19 TYR 0.036 0.002 TYR O 178 PHE 0.015 0.001 PHE A 131 TRP 0.021 0.001 TRP M 74 HIS 0.015 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (22334) covalent geometry : angle 0.80499 / 0.40 (30163) hydrogen bonds : bond 0.04173 / 2.69 ( 627) hydrogen bonds : angle 5.80733 / 3.99 ( 1665) *********************** 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 692 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 573 time to evaluate : 0.897 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: A 84 GLN cc_start: 0.8520 (pt0) cc_final: 0.7427 (mp10) REVERT: A 127 LYS cc_start: 0.9542 (mptm) cc_final: 0.9040 (mmmt) REVERT: A 160 ILE cc_start: 0.9463 (pp) cc_final: 0.9128 (mt) REVERT: A 234 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8623 (mmmt) REVERT: A 261 ILE cc_start: 0.8701 (mp) cc_final: 0.8190 (mm) REVERT: A 275 ASP cc_start: 0.8748 (t70) cc_final: 0.8444 (t0) REVERT: A 357 LYS cc_start: 0.9541 (mtpp) cc_final: 0.9176 (mtpp) REVERT: A 361 LYS cc_start: 0.9488 (mmmt) cc_final: 0.9173 (mmmt) REVERT: A 375 TRP cc_start: 0.8816 (m-90) cc_final: 0.8465 (m-10) REVERT: B 39 TRP cc_start: 0.9542 (t-100) cc_final: 0.9305 (t-100) REVERT: B 66 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9290 (pp) REVERT: B 92 MET cc_start: 0.8921 (mmm) cc_final: 0.8627 (mmm) REVERT: B 99 MET cc_start: 0.8264 (ppp) cc_final: 0.7685 (tmm) REVERT: B 127 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8971 (mmmt) REVERT: B 139 ARG cc_start: 0.8576 (mmt90) cc_final: 0.8172 (mtp-110) REVERT: B 158 LYS cc_start: 0.9540 (tppt) cc_final: 0.9198 (tptp) REVERT: B 168 GLU cc_start: 0.8636 (tt0) cc_final: 0.8305 (tt0) REVERT: B 170 GLU cc_start: 0.8918 (pp20) cc_final: 0.8609 (pp20) REVERT: B 220 ARG cc_start: 0.8434 (ttm110) cc_final: 0.7827 (mtt180) REVERT: B 236 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8740 (tppt) REVERT: B 238 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.8974 (mp) REVERT: B 354 ARG cc_start: 0.8885 (ttp-170) cc_final: 0.8019 (ttm170) REVERT: B 375 TRP cc_start: 0.8928 (m-90) cc_final: 0.8451 (m-10) REVERT: C 45 MET cc_start: 0.7935 (mpm) cc_final: 0.7544 (mpp) REVERT: C 77 LYS cc_start: 0.9451 (mmmm) cc_final: 0.8943 (mmmm) REVERT: C 79 GLN cc_start: 0.8933 (pm20) cc_final: 0.8126 (pm20) REVERT: C 99 MET cc_start: 0.8369 (pmm) cc_final: 0.7856 (pmm) REVERT: C 108 MET cc_start: 0.8628 (mmm) cc_final: 0.8136 (mmt) REVERT: C 123 ASN cc_start: 0.9267 (p0) cc_final: 0.9018 (p0) REVERT: C 167 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8768 (tp30) REVERT: C 168 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.9125 (pp20) REVERT: C 170 GLU cc_start: 0.8682 (pp20) cc_final: 0.8439 (pp20) REVERT: C 171 MET cc_start: 0.9269 (tpp) cc_final: 0.9045 (tpp) REVERT: C 172 ARG cc_start: 0.9263 (ttp80) cc_final: 0.8465 (ptt90) REVERT: C 174 MET cc_start: 0.6685 (mmp) cc_final: 0.6038 (tpt) REVERT: C 237 ASP cc_start: 0.7425 (p0) cc_final: 0.6713 (p0) REVERT: C 244 ASP cc_start: 0.8222 (m-30) cc_final: 0.7953 (m-30) REVERT: C 285 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8052 (tm-30) REVERT: C 346 ASP cc_start: 0.7516 (t0) cc_final: 0.6618 (t0) REVERT: J 1 MET cc_start: 0.7489 (tmm) cc_final: 0.6840 (tmm) REVERT: J 10 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7326 (mmm) REVERT: J 21 ASN cc_start: 0.9152 (t0) cc_final: 0.8655 (t0) REVERT: J 36 LYS cc_start: 0.8888 (tmmm) cc_final: 0.8486 (pttt) REVERT: I 10 MET cc_start: 0.8277 (mpp) cc_final: 0.7688 (mpp) REVERT: I 39 ASP cc_start: 0.8882 (p0) cc_final: 0.8546 (p0) REVERT: M 92 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7478 (mtp) REVERT: M 129 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7511 (tp-100) REVERT: M 158 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8878 (tttt) REVERT: M 203 GLU cc_start: 0.8955 (tp30) cc_final: 0.8749 (tp30) REVERT: M 289 GLN cc_start: 0.8760 (mp10) cc_final: 0.8449 (mp-120) REVERT: M 291 GLN cc_start: 0.9237 (tp-100) cc_final: 0.8615 (tp-100) REVERT: M 295 ASP cc_start: 0.9017 (p0) cc_final: 0.8584 (p0) REVERT: M 351 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8886 (mmtt) REVERT: N 28 ASP cc_start: 0.8638 (p0) cc_final: 0.8404 (p0) REVERT: N 45 MET cc_start: 0.8455 (pmm) cc_final: 0.8157 (mpp) REVERT: N 51 ASN cc_start: 0.9171 (m110) cc_final: 0.8697 (t0) REVERT: N 88 GLU cc_start: 0.7253 (pm20) cc_final: 0.7046 (pm20) REVERT: N 92 MET cc_start: 0.9299 (mmm) cc_final: 0.9013 (mmm) REVERT: N 110 LYS cc_start: 0.9368 (tppt) cc_final: 0.9124 (mmtt) REVERT: N 115 ARG cc_start: 0.8693 (mtp85) cc_final: 0.8399 (mtm180) REVERT: N 128 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8545 (mmmm) REVERT: N 139 ARG cc_start: 0.8481 (mmt90) cc_final: 0.7870 (mtp-110) REVERT: N 156 TYR cc_start: 0.9086 (t80) cc_final: 0.8862 (t80) REVERT: N 168 GLU cc_start: 0.9399 (pp20) cc_final: 0.8938 (pp20) REVERT: N 171 MET cc_start: 0.9161 (ppp) cc_final: 0.8726 (ppp) REVERT: N 203 GLU cc_start: 0.8933 (pp20) cc_final: 0.8674 (tm-30) REVERT: N 217 GLU cc_start: 0.7736 (tp30) cc_final: 0.7269 (tp30) REVERT: N 220 ARG cc_start: 0.8919 (mtt180) cc_final: 0.8667 (mtm180) REVERT: N 234 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8343 (mmmt) REVERT: N 237 ASP cc_start: 0.8318 (p0) cc_final: 0.7563 (p0) REVERT: N 284 LYS cc_start: 0.9258 (mtmt) cc_final: 0.8942 (mtmm) REVERT: N 325 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8510 (ptmm) REVERT: N 346 ASP cc_start: 0.8633 (p0) cc_final: 0.8107 (p0) REVERT: O 39 TRP cc_start: 0.9336 (t-100) cc_final: 0.9096 (t-100) REVERT: O 40 ASP cc_start: 0.9208 (t0) cc_final: 0.8960 (t0) REVERT: O 79 GLN cc_start: 0.8545 (mm110) cc_final: 0.8255 (mm-40) REVERT: O 92 MET cc_start: 0.8844 (mpp) cc_final: 0.8635 (mpp) REVERT: O 93 ASP cc_start: 0.8903 (m-30) cc_final: 0.8109 (m-30) REVERT: O 167 GLU cc_start: 0.8301 (tp30) cc_final: 0.7818 (tp30) REVERT: O 174 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6598 (mmm) REVERT: O 197 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9026 (tp) REVERT: O 203 GLU cc_start: 0.8770 (pp20) cc_final: 0.8426 (pp20) REVERT: O 207 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8338 (m-40) REVERT: O 236 LYS cc_start: 0.9254 (pttp) cc_final: 0.8951 (ptpt) REVERT: Q 23 ARG cc_start: 0.8363 (pmm150) cc_final: 0.7950 (pmt170) REVERT: Q 33 ASP cc_start: 0.8267 (t70) cc_final: 0.7688 (t70) REVERT: S 10 MET cc_start: 0.7883 (mpt) cc_final: 0.5891 (ptm) REVERT: S 21 ASN cc_start: 0.7947 (p0) cc_final: 0.7628 (p0) REVERT: S 27 ASN cc_start: 0.8444 (t0) cc_final: 0.8201 (p0) REVERT: S 31 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8757 (p) REVERT: S 49 SER cc_start: 0.8966 (t) cc_final: 0.8745 (p) outliers start: 119 outliers final: 64 residues processed: 639 average time/residue: 0.1687 time to fit residues: 163.7867 Evaluate side-chains 606 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 530 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 144 THR 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 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 66 ILE 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 209 GLN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 350 ILE 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 149 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 168 GLU 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 344 ILE Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 18 SER Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 34 THR 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 M residue 92 MET 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 158 LYS Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 236 LYS 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 359 MET Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain N residue 153 LEU 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 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 297 LEU 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 N residue 350 ILE Chi-restraints excluded: chain O residue 116 MET Chi-restraints excluded: chain O residue 145 LEU Chi-restraints excluded: chain O residue 174 MET Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 207 ASN Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 287 LYS Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain S residue 31 SER 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 167 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 265 optimal weight: 50.0000 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 267 optimal weight: 30.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN J 29 ASN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 HIS ** N 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.072987 restraints weight = 73402.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.075203 restraints weight = 39627.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076730 restraints weight = 25752.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077768 restraints weight = 18647.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.078505 restraints weight = 14553.954| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22334 Z= 0.219 Angle : 0.829 10.235 30163 Z= 0.419 Chirality : 0.049 0.278 3370 Planarity : 0.004 0.034 3876 Dihedral : 6.338 34.415 2975 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 5.25 % Allowed : 23.02 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.16), residues: 2555 helix: -0.82 (0.22), residues: 524 sheet: -1.86 (0.23), residues: 447 loop : -2.30 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 115 TYR 0.031 0.002 TYR O 178 PHE 0.019 0.001 PHE A 202 TRP 0.021 0.002 TRP M 74 HIS 0.015 0.002 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (22334) covalent geometry : angle 0.82873 / 0.42 (30163) hydrogen bonds : bond 0.04249 / 2.75 ( 627) hydrogen bonds : angle 5.74920 / 3.94 ( 1665) *********************** 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 671 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 549 time to evaluate : 0.866 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 127 LYS cc_start: 0.9538 (mptm) cc_final: 0.9070 (mmmm) REVERT: A 160 ILE cc_start: 0.9517 (pp) cc_final: 0.9175 (mt) REVERT: A 168 GLU cc_start: 0.9261 (tt0) cc_final: 0.9024 (tt0) REVERT: A 234 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8671 (mmmt) REVERT: A 238 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8870 (mp) REVERT: A 261 ILE cc_start: 0.8729 (mp) cc_final: 0.8134 (mm) REVERT: A 275 ASP cc_start: 0.8823 (t70) cc_final: 0.8553 (t0) REVERT: A 357 LYS cc_start: 0.9559 (mtpp) cc_final: 0.9217 (mtpp) REVERT: A 361 LYS cc_start: 0.9554 (mmmt) cc_final: 0.9274 (mmmt) REVERT: A 375 TRP cc_start: 0.8837 (m-90) cc_final: 0.8465 (m-10) REVERT: B 66 ILE cc_start: 0.9563 (OUTLIER) cc_final: 0.9325 (pp) REVERT: B 92 MET cc_start: 0.8923 (mmm) cc_final: 0.8657 (mmm) REVERT: B 99 MET cc_start: 0.8372 (ppp) cc_final: 0.7817 (tmm) REVERT: B 127 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8978 (mmmm) REVERT: B 139 ARG cc_start: 0.8644 (mmt90) cc_final: 0.8283 (mtp-110) REVERT: B 158 LYS cc_start: 0.9572 (tppt) cc_final: 0.9173 (tptp) REVERT: B 170 GLU cc_start: 0.8918 (pp20) cc_final: 0.8623 (pp20) REVERT: B 236 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8735 (tppt) REVERT: B 238 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9085 (mp) REVERT: B 375 TRP cc_start: 0.8954 (m-90) cc_final: 0.8501 (m-10) REVERT: C 45 MET cc_start: 0.7917 (mpm) cc_final: 0.7444 (mpp) REVERT: C 77 LYS cc_start: 0.9491 (mmmm) cc_final: 0.9122 (mmmm) REVERT: C 79 GLN cc_start: 0.9038 (pm20) cc_final: 0.8302 (pm20) REVERT: C 99 MET cc_start: 0.8455 (pmm) cc_final: 0.7913 (pmm) REVERT: C 108 MET cc_start: 0.8551 (mmm) cc_final: 0.8076 (mmt) REVERT: C 123 ASN cc_start: 0.9289 (p0) cc_final: 0.9016 (p0) REVERT: C 167 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8665 (tp30) REVERT: C 168 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.9091 (pp20) REVERT: C 170 GLU cc_start: 0.8689 (pp20) cc_final: 0.8367 (pp20) REVERT: C 171 MET cc_start: 0.9278 (tpp) cc_final: 0.9045 (tpp) REVERT: C 172 ARG cc_start: 0.9267 (ttp80) cc_final: 0.8456 (ptt90) REVERT: C 285 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 369 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7858 (t80) REVERT: J 1 MET cc_start: 0.7469 (tmm) cc_final: 0.7124 (tmt) REVERT: J 10 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7409 (mmm) REVERT: J 21 ASN cc_start: 0.9093 (t0) cc_final: 0.8769 (t0) REVERT: I 10 MET cc_start: 0.8303 (mpp) cc_final: 0.7689 (mpp) REVERT: D 35 ASN cc_start: 0.8712 (t0) cc_final: 0.8364 (t0) REVERT: D 46 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6647 (t70) REVERT: E 36 LYS cc_start: 0.7902 (pttm) cc_final: 0.7602 (pttm) REVERT: M 129 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7677 (tp-100) REVERT: M 159 LYS cc_start: 0.9634 (ttmm) cc_final: 0.9422 (tppp) REVERT: M 203 GLU cc_start: 0.8919 (tp30) cc_final: 0.8516 (tp30) REVERT: M 234 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8382 (tptp) REVERT: M 289 GLN cc_start: 0.8761 (mp10) cc_final: 0.8443 (mp-120) REVERT: M 291 