Starting phenix.real_space_refine on Sat Mar 7 05:15:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uws_26841/03_2026/7uws_26841.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uws_26841/03_2026/7uws_26841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uws_26841/03_2026/7uws_26841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uws_26841/03_2026/7uws_26841.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uws_26841/03_2026/7uws_26841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uws_26841/03_2026/7uws_26841.map" } resolution = 3.47 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= 0.001 sd= 0.014 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: 5 Type Number sf(0) Gaussians P 68 5.49 5 S 201 5.16 5 C 25140 2.51 5 N 6464 2.21 5 O 7543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39416 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3003 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 16, 'TRANS': 362} Chain breaks: 2 Chain: "B" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3173 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 19, 'TRANS': 380} Chain breaks: 2 Chain: "C" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3117 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 17, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3029 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3322 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 401} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3322 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 401} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3033 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain breaks: 2 Chain: "H" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1344 Classifications: {'RNA': 68} Modifications used: {'rna2p_pyr': 9, 'rna3p_pyr': 59} Link IDs: {'rna2p': 9, 'rna3p': 58} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1278 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1410 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 162} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1279 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1532 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 177} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1532 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 177} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1532 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 177} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1410 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1415 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Chain: "T" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1415 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 9.38, per 1000 atoms: 0.24 Number of scatterers: 39416 At special positions: 0 Unit cell: (143.1, 161.65, 135.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 201 16.00 P 68 15.00 O 7543 8.00 N 6464 7.00 C 25140 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: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8894 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 50 sheets defined 42.4% alpha, 11.2% beta 0 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 47 through 62 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.651A pdb=" N ASP A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 107 " --> pdb=" O ILE A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.912A pdb=" N TYR A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.812A pdb=" N THR A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 294 through 308 removed outlier: 3.519A pdb=" N HIS A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 341 Processing helix chain 'A' and resid 392 through 402 Processing helix chain 'A' and resid 411 through 420 Processing helix chain 'B' and resid 27 through 35 Processing helix chain 'B' and resid 47 through 62 Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.880A pdb=" N LEU B 107 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 108 " --> pdb=" O PHE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 145 removed outlier: 4.019A pdb=" N TYR B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 removed outlier: 3.617A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 188 through 205 removed outlier: 3.524A pdb=" N THR B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 218 removed outlier: 4.144A pdb=" N THR B 217 " --> pdb=" O PHE B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 225 through 238 Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.882A pdb=" N THR B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 324 through 341 removed outlier: 3.562A pdb=" N SER B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 3.551A pdb=" N GLN B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 411 through 420 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 62 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.877A pdb=" N LEU C 107 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 4.025A pdb=" N TYR C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.545A pdb=" N GLY C 186 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 205 removed outlier: 3.856A pdb=" N THR C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 213 through 218 removed outlier: 4.316A pdb=" N THR C 217 " --> pdb=" O PHE C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 225 through 239 removed outlier: 3.723A pdb=" N GLY C 239 " --> pdb=" O CYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.634A pdb=" N THR C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.769A pdb=" N ASP C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.851A pdb=" N GLU C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 294 through 308 Processing helix chain 'C' and resid 324 through 341 Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.585A pdb=" N TRP C 378 " --> pdb=" O ASP C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 402 Processing helix chain 'C' and resid 411 through 420 Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.895A pdb=" N LEU D 107 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 108 " --> pdb=" O PHE D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.620A pdb=" N TYR D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 180 through 187 removed outlier: 3.505A pdb=" N VAL D 184 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 186 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 205 Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.814A pdb=" N GLY D 239 " --> pdb=" O CYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 253 through 262 Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.592A pdb=" N GLN D 266 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 267' Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'D' and resid 294 through 308 removed outlier: 3.714A pdb=" N HIS D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.670A pdb=" N SER D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 411 through 420 Processing helix chain 'E' and resid 27 through 35 Processing helix chain 'E' and resid 47 through 62 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.981A pdb=" N LEU E 107 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 removed outlier: 3.794A pdb=" N TYR E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 169 removed outlier: 4.499A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 167 " --> pdb=" O GLN E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 removed outlier: 3.790A pdb=" N GLY E 186 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 205 removed outlier: 3.639A pdb=" N THR E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 215 Processing helix chain 'E' and resid 217 through 221 Processing helix chain 'E' and resid 225 through 238 Processing helix chain 'E' and resid 241 through 248 removed outlier: 4.061A pdb=" N THR E 246 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR E 247 " --> pdb=" O GLU E 243 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 262 removed outlier: 4.193A pdb=" N ASP E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 removed outlier: 4.093A pdb=" N GLU E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 Processing helix chain 'E' and resid 294 through 308 removed outlier: 3.692A pdb=" N HIS E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 341 removed outlier: 3.506A pdb=" N SER E 340 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER E 341 " --> pdb=" O ALA E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 385 Processing helix chain 'E' and resid 390 through 402 Processing helix chain 'E' and resid 411 through 420 Processing helix chain 'F' and resid 27 through 35 Processing helix chain 'F' and resid 47 through 62 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.864A pdb=" N LEU F 107 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 108 " --> pdb=" O PHE F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 104 through 108' Processing helix chain 'F' and resid 133 through 145 removed outlier: 3.650A pdb=" N TYR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 168 removed outlier: 3.846A pdb=" N ILE F 167 " --> pdb=" O GLN F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 187 removed outlier: 3.620A pdb=" N GLY F 186 " --> pdb=" O ASP F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 205 Processing helix chain 'F' and resid 210 through 215 Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 225 through 239 removed outlier: 3.670A pdb=" N GLY F 239 " --> pdb=" O CYS F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 253 through 262 removed outlier: 3.621A pdb=" N GLU F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 294 through 308 Processing helix chain 'F' and resid 324 through 341 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 390 through 402 Processing helix chain 'F' and resid 411 through 420 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 47 through 62 Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.921A pdb=" N LEU G 107 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 108 " --> pdb=" O PHE G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 145 removed outlier: 4.056A pdb=" N TRP G 133 " --> pdb=" O ALA G 129 " (cutoff:3.500A) Proline residue: G 135 - end of helix removed outlier: 3.741A pdb=" N TYR G 142 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 164 Processing helix chain 'G' and resid 183 through 187 removed outlier: 3.508A pdb=" N GLY G 186 " --> pdb=" O ASP G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 205 removed outlier: 3.748A pdb=" N THR G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 212 No H-bonds generated for 'chain 'G' and resid 210 through 212' Processing helix chain 'G' and resid 213 through 218 removed outlier: 4.187A pdb=" N THR G 217 " --> pdb=" O PHE G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 225 through 239 removed outlier: 3.752A pdb=" N THR G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY G 239 " --> pdb=" O CYS G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 246 removed outlier: 3.657A pdb=" N THR G 246 " --> pdb=" O THR G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 252 through 262 removed outlier: 3.773A pdb=" N ASP G 256 " --> pdb=" O ARG G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 308 Processing helix chain 'G' and resid 323 through 339 removed outlier: 4.181A pdb=" N LEU G 327 " --> pdb=" O GLU G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 384 Processing helix chain 'G' and resid 390 through 402 Processing helix chain 'G' and resid 411 through 421 Processing helix chain 'J' and resid 80 through 89 Processing helix chain 'J' and resid 90 through 93 Processing helix chain 'J' and resid 101 through 115 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 200 through 207 removed outlier: 3.519A pdb=" N LEU J 206 " --> pdb=" O GLN J 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 89 Processing helix chain 'K' and resid 90 through 93 removed outlier: 3.659A pdb=" N ASN K 93 " --> pdb=" O GLN K 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 90 through 93' Processing helix chain 'K' and resid 98 through 100 No H-bonds generated for 'chain 'K' and resid 98 through 100' Processing helix chain 'K' and resid 101 through 115 Processing helix chain 'K' and resid 119 through 123 Processing helix chain 'K' and resid 188 through 193 removed outlier: 3.852A pdb=" N MET K 193 " --> pdb=" O TRP K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 205 Processing helix chain 'L' and resid 80 through 89 Processing helix chain 'L' and resid 90 through 93 removed outlier: 3.510A pdb=" N ASN L 93 " --> pdb=" O GLN L 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 90 through 93' Processing helix chain 'L' and resid 98 through 100 No H-bonds generated for 'chain 'L' and resid 98 through 100' Processing helix chain 'L' and resid 101 through 115 Processing helix chain 'L' and resid 119 through 123 Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.714A pdb=" N MET L 193 " --> pdb=" O TRP L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 208 Processing helix chain 'M' and resid 80 through 89 Processing helix chain 'M' and resid 101 through 115 Processing helix chain 'M' and resid 119 through 123 removed outlier: 3.607A pdb=" N LEU M 123 " --> pdb=" O PRO M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 193 removed outlier: 3.512A pdb=" N MET M 193 " --> pdb=" O TRP M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 208 removed outlier: 3.709A pdb=" N GLU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE M 208 " --> pdb=" O GLU M 204 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 removed outlier: 4.307A pdb=" N GLN N 90 " --> pdb=" O ALA N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 115 Processing helix chain 'N' and resid 119 through 123 Processing helix chain 'N' and resid 188 through 193 removed outlier: 3.576A pdb=" N MET N 193 " --> pdb=" O TRP N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 205 Processing helix chain 'O' and resid 80 through 89 Processing helix chain 'O' and resid 90 through 93 removed outlier: 3.699A pdb=" N ASN O 93 " --> pdb=" O GLN O 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 90 through 93' Processing helix chain 'O' and resid 101 through 115 Processing helix chain 'O' and resid 119 through 123 Processing helix chain 'O' and resid 188 through 193 removed outlier: 3.503A pdb=" N MET O 193 " --> pdb=" O TRP O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 200 through 208 removed outlier: 4.090A pdb=" N LEU O 206 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE O 208 " --> pdb=" O GLU O 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 90 removed outlier: 3.529A pdb=" N VAL P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN P 90 " --> pdb=" O ALA P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 93 No H-bonds generated for 'chain 'P' and resid 91 through 93' Processing helix chain 'P' and resid 101 through 115 Processing helix chain 'P' and resid 120 through 123 Processing helix chain 'P' and resid 189 through 193 removed outlier: 3.563A pdb=" N MET P 193 " --> pdb=" O TRP P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 200 through 207 Processing helix chain 'Q' and resid 80 through 89 Processing helix chain 'Q' and resid 98 through 100 No H-bonds generated for 'chain 'Q' and resid 98 through 100' Processing helix chain 'Q' and resid 101 through 115 Processing helix chain 'Q' and resid 200 through 205 Processing helix chain 'Q' and resid 206 through 208 No H-bonds generated for 'chain 'Q' and resid 206 through 208' Processing helix chain 'R' and resid 80 through 89 Processing helix chain 'R' and resid 101 through 115 Processing helix chain 'R' and resid 201 through 208 removed outlier: 3.868A pdb=" N LEU R 206 " --> pdb=" O GLN R 202 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 90 removed outlier: 4.020A pdb=" N GLN S 90 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 93 No H-bonds generated for 'chain 'S' and resid 91 through 93' Processing helix chain 'S' and resid 101 through 115 Processing helix chain 'S' and resid 189 through 193 removed outlier: 3.677A pdb=" N MET S 193 " --> pdb=" O TRP S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 205 removed outlier: 3.641A pdb=" N GLY S 205 " --> pdb=" O ILE S 201 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 208 No