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8820 (tp-100) REVERT: M 295 ASP cc_start: 0.8968 (p0) cc_final: 0.8703 (p0) REVERT: N 28 ASP cc_start: 0.8701 (p0) cc_final: 0.8419 (p0) REVERT: N 45 MET cc_start: 0.8559 (pmm) cc_final: 0.8157 (mpp) REVERT: N 51 ASN cc_start: 0.9157 (m110) cc_final: 0.8809 (t0) REVERT: N 92 MET cc_start: 0.9279 (mmm) cc_final: 0.8763 (mmm) REVERT: N 110 LYS cc_start: 0.9501 (tppt) cc_final: 0.9043 (mmtt) REVERT: N 115 ARG cc_start: 0.8682 (mtp85) cc_final: 0.8376 (mtm180) REVERT: N 128 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8501 (mmmm) REVERT: N 139 ARG cc_start: 0.8371 (mmt90) cc_final: 0.7923 (mtp-110) REVERT: N 156 TYR cc_start: 0.9157 (t80) cc_final: 0.8882 (t80) REVERT: N 168 GLU cc_start: 0.9410 (pp20) cc_final: 0.9101 (pp20) REVERT: N 203 GLU cc_start: 0.8821 (pp20) cc_final: 0.8589 (pp20) REVERT: N 217 GLU cc_start: 0.7807 (tp30) cc_final: 0.7363 (tp30) REVERT: N 220 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8582 (mtm180) REVERT: N 234 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8432 (mmmt) REVERT: N 237 ASP cc_start: 0.8358 (p0) cc_final: 0.7706 (p0) REVERT: N 252 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8762 (p0) REVERT: N 284 LYS cc_start: 0.9317 (mtmt) cc_final: 0.8980 (mtmm) REVERT: N 346 ASP cc_start: 0.8623 (p0) cc_final: 0.8209 (p0) REVERT: O 39 TRP cc_start: 0.9297 (t-100) cc_final: 0.9063 (t-100) REVERT: O 40 ASP cc_start: 0.9211 (t0) cc_final: 0.8989 (t0) REVERT: O 93 ASP cc_start: 0.8888 (m-30) cc_final: 0.7989 (m-30) REVERT: O 99 MET cc_start: 0.7429 (ppp) cc_final: 0.7148 (ppp) REVERT: O 167 GLU cc_start: 0.8135 (tp30) cc_final: 0.7666 (tp30) REVERT: O 197 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8983 (tp) REVERT: O 202 PHE cc_start: 0.9411 (t80) cc_final: 0.9173 (t80) REVERT: O 236 LYS cc_start: 0.9269 (pttp) cc_final: 0.8971 (ptpt) REVERT: Q 21 ASN cc_start: 0.8375 (t0) cc_final: 0.8091 (t0) REVERT: Q 23 ARG cc_start: 0.8425 (pmm150) cc_final: 0.7934 (pmt170) REVERT: Q 33 ASP cc_start: 0.8372 (t70) cc_final: 0.7554 (t0) REVERT: S 10 MET cc_start: 0.7858 (mpt) cc_final: 0.6008 (ptm) REVERT: S 21 ASN cc_start: 0.8036 (p0) cc_final: 0.7741 (p0) REVERT: S 31 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8905 (p) REVERT: S 49 SER cc_start: 0.9076 (t) cc_final: 0.8856 (p) outliers start: 122 outliers final: 73 residues processed: 622 average time/residue: 0.1688 time to fit residues: 159.7721 Evaluate side-chains 611 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 528 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 144 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 276 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 66 ILE 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 180 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 350 ILE 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 133 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 168 GLU 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 345 LEU Chi-restraints excluded: chain C residue 369 PHE 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 29 ASN Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain I residue 14 SER 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 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 175 LEU Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 392 LEU Chi-restraints excluded: chain N residue 144 THR 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 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 323 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 197 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 287 LYS Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain S residue 31 SER 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 26 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN B 182 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS J 29 ASN ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 211 ASN S 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.087871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074077 restraints weight = 71535.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.076326 restraints weight = 38525.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.077855 restraints weight = 24901.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.078904 restraints weight = 17965.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079664 restraints weight = 13994.513| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22334 Z= 0.160 Angle : 0.816 11.824 30163 Z= 0.407 Chirality : 0.048 0.254 3370 Planarity : 0.004 0.038 3876 Dihedral : 6.231 39.294 2975 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 5.12 % Allowed : 23.58 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.16), residues: 2555 helix: -0.72 (0.23), residues: 520 sheet: -1.75 (0.23), residues: 447 loop : -2.23 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 115 TYR 0.032 0.002 TYR S 41 PHE 0.016 0.001 PHE M 266 TRP 0.023 0.002 TRP M 74 HIS 0.022 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (22334) covalent geometry : angle 0.81586 / 0.41 (30163) hydrogen bonds : bond 0.04165 / 2.69 ( 627) hydrogen bonds : angle 5.70729 / 3.90 ( 1665) *********************** 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 690 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 571 time to evaluate : 0.937 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: A 71 ARG cc_start: 0.9194 (ptm160) cc_final: 0.8816 (ptm160) REVERT: A 127 LYS cc_start: 0.9533 (mptm) cc_final: 0.9046 (mmmm) REVERT: A 160 ILE cc_start: 0.9483 (pp) cc_final: 0.9275 (mt) REVERT: A 234 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8561 (mmmt) REVERT: A 235 LEU cc_start: 0.9218 (tp) cc_final: 0.8978 (tt) REVERT: A 261 ILE cc_start: 0.8669 (mp) cc_final: 0.8181 (mm) REVERT: A 275 ASP cc_start: 0.8832 (t70) cc_final: 0.8546 (t0) REVERT: A 357 LYS cc_start: 0.9536 (mtpp) cc_final: 0.9164 (mtpp) REVERT: A 361 LYS cc_start: 0.9555 (mmmt) cc_final: 0.9305 (mmmt) REVERT: A 375 TRP cc_start: 0.8783 (m-90) cc_final: 0.8441 (m-10) REVERT: B 66 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9310 (pp) REVERT: B 92 MET cc_start: 0.8946 (mmm) cc_final: 0.8668 (mmm) REVERT: B 99 MET cc_start: 0.8387 (ppp) cc_final: 0.7842 (tmm) REVERT: B 139 ARG cc_start: 0.8605 (mmt90) cc_final: 0.8238 (mtp-110) REVERT: B 158 LYS cc_start: 0.9533 (tppt) cc_final: 0.9126 (tptp) REVERT: B 170 GLU cc_start: 0.8925 (pp20) cc_final: 0.8724 (pp20) REVERT: B 236 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8679 (tppt) REVERT: B 238 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9017 (mp) REVERT: B 357 LYS cc_start: 0.8859 (mtmp) cc_final: 0.8343 (mtmm) REVERT: B 375 TRP cc_start: 0.8889 (m-90) cc_final: 0.8410 (m-10) REVERT: B 382 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6951 (pptt) REVERT: C 45 MET cc_start: 0.7909 (mpm) cc_final: 0.7444 (mpp) REVERT: C 77 LYS cc_start: 0.9502 (mmmm) cc_final: 0.9147 (mmmm) REVERT: C 79 GLN cc_start: 0.8967 (pm20) cc_final: 0.8329 (pm20) REVERT: C 99 MET cc_start: 0.8448 (pmm) cc_final: 0.7815 (pmm) REVERT: C 108 MET cc_start: 0.8610 (mmm) cc_final: 0.8206 (mmt) REVERT: C 123 ASN cc_start: 0.9257 (p0) cc_final: 0.9045 (p0) REVERT: C 167 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8711 (tp30) REVERT: C 168 GLU cc_start: 0.9447 (OUTLIER) cc_final: 0.9068 (pp20) REVERT: C 170 GLU cc_start: 0.8831 (pp20) cc_final: 0.8361 (pp20) REVERT: C 171 MET cc_start: 0.9319 (tpp) cc_final: 0.9083 (tpp) REVERT: C 172 ARG cc_start: 0.9272 (ttp80) cc_final: 0.8435 (ptt90) REVERT: C 254 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.9333 (mmtt) REVERT: C 285 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 369 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7906 (t80) REVERT: J 10 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7124 (mmm) REVERT: J 21 ASN cc_start: 0.9152 (t0) cc_final: 0.8813 (t0) REVERT: J 30 MET cc_start: 0.8792 (tpp) cc_final: 0.8347 (tmm) REVERT: I 10 MET cc_start: 0.8263 (mpp) cc_final: 0.7618 (mpp) REVERT: D 35 ASN cc_start: 0.8650 (t0) cc_final: 0.8326 (t0) REVERT: D 46 HIS cc_start: 0.6648 (OUTLIER) cc_final: 0.6432 (t70) REVERT: E 22 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8398 (mmpt) REVERT: M 93 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: M 99 MET cc_start: 0.8182 (mmm) cc_final: 0.7590 (tpt) REVERT: M 129 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7691 (tp-100) REVERT: M 159 LYS cc_start: 0.9644 (ttmm) cc_final: 0.9432 (tppp) REVERT: M 177 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8803 (p0) REVERT: M 203 GLU cc_start: 0.8895 (tp30) cc_final: 0.8430 (tp30) REVERT: M 234 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8062 (tptt) REVERT: M 289 GLN cc_start: 0.8750 (mp10) cc_final: 0.8393 (mp-120) REVERT: M 291 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8809 (tp-100) REVERT: M 295 ASP cc_start: 0.8985 (p0) cc_final: 0.8741 (p0) REVERT: N 28 ASP cc_start: 0.8694 (p0) cc_final: 0.8403 (p0) REVERT: N 45 MET cc_start: 0.8527 (pmm) cc_final: 0.8048 (mpp) REVERT: N 51 ASN cc_start: 0.9124 (m110) cc_final: 0.8790 (t0) REVERT: N 110 LYS cc_start: 0.9483 (tppt) cc_final: 0.9011 (mmtt) REVERT: N 115 ARG cc_start: 0.8633 (mtp85) cc_final: 0.8432 (mtm180) REVERT: N 128 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8594 (mmmm) REVERT: N 139 ARG cc_start: 0.8330 (mmt90) cc_final: 0.7824 (mtp-110) REVERT: N 156 TYR cc_start: 0.9112 (t80) cc_final: 0.8904 (t80) REVERT: N 168 GLU cc_start: 0.9447 (pp20) cc_final: 0.9141 (pp20) REVERT: N 203 GLU cc_start: 0.8878 (pp20) cc_final: 0.8615 (pp20) REVERT: N 217 GLU cc_start: 0.7791 (tp30) cc_final: 0.7290 (tp30) REVERT: N 220 ARG cc_start: 0.8889 (mtt180) cc_final: 0.8568 (mtm180) REVERT: N 234 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8337 (mmmt) REVERT: N 237 ASP cc_start: 0.8319 (p0) cc_final: 0.7611 (p0) REVERT: N 284 LYS cc_start: 0.9298 (mtmt) cc_final: 0.8944 (mtmm) REVERT: N 346 ASP cc_start: 0.8607 (p0) cc_final: 0.8168 (p0) REVERT: O 39 TRP cc_start: 0.9246 (t-100) cc_final: 0.9043 (t-100) REVERT: O 40 ASP cc_start: 0.9166 (t0) cc_final: 0.8935 (t0) REVERT: O 93 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: O 197 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8968 (tp) REVERT: O 202 PHE cc_start: 0.9415 (t80) cc_final: 0.9161 (t80) REVERT: O 217 GLU cc_start: 0.8238 (pm20) cc_final: 0.8010 (pm20) REVERT: O 236 LYS cc_start: 0.9264 (pttp) cc_final: 0.8953 (ptpt) REVERT: O 261 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8404 (pp) REVERT: O 371 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: Q 21 ASN cc_start: 0.8371 (t0) cc_final: 0.8054 (t0) REVERT: Q 23 ARG cc_start: 0.8389 (pmm150) cc_final: 0.7889 (pmt170) REVERT: Q 33 ASP cc_start: 0.8402 (t70) cc_final: 0.7567 (t0) REVERT: S 10 MET cc_start: 0.7718 (mpt) cc_final: 0.5848 (ptt) REVERT: S 49 SER cc_start: 0.9059 (t) cc_final: 0.8824 (p) outliers start: 119 outliers final: 72 residues processed: 635 average time/residue: 0.1599 time to fit residues: 155.1399 Evaluate side-chains 616 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 529 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 118 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 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 66 ILE 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 209 GLN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 350 ILE 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 149 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 369 PHE 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 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 52 SER Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 93 ASP 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 275 ASP Chi-restraints excluded: chain M residue 321 VAL 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 M residue 392 LEU Chi-restraints excluded: chain N residue 144 THR 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 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 N residue 285 GLU Chi-restraints excluded: chain N residue 297 LEU 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 87 GLU 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 133 LEU 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 261 ILE Chi-restraints excluded: chain O residue 287 LYS Chi-restraints excluded: chain O residue 371 GLU Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 179 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 129 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 211 ASN O 182 GLN Q 35 ASN S 5 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.087805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073925 restraints weight = 71504.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076165 restraints weight = 38724.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077669 restraints weight = 25134.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078764 restraints weight = 18253.