H-bonds generated for 'chain 'S' and resid 206 through 208' Processing helix chain 'T' and resid 80 through 89 Processing helix chain 'T' and resid 98 through 100 No H-bonds generated for 'chain 'T' and resid 98 through 100' Processing helix chain 'T' and resid 101 through 115 Processing helix chain 'T' and resid 189 through 193 Processing helix chain 'T' and resid 200 through 208 removed outlier: 3.511A pdb=" N LEU T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 89 Processing helix chain 'U' and resid 98 through 100 No H-bonds generated for 'chain 'U' and resid 98 through 100' Processing helix chain 'U' and resid 101 through 115 removed outlier: 3.526A pdb=" N HIS U 115 " --> pdb=" O ILE U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 189 through 193 removed outlier: 3.501A pdb=" N MET U 193 " --> pdb=" O TRP U 190 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.715A pdb=" N ILE A 42 " --> pdb=" O LYS A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 42 removed outlier: 5.875A pdb=" N LEU B 40 " --> pdb=" O LYS B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AA6, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.152A pdb=" N LEU D 40 " --> pdb=" O LYS D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 348 through 349 Processing sheet with id=AA8, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.726A pdb=" N THR E 12 " --> pdb=" O ARG E 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 41 through 42 removed outlier: 3.788A pdb=" N ILE E 42 " --> pdb=" O LYS E 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 89 through 90 Processing sheet with id=AB2, first strand: chain 'E' and resid 348 through 349 Processing sheet with id=AB3, first strand: chain 'F' and resid 39 through 42 removed outlier: 6.154A pdb=" N LEU F 40 " --> pdb=" O LYS F 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 89 through 90 Processing sheet with id=AB5, first strand: chain 'G' and resid 39 through 42 removed outlier: 6.009A pdb=" N LEU G 40 " --> pdb=" O LYS G 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 89 through 90 Processing sheet with id=AB7, first strand: chain 'J' and resid 136 through 137 removed outlier: 4.045A pdb=" N GLY J 137 " --> pdb=" O PHE J 66 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE J 66 " --> pdb=" O GLY J 137 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER J 178 " --> pdb=" O ARG J 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 70 through 73 removed outlier: 3.680A pdb=" N ALA J 133 " --> pdb=" O MET J 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 137 through 143 Processing sheet with id=AC1, first strand: chain 'K' and resid 130 through 134 removed outlier: 3.531A pdb=" N ALA K 133 " --> pdb=" O MET K 70 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU K 156 " --> pdb=" O PHE K 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 211 through 214 removed outlier: 6.890A pdb=" N ILE K 211 " --> pdb=" O ASP K 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 130 through 141 Processing sheet with id=AC4, first strand: chain 'L' and resid 156 through 158 removed outlier: 3.577A pdb=" N GLU L 156 " --> pdb=" O PHE L 175 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE L 158 " --> pdb=" O PHE L 173 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 162 through 163 removed outlier: 3.637A pdb=" N GLY L 169 " --> pdb=" O PHE L 162 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 130 through 143 removed outlier: 3.809A pdb=" N LEU M 141 " --> pdb=" O GLU M 62 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU M 62 " --> pdb=" O LEU M 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 130 through 143 removed outlier: 3.809A pdb=" N LEU M 141 " --> pdb=" O GLU M 62 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU M 62 " --> pdb=" O LEU M 141 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 156 through 158 removed outlier: 3.677A pdb=" N PHE M 158 " --> pdb=" O PHE M 173 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 212 through 214 removed outlier: 3.601A pdb=" N SER M 213 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL M 221 " --> pdb=" O SER M 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'N' and resid 130 through 143 removed outlier: 3.512A pdb=" N ALA N 133 " --> pdb=" O MET N 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU N 62 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU N 156 " --> pdb=" O PHE N 175 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 130 through 143 removed outlier: 3.512A pdb=" N ALA N 133 " --> pdb=" O MET N 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU N 62 " --> pdb=" O LEU N 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 211 through 214 removed outlier: 6.930A pdb=" N ILE N 211 " --> pdb=" O ASP N 223 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER N 213 " --> pdb=" O VAL N 221 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 130 through 143 removed outlier: 3.534A pdb=" N LEU O 141 " --> pdb=" O GLU O 62 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU O 62 " --> pdb=" O LEU O 141 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE O 175 " --> pdb=" O GLU O 156 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU O 156 " --> pdb=" O PHE O 175 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 130 through 143 removed outlier: 3.534A pdb=" N LEU O 141 " --> pdb=" O GLU O 62 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU O 62 " --> pdb=" O LEU O 141 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 211 through 214 removed outlier: 6.724A pdb=" N ILE O 211 " --> pdb=" O ASP O 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 137 through 143 removed outlier: 3.830A pdb=" N GLU P 62 " --> pdb=" O LEU P 141 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 117 through 118 removed outlier: 3.607A pdb=" N TYR P 132 " --> pdb=" O GLN P 117 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL P 72 " --> pdb=" O TYR P 131 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA P 133 " --> pdb=" O MET P 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR P 174 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE P 158 " --> pdb=" O PHE P 173 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 210 through 213 removed outlier: 7.174A pdb=" N ILE P 211 " --> pdb=" O ASP P 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 117 through 118 removed outlier: 3.505A pdb=" N TYR Q 132 " --> pdb=" O GLN Q 117 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 210 through 212 removed outlier: 6.923A pdb=" N ILE Q 211 " --> pdb=" O ASP Q 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 130 through 135 removed outlier: 3.501A pdb=" N ALA R 133 " --> pdb=" O MET R 70 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 117 through 118 removed outlier: 3.548A pdb=" N GLN S 117 " --> pdb=" O TYR S 132 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL S 72 " --> pdb=" O TYR S 131 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY S 137 " --> pdb=" O PHE S 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE S 66 " --> pdb=" O GLY S 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS S 139 " --> pdb=" O PHE S 64 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR S 174 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE S 158 " --> pdb=" O PHE S 173 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE S 175 " --> pdb=" O GLU S 156 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 117 through 118 removed outlier: 3.548A pdb=" N GLN S 117 " --> pdb=" O TYR S 132 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL S 72 " --> pdb=" O TYR S 131 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY S 137 " --> pdb=" O PHE S 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE S 66 " --> pdb=" O GLY S 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS S 139 " --> pdb=" O PHE S 64 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 162 through 163 removed outlier: 4.095A pdb=" N GLY S 169 " --> pdb=" O PHE S 162 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 210 through 213 removed outlier: 6.694A pdb=" N ILE S 211 " --> pdb=" O ASP S 223 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER S 213 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL S 221 " --> pdb=" O SER S 213 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 117 through 118 removed outlier: 3.599A pdb=" N TYR T 132 " --> pdb=" O GLN T 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA T 133 " --> pdb=" O MET T 70 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY T 137 " --> pdb=" O PHE T 66 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 117 through 118 removed outlier: 3.599A pdb=" N TYR T 132 " --> pdb=" O GLN T 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA T 133 " --> pdb=" O MET T 70 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY T 137 " --> pdb=" O PHE T 66 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 162 through 163 Processing sheet with id=AF2, first strand: chain 'T' and resid 210 through 213 removed outlier: 6.741A pdb=" N ILE T 211 " --> pdb=" O ASP T 223 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER T 213 " --> pdb=" O VAL T 221 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL T 221 " --> pdb=" O SER T 213 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 60 through 65 removed outlier: 3.709A pdb=" N HIS U 143 " --> pdb=" O ARG U 60 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU U 62 " --> pdb=" O LEU U 141 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 71 through 73 Processing sheet with id=AF5, first strand: chain 'U' and resid 162 through 163 1441 hydrogen bonds defined for protein. 3915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 8.47 Time building geometry restraints manager: 4.05 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: 11012 1.34 - 1.45: 7412 1.45 - 1.57: 21574 1.57 - 1.69: 135 1.69 - 1.81: 359 Bond restraints: 40492 Sorted by residual: bond pdb=" N ASN A 190 " pdb=" CA ASN A 190 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.05e+00 bond pdb=" N ASP A 180 " pdb=" CA ASP A 180 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.25e-02 6.40e+03 5.93e+00 bond pdb=" N TYR J 95 " pdb=" CA TYR J 95 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.28e-02 6.10e+03 5.79e+00 bond pdb=" N LYS T 207 " pdb=" CA LYS T 207 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.28e-02 6.10e+03 5.14e+00 bond pdb=" C LYS C 388 " pdb=" N PRO C 389 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.30e-02 5.92e+03 5.10e+00 ... (remaining 40487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 53784 1.93 - 3.86: 1085 3.86 - 5.79: 150 5.79 - 7.72: 16 7.72 - 9.64: 4 Bond angle restraints: 55039 Sorted by residual: angle pdb=" N ILE M 96 " pdb=" CA ILE M 96 " pdb=" C ILE M 96 " ideal model delta sigma weight residual 113.53 108.10 5.43 9.80e-01 1.04e+00 3.07e+01 angle pdb=" N PHE T 208 " pdb=" CA PHE T 208 " pdb=" C