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079529 restraints weight = 14170.874| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4069 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= 0.174 Angle : 0.831 12.505 30163 Z= 0.416 Chirality : 0.049 0.218 3370 Planarity : 0.004 0.040 3876 Dihedral : 6.162 40.502 2975 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 4.82 % Allowed : 24.53 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.16), residues: 2555 helix: -0.69 (0.23), residues: 521 sheet: -1.69 (0.23), residues: 447 loop : -2.19 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 115 TYR 0.033 0.002 TYR O 178 PHE 0.022 0.001 PHE A 202 TRP 0.019 0.002 TRP M 74 HIS 0.026 0.002 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (22334) covalent geometry : angle 0.83124 / 0.42 (30163) hydrogen bonds : bond 0.04189 / 2.70 ( 627) hydrogen bonds : angle 5.66379 / 3.87 ( 1665) *********************** 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 661 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 549 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.0377 (OUTLIER) cc_final: -0.1505 (t0) REVERT: A 127 LYS cc_start: 0.9530 (mptm) cc_final: 0.9033 (mmmm) REVERT: A 160 ILE cc_start: 0.9583 (pp) cc_final: 0.9268 (mt) REVERT: A 167 GLU cc_start: 0.8353 (pm20) cc_final: 0.8109 (pp20) REVERT: A 234 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8390 (mmmt) REVERT: A 235 LEU cc_start: 0.9239 (tp) cc_final: 0.8980 (tt) REVERT: A 261 ILE cc_start: 0.8696 (mp) cc_final: 0.8152 (mm) REVERT: A 275 ASP cc_start: 0.8820 (t70) cc_final: 0.8557 (t0) REVERT: A 357 LYS cc_start: 0.9505 (mtpp) cc_final: 0.9142 (mtpp) REVERT: A 361 LYS cc_start: 0.9555 (mmmt) cc_final: 0.9334 (mmmt) REVERT: A 375 TRP cc_start: 0.8793 (m-90) cc_final: 0.8444 (m-10) REVERT: B 66 ILE cc_start: 0.9561 (OUTLIER) cc_final: 0.9319 (pp) REVERT: B 92 MET cc_start: 0.8946 (mmm) cc_final: 0.8659 (mmm) REVERT: B 99 MET cc_start: 0.8332 (ppp) cc_final: 0.7621 (tmm) REVERT: B 127 LYS cc_start: 0.9158 (mmmm) cc_final: 0.8754 (mmmt) REVERT: B 139 ARG cc_start: 0.8599 (mmt90) cc_final: 0.8242 (mtp-110) REVERT: B 158 LYS cc_start: 0.9523 (tppt) cc_final: 0.8997 (tptp) REVERT: B 203 GLU cc_start: 0.8813 (pp20) cc_final: 0.8610 (pp20) REVERT: B 236 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8688 (tppt) REVERT: B 238 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9043 (mp) REVERT: B 357 LYS cc_start: 0.8876 (mtmp) cc_final: 0.8299 (mtmm) REVERT: B 375 TRP cc_start: 0.8887 (m-90) cc_final: 0.8406 (m-10) REVERT: B 382 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7019 (pptt) REVERT: C 45 MET cc_start: 0.7858 (mpm) cc_final: 0.7370 (mpp) REVERT: C 77 LYS cc_start: 0.9487 (mmmm) cc_final: 0.9137 (mmmm) REVERT: C 79 GLN cc_start: 0.8998 (pm20) cc_final: 0.8388 (pm20) REVERT: C 99 MET cc_start: 0.8577 (pmm) cc_final: 0.7815 (pmm) REVERT: C 108 MET cc_start: 0.8566 (mmm) cc_final: 0.8186 (mmt) REVERT: C 123 ASN cc_start: 0.9247 (p0) cc_final: 0.9028 (p0) REVERT: C 167 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8667 (tp30) REVERT: C 168 GLU cc_start: 0.9448 (OUTLIER) cc_final: 0.9097 (pp20) REVERT: C 170 GLU cc_start: 0.8862 (pp20) cc_final: 0.8394 (pp20) REVERT: C 171 MET cc_start: 0.9334 (tpp) cc_final: 0.9121 (tpp) REVERT: C 172 ARG cc_start: 0.9299 (ttp80) cc_final: 0.8547 (ptt90) REVERT: C 254 LYS cc_start: 0.9567 (OUTLIER) cc_final: 0.9348 (mmtt) REVERT: C 285 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8054 (tm-30) REVERT: C 369 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8029 (t80) REVERT: J 10 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7131 (mmm) REVERT: J 23 ARG cc_start: 0.8241 (mpp-170) cc_final: 0.7855 (mpt180) REVERT: J 30 MET cc_start: 0.8832 (tpp) cc_final: 0.8355 (tmm) REVERT: J 36 LYS cc_start: 0.8776 (tmmm) cc_final: 0.8489 (pttm) REVERT: I 10 MET cc_start: 0.8245 (mpp) cc_final: 0.7567 (mpp) REVERT: I 39 ASP cc_start: 0.8713 (p0) cc_final: 0.8460 (p0) REVERT: D 35 ASN cc_start: 0.8658 (t0) cc_final: 0.8348 (t0) REVERT: D 46 HIS cc_start: 0.7138 (OUTLIER) cc_final: 0.6437 (t-90) REVERT: E 22 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8394 (mmpt) REVERT: M 93 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: M 99 MET cc_start: 0.8262 (mmm) cc_final: 0.8053 (tpp) REVERT: M 129 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7761 (tp-100) REVERT: M 177 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8826 (p0) REVERT: M 203 GLU cc_start: 0.8903 (tp30) cc_final: 0.8672 (tp30) REVERT: M 234 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7986 (tptp) REVERT: M 289 GLN cc_start: 0.8745 (mp10) cc_final: 0.8404 (mp-120) REVERT: N 28 ASP cc_start: 0.8680 (p0) cc_final: 0.8402 (p0) REVERT: N 45 MET cc_start: 0.8532 (pmm) cc_final: 0.8088 (mpp) REVERT: N 51 ASN cc_start: 0.9129 (m110) cc_final: 0.8765 (t0) REVERT: N 115 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8215 (mtm180) REVERT: N 128 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8468 (mmmm) REVERT: N 139 ARG cc_start: 0.8345 (mmt90) cc_final: 0.7923 (mtp-110) REVERT: N 156 TYR cc_start: 0.9121 (t80) cc_final: 0.8915 (t80) REVERT: N 168 GLU cc_start: 0.9436 (pp20) cc_final: 0.9153 (pp20) REVERT: N 203 GLU cc_start: 0.8865 (pp20) cc_final: 0.8587 (pp20) REVERT: N 217 GLU cc_start: 0.7809 (tp30) cc_final: 0.7275 (tp30) REVERT: N 220 ARG cc_start: 0.8876 (mtt180) cc_final: 0.8567 (mtm180) REVERT: N 234 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8291 (mmmt) REVERT: N 237 ASP cc_start: 0.8362 (p0) cc_final: 0.7655 (p0) REVERT: N 284 LYS cc_start: 0.9296 (mtmt) cc_final: 0.8973 (mtmm) REVERT: N 346 ASP cc_start: 0.8633 (p0) cc_final: 0.8202 (p0) REVERT: O 40 ASP cc_start: 0.9188 (t0) cc_final: 0.8958 (t0) REVERT: O 93 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.6985 (m-30) REVERT: O 197 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8996 (tp) REVERT: O 236 LYS cc_start: 0.9269 (pttp) cc_final: 0.8952 (ptpt) REVERT: O 261 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8476 (pp) REVERT: O 371 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: Q 21 ASN cc_start: 0.8387 (t0) cc_final: 0.8112 (t0) REVERT: Q 23 ARG cc_start: 0.8392 (pmm150) cc_final: 0.7831 (pmm150) REVERT: Q 33 ASP cc_start: 0.8422 (t70) cc_final: 0.7887 (t70) REVERT: S 10 MET cc_start: 0.7685 (mpt) cc_final: 0.5790 (ptm) REVERT: S 49 SER cc_start: 0.9085 (t) cc_final: 0.8843 (p) outliers start: 112 outliers final: 70 residues processed: 614 average time/residue: 0.1651 time to fit residues: 154.9949 Evaluate side-chains 614 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 528 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 100 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 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 31 LYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 66 ILE 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 209 GLN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 350 ILE 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 149 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 369 PHE 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 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 52 SER Chi-restraints excluded: chain M residue 65 ASP Chi-restraints excluded: chain M residue 93 ASP 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 236 LYS Chi-restraints excluded: chain M residue 240 ILE Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 392 LEU 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 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 285 GLU Chi-restraints excluded: chain N residue 297 LEU 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 87 GLU 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 145 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 261 ILE Chi-restraints excluded: chain O residue 371 GLU Chi-restraints excluded: chain Q residue 47 SER 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 154 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 268 optimal weight: 50.0000 chunk 109 optimal weight: 8.9990 chunk 267 optimal weight: 30.0000 chunk 101 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 265 optimal weight: 40.0000 chunk 169 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.086271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072715 restraints weight = 72531.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.074898 restraints weight = 39135.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.076369 restraints weight = 25374.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077406 restraints weight = 18394.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078125 restraints weight = 14346.960| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22334 Z= 0.220 Angle : 0.867 12.523 30163 Z= 0.437 Chirality : 0.050 0.221 3370 Planarity : 0.004 0.043 3876 Dihedral : 6.224 42.832 2975 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 4.48 % Allowed : 25.30 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.16), residues: 2555 helix: -0.74 (0.22), residues: 529 sheet: -1.65 (0.23), residues: 453 loop : -2.16 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG J 19 TYR 0.036 0.002 TYR O 178 PHE 0.017 0.001 PHE M 266 TRP 0.017 0.002 TRP M 74 HIS 0.018 0.002 HIS N 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (22334) covalent geometry : angle 0.86710 / 0.44 (30163) hydrogen bonds : bond 0.04244 / 2.76 ( 627) hydrogen bonds : angle 5.67018 / 3.87 ( 1665) *********************** 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 630 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 526 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.0603 (OUTLIER) cc_final: -0.1327 (t0) REVERT: A 127 LYS cc_start: 0.9527 (mptm) cc_final: 0.9052 (mmmm) REVERT: A 160 ILE cc_start: 0.9599 (pp) cc_final: 0.9256 (mt) REVERT: A 167 GLU cc_start: 0.8334 (pm20) cc_final: 0.8013 (pp20) REVERT: A 234 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8436 (mmmt) REVERT: A 235 LEU cc_start: 0.9136 (tp) cc_final: 0.8912 (tt) REVERT: A 261 ILE cc_start: 0.8769 (mp) cc_final: 0.8453 (mp) REVERT: A 275 ASP cc_start: 0.8879 (t70) cc_final: 0.8619 (t0) REVERT: A 357 LYS cc_start: 0.9532 (mtpp) cc_final: 0.9077 (mtpp) REVERT: A 361 LYS cc_start: 0.9528 (mmmt) cc_final: 0.9318 (mmmt) REVERT: A 375 TRP cc_start: 0.8770 (m-90) cc_final: 0.8314 (m-10) REVERT: B 66 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9363 (pp) REVERT: B 79 GLN cc_start: 0.7970 (pm20) cc_final: 0.7703 (pm20) REVERT: B 92 MET cc_start: 0.8970 (mmm) cc_final: 0.8656 (mmm) REVERT: B 99 MET cc_start: 0.8361 (ppp) cc_final: 0.7628 (tmm) REVERT: B 127 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8883 (mmmt) REVERT: B 139 ARG cc_start: 0.8732 (mmt90) cc_final: 0.8294 (mtp-110) REVERT: B 158 LYS cc_start: 0.9535 (tppt) cc_final: 0.9176 (tptp) REVERT: B 236 LYS cc_start: 0.9064 (mmmt) cc_final: 0.8633 (tppt) REVERT: B 238 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9111 (mp) REVERT: B 357 LYS cc_start: 0.8929 (mtmp) cc_final: 0.8332 (mtmm) REVERT: B 375 TRP cc_start: 0.8924 (m-90) cc_final: 0.8461 (m-10) REVERT: B 382 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7009 (pptt) REVERT: C 45 MET cc_start: 0.7875 (mpm) cc_final: 0.7337 (mpp) REVERT: C 77 LYS cc_start: 0.9491 (mmmm) cc_final: 0.9136 (mmmm) REVERT: C 79 GLN cc_start: 0.9018 (pm20) cc_final: 0.8432 (pm20) REVERT: C 99 MET cc_start: 0.8628 (pmm) cc_final: 0.7935 (pmm) REVERT: C 108 MET cc_start: 0.8491 (mmm) cc_final: 0.8230 (mmt) REVERT: C 167 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8658 (tp30) REVERT: C 168 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.9054 (pp20) REVERT: C 170 GLU cc_start: 0.8873 (pp20) cc_final: 0.8466 (pp20) REVERT: C 171 MET cc_start: 0.9349 (tpp) cc_final: 0.9126 (tpp) REVERT: C 172 ARG cc_start: 0.9308 (ttp80) cc_final: 0.8545 (ptt90) REVERT: C 254 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9324 (mmtt) REVERT: C 285 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8042 (tm-30) REVERT: C 346 ASP cc_start: 0.7601 (t0) cc_final: 0.7213 (t0) REVERT: C 369 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8072 (t80) REVERT: J 10 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7240 (mmm) REVERT: J 19 ARG cc_start: 0.7276 (tmm160) cc_final: 0.7039 (tmm160) REVERT: J 20 LEU cc_start: 0.9070 (tp) cc_final: 0.8095 (tp) REVERT: J 21 ASN cc_start: 0.9060 (t0) cc_final: 0.8499 (t0) REVERT: J 23 ARG cc_start: 0.8276 (mpp-170) cc_final: 0.7984 (mpt180) REVERT: I 10 MET cc_start: 0.8290 (mpp) cc_final: 0.7633 (mpp) REVERT: I 36 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7774 (pttm) REVERT: D 35 ASN cc_start: 0.8661 (t0) cc_final: 0.8354 (t0) REVERT: D 46 HIS cc_start: 0.6967 (OUTLIER) cc_final: 0.6719 (t70) REVERT: E 22 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8435 (mmpt) REVERT: M 99 MET cc_start: 0.8300 (mmm) cc_final: 0.8012 (tpp) REVERT: M 177 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8866 (p0) REVERT: M 203 GLU cc_start: 0.8919 (tp30) cc_final: 0.8676 (tp30) REVERT: M 234 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8042 (tptp) REVERT: M 289 GLN cc_start: 0.8755 (mp10) cc_final: 0.8438 (mp-120) REVERT: N 28 ASP cc_start: 0.8671 (p0) cc_final: 0.8390 (p0) REVERT: N 45 MET cc_start: 0.8648 (pmm) cc_final: 0.8256 (mpp) REVERT: N 51 ASN cc_start: 0.9105 (m110) cc_final: 0.8733 (t0) REVERT: N 115 ARG cc_start: 0.8786 (mtp85) cc_final: 0.8571 (mtm180) REVERT: N 128 LYS cc_start: 0.9061 (mmmm) cc_final: 0.8772 (mmmm) REVERT: N 139 ARG cc_start: 0.8325 (mmt90) cc_final: 0.7938 (mtp-110) REVERT: N 156 TYR cc_start: 0.9166 (t80) cc_final: 0.8932 (t80) REVERT: N 168 GLU cc_start: 0.9437 (pp20) cc_final: 0.9118 (pp20) REVERT: N 203 GLU cc_start: 0.8884 (pp20) cc_final: 0.8615 (pp20) REVERT: N 217 GLU cc_start: 0.7870 (tp30) cc_final: 0.7333 (tp30) REVERT: N 220 ARG cc_start: 0.8863 (mtt180) cc_final: 0.8564 (mtm180) REVERT: N 234 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8456 (mmmt) REVERT: N 237 ASP cc_start: 0.8381 (p0) cc_final: 0.7669 (p0) REVERT: N 252 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8770 (p0) REVERT: N 284 LYS cc_start: 0.9327 (mtmt) cc_final: 0.9042 (mtmm) REVERT: N 346 ASP cc_start: 0.8638 (p0) cc_final: 0.8218 (p0) REVERT: N 375 TRP cc_start: 0.9302 (m-90) cc_final: 0.8756 (m-90) REVERT: O 167 GLU cc_start: 0.8164 (tp30) cc_final: 0.7711 (tp30) REVERT: O 197 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9010 (tp) REVERT: O 236 LYS cc_start: 0.9297 (pttp) cc_final: 0.8961 (ptpt) REVERT: O 261 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8525 (pp) REVERT: Q 21 ASN cc_start: 0.8362 (t0) cc_final: 0.8061 (t0) REVERT: Q 23 ARG cc_start: 0.8402 (pmm150) cc_final: 0.7838 (pmm150) REVERT: Q 33 ASP cc_start: 0.8393 (t70) cc_final: 0.7584 (t0) REVERT: S 10 MET cc_start: 0.7722 (mpt) cc_final: 0.5885 (ptm) REVERT: S 49 SER cc_start: 0.9185 (t) cc_final: 0.8951 (p) outliers start: 104 outliers final: 74 residues processed: 588 average time/residue: 0.1677 time to fit residues: 150.6946 Evaluate side-chains 603 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 514 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 91 ILE 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 144 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 276 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 66 ILE 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 209 GLN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 350 ILE 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 149 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 369 PHE 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 14 SER 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 43 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 45 ILE 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 153 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 177 ASP Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 392 LEU 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 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 N residue 285 GLU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 323 LYS Chi-restraints excluded: chain N residue 337 LYS Chi-restraints excluded: chain O residue 87 GLU 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 197 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 261 ILE Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain Q residue 47 SER 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 175 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 251 optimal weight: 30.0000 chunk 63 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 255 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.072996 restraints weight = 72536.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.075193 restraints weight = 39105.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076702 restraints weight = 25333.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077718 restraints weight = 18294.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078475 restraints weight = 14288.360| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22334 Z= 0.199 Angle : 0.877 13.617 30163 Z= 0.439 Chirality : 0.050 0.222 3370 Planarity : 0.004 0.041 3876 Dihedral : 6.222 42.601 2975 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 4.09 % Allowed : 25.99 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.16), residues: 2555 helix: -0.76 (0.22), residues: 522 sheet: -1.60 (0.23), residues: 453 loop : -2.09 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 115 TYR 0.033 0.002 TYR O 178 PHE 0.020 0.001 PHE A 202 TRP 0.016 0.002 TRP M 74 HIS 0.017 0.001 HIS N 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (22334) covalent geometry : angle 0.87720 / 0.44 (30163) hydrogen bonds : bond 0.04264 / 2.77 ( 627) hydrogen bonds : angle 5.67308 / 3.87 ( 1665) ********************** 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 636 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 541 time to evaluate : 0.869 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: A 100 ASP cc_start: 0.0644 (OUTLIER) cc_final: -0.1242 (m-30) REVERT: A 127 LYS cc_start: 0.9521 (mptm) cc_final: 0.9056 (mmmm) REVERT: A 160 ILE cc_start: 0.9577 (pp) cc_final: 0.9239 (mt) REVERT: A 167 GLU cc_start: 0.8324 (pm20) cc_final: 0.7985 (pp20) REVERT: A 234 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8467 (mmmt) REVERT: A 261 ILE cc_start: 0.8777 (mp) cc_final: 0.8455 (mp) REVERT: A 275 ASP cc_start: 0.8874 (t70) cc_final: 0.8614 (t0) REVERT: A 357 LYS cc_start: 0.9508 (mtpp) cc_final: 0.8886 (mtpp) REVERT: A 361 LYS cc_start: 0.9539 (mmmt) cc_final: 0.9339 (mmmt) REVERT: A 375 TRP cc_start: 0.8791 (m-90) cc_final: 0.8301 (m-10) REVERT: B 66 ILE cc_start: 0.9599 (OUTLIER) cc_final: 0.9392 (pp) REVERT: B 78 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8333 (mm-30) REVERT: B 92 MET cc_start: 0.8973 (mmm) cc_final: 0.8659 (mmm) REVERT: B 99 MET cc_start: 0.8391 (ppp) cc_final: 0.7676 (tmm) REVERT: B 127 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8838 (mmmt) REVERT: B 139 ARG cc_start: 0.8595 (mmt90) cc_final: 0.8301 (mtp-110) REVERT: B 158 LYS cc_start: 0.9536 (tppt) cc_final: 0.9168 (tptp) REVERT: B 168 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: B 203 GLU cc_start: 0.8753 (pp20) cc_final: 0.8513 (pp20) REVERT: B 236 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8676 (tppt) REVERT: B 238 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9102 (mp) REVERT: B 360 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8884 (mm) REVERT: B 375 TRP cc_start: 0.8907 (m-90) cc_final: 0.8447 (m-10) REVERT: B 382 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7070 (pptt) REVERT: C 45 MET cc_start: 0.7869 (mpm) cc_final: 0.7391 (mpp) REVERT: C 77 LYS cc_start: 0.9478 (mmmm) cc_final: 0.9143 (mmmm) REVERT: C 79 GLN cc_start: 0.8980 (pm20) cc_final: 0.8443 (pm20) REVERT: C 99 MET cc_start: 0.8621 (pmm) cc_final: 0.7790 (pmm) REVERT: C 108 MET cc_start: 0.8450 (mmm) cc_final: 0.8153 (mmt) REVERT: C 167 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8672 (tp30) REVERT: C 168 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.9070 (pp20) REVERT: C 170 GLU cc_start: 0.8872 (pp20) cc_final: 0.8475 (pp20) REVERT: C 171 MET cc_start: 0.9368 (tpp) cc_final: 0.9149 (tpp) REVERT: C 172 ARG cc_start: 0.9306 (ttp80) cc_final: 0.8534 (ptt90) REVERT: C 254 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9324 (mmtt) REVERT: C 285 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 369 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8032 (t80) REVERT: J 10 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7202 (mmm) REVERT: J 21 ASN cc_start: 0.9089 (t0) cc_final: 0.8640 (t0) REVERT: J 23 ARG cc_start: 0.8308 (mpp-170) cc_final: 0.7850 (mpt180) REVERT: J 36 LYS cc_start: 0.8778 (tmmm) cc_final: 0.8481 (pttm) REVERT: I 10 MET cc_start: 0.8266 (mpp) cc_final: 0.7590 (mpp) REVERT: D 35 ASN cc_start: 0.8661 (t0) cc_final: 0.8365 (t0) REVERT: E 22 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8407 (mmpt) REVERT: M 99 MET cc_start: 0.8247 (mmm) cc_final: 0.7978 (tpp) REVERT: M 177 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8849 (p0) REVERT: M 203 GLU cc_start: 0.8915 (tp30) cc_final: 0.8664 (tp30) REVERT: M 234 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8030 (tptp) REVERT: M 289 GLN cc_start: 0.8747 (mp10) cc_final: 0.8415 (mp-120) REVERT: N 28 ASP cc_start: 0.8677 (p0) cc_final: 0.8389 (p0) REVERT: N 45 MET cc_start: 0.8644 (pmm) cc_final: 0.8244 (mpp) REVERT: N 51 ASN cc_start: 0.9102 (m110) cc_final: 0.8753 (t0) REVERT: N 128 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8749 (mmmm) REVERT: N 139 ARG cc_start: 0.8352 (mmt90) cc_final: 0.7979 (mtp-110) REVERT: N 156 TYR cc_start: 0.9143 (t80) cc_final: 0.8899 (t80) REVERT: N 168 GLU cc_start: 0.9380 (pp20) cc_final: 0.9133 (pp20) REVERT: N 217 GLU cc_start: 0.7954 (tp30) cc_final: 0.7424 (tp30) REVERT: N 220 ARG cc_start: 0.8847 (mtt180) cc_final: 0.8533 (mtm180) REVERT: N 234 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8440 (mmmt) REVERT: N 237 ASP cc_start: 0.8368 (p0) cc_final: 0.7645 (p0) REVERT: N 252 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8737 (p0) REVERT: N 284 LYS cc_start: 0.9325 (mtmt) cc_final: 0.9014 (mtmm) REVERT: N 346 ASP cc_start: 0.8648 (p0) cc_final: 0.8221 (p0) REVERT: N 375 TRP cc_start: 0.9305 (m-90) cc_final: 0.8783 (m-90) REVERT: O 167 GLU cc_start: 0.8149 (tp30) cc_final: 0.7946 (tp30) REVERT: O 197 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9005 (tp) REVERT: O 236 LYS cc_start: 0.9298 (pttp) cc_final: 0.8994 (ptpt) REVERT: O 261 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8544 (pp) REVERT: O 371 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: Q 21 ASN cc_start: 0.8330 (t0) cc_final: 0.8043 (t0) REVERT: Q 23 ARG cc_start: 0.8418 (pmm150) cc_final: 0.7882 (pmm150) REVERT: Q 33 ASP cc_start: 0.8362 (t70) cc_final: 0.7550 (t0) REVERT: S 10 MET cc_start: 0.7468 (mpt) cc_final: 0.5702 (ptm) REVERT: S 49 SER cc_start: 0.9221 (t) cc_final: 0.8989 (p) outliers start: 95 outliers final: 70 residues processed: 598 average time/residue: 0.1721 time to fit residues: 156.5039 Evaluate side-chains 613 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 527 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 91 ILE 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 144 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 66 ILE 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 168 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 350 ILE 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 149 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 369 PHE 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 14 SER 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 E residue 22 LYS 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 153 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 177 ASP Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 236 LYS Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 392 LEU 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 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 N residue 285 GLU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 323 LYS Chi-restraints excluded: chain N residue 337 LYS Chi-restraints excluded: chain O residue 87 GLU 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 197 LEU Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 243 THR Chi-restraints excluded: chain O residue 261 ILE Chi-restraints excluded: chain O residue 344 ILE Chi-restraints excluded: chain O residue 371 GLU Chi-restraints excluded: chain Q residue 47 SER 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 86 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 264 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 120 optimal weight: 0.0980 chunk 168 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 ASN N 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.088563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.074837 restraints weight = 71708.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077097 restraints weight = 38643.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078637 restraints weight = 24960.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079686 restraints weight = 18037.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.080428 restraints weight = 14068.941| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 22334 Z= 0.155 Angle : 0.883 17.051 30163 Z= 0.436 Chirality : 0.049 0.358 3370 Planarity : 0.004 0.038 3876 Dihedral : 6.113 40.936 2975 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 3.74 % Allowed : 26.64 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.16), residues: 2555 helix: -0.77 (0.22), residues: 522 sheet: -1.51 (0.23), residues: 469 loop : -2.03 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 115 TYR 0.043 0.002 TYR O 178 PHE 0.017 0.001 PHE I 53 TRP 0.017 0.001 TRP M 74 HIS 0.017 0.001 HIS N 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (22334) covalent geometry : angle 0.88325 / 0.44 (30163) hydrogen bonds : bond 0.04205 / 2.73 ( 627) hydrogen bonds : angle 5.62801 / 3.84 ( 1665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4203.64 seconds wall clock time: 73 minutes 47.81 seconds (4427.81 seconds total)