PHE T 208 " ideal model delta sigma weight residual 113.19 107.06 6.13 1.19e+00 7.06e-01 2.66e+01 angle pdb=" N ILE E 8 " pdb=" CA ILE E 8 " pdb=" C ILE E 8 " ideal model delta sigma weight residual 106.21 111.60 -5.39 1.07e+00 8.73e-01 2.54e+01 angle pdb=" N TYR E 152 " pdb=" CA TYR E 152 " pdb=" C TYR E 152 " ideal model delta sigma weight residual 113.55 107.32 6.23 1.26e+00 6.30e-01 2.45e+01 angle pdb=" N ILE K 96 " pdb=" CA ILE K 96 " pdb=" C ILE K 96 " ideal model delta sigma weight residual 113.53 109.00 4.53 9.80e-01 1.04e+00 2.14e+01 ... (remaining 55034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 23764 35.73 - 71.47: 545 71.47 - 107.20: 30 107.20 - 142.93: 2 142.93 - 178.67: 17 Dihedral angle restraints: 24358 sinusoidal: 10494 harmonic: 13864 Sorted by residual: dihedral pdb=" O4' U H 127 " pdb=" C1' U H 127 " pdb=" N1 U H 127 " pdb=" C2 U H 127 " ideal model delta sinusoidal sigma weight residual 200.00 38.88 161.12 1 1.50e+01 4.44e-03 8.30e+01 dihedral pdb=" O4' U H 118 " pdb=" C1' U H 118 " pdb=" N1 U H 118 " pdb=" C2 U H 118 " ideal model delta sinusoidal sigma weight residual -160.00 -2.93 -157.07 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" O4' U H 469 " pdb=" C1' U H 469 " pdb=" N1 U H 469 " pdb=" C2 U H 469 " ideal model delta sinusoidal sigma weight residual 200.00 45.52 154.48 1 1.50e+01 4.44e-03 8.12e+01 ... (remaining 24355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 5036 0.053 - 0.105: 882 0.105 - 0.158: 109 0.158 - 0.210: 6 0.210 - 0.263: 1 Chirality restraints: 6034 Sorted by residual: chirality pdb=" CA LYS C 388 " pdb=" N LYS C 388 " pdb=" C LYS C 388 " pdb=" CB LYS C 388 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C3' U H 129 " pdb=" C4' U H 129 " pdb=" O3' U H 129 " pdb=" C2' U H 129 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" C3' U H 454 " pdb=" C4' U H 454 " pdb=" O3' U H 454 " pdb=" C2' U H 454 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 6031 not shown) Planarity restraints: 6770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO U 149 " 0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO U 150 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO U 150 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO U 150 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 148 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO J 149 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO J 149 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO J 149 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE U 148 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO U 149 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO U 149 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO U 149 " 0.034 5.00e-02 4.00e+02 ... (remaining 6767 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2829 2.74 - 3.28: 40924 3.28 - 3.82: 65998 3.82 - 4.36: 78968 4.36 - 4.90: 132552 Nonbonded interactions: 321271 Sorted by model distance: nonbonded pdb=" OD1 ASN E 251 " pdb=" OG SER E 326 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR A 336 " pdb=" OD2 ASP A 392 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP D 199 " pdb=" OH TYR D 277 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN D 94 " pdb=" NZ LYS D 97 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR D 336 " pdb=" OD2 ASP D 392 " model vdw 2.203 3.040 ... (remaining 321266 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 22 through 164 or resid 173 through 319 or resid 327 throu \ gh 339 or resid 371 or resid 373 or resid 392 through 421)) selection = (chain 'B' and (resid 22 through 164 or resid 173 through 319 or resid 327 throu \ gh 339 or resid 371 or resid 373 or resid 392 through 421)) selection = (chain 'C' and (resid 22 through 164 or resid 173 through 319 or resid 327 throu \ gh 339 or resid 385 or resid 387 or resid 392 through 421)) selection = (chain 'D' and (resid 22 through 164 or resid 173 through 339 or resid 371 or re \ sid 373 or resid 392 through 421)) selection = (chain 'E' and (resid 22 through 164 or resid 173 through 319 or resid 327 throu \ gh 339 or resid 371 or resid 373 or resid 392 through 421)) selection = (chain 'F' and (resid 22 through 164 or resid 173 through 319 or resid 327 throu \ gh 339 or resid 371 or resid 373 or resid 392 through 421)) selection = (chain 'G' and (resid 22 through 319 or resid 327 through 339 or resid 385 or re \ sid 387 or resid 392 through 421)) } ncs_group { reference = (chain 'J' and (resid 62 through 122 or resid 127 through 143 or resid 148 throu \ gh 162 or resid 169 through 194 or resid 201 through 212 or resid 220 through 22 \ 5)) selection = (chain 'K' and (resid 62 through 122 or resid 127 through 143 or resid 148 throu \ gh 162 or resid 169 through 180 or resid 186 through 194 or resid 201 through 21 \ 2 or resid 220 through 225)) selection = (chain 'L' and (resid 62 through 122 or resid 127 through 162 or resid 169 throu \ gh 180 or resid 186 through 194 or resid 201 through 212 or resid 220 through 22 \ 5)) selection = (chain 'P' and (resid 62 through 122 or resid 127 through 143 or resid 148 throu \ gh 180 or resid 186 through 194 or resid 201 through 212 or resid 220 through 22 \ 5)) selection = (chain 'S' and (resid 62 through 143 or resid 148 through 162 or resid 169 throu \ gh 180 or resid 186 through 194 or resid 201 through 212 or resid 220 through 22 \ 5)) selection = (chain 'T' and (resid 62 through 143 or resid 148 through 162 or resid 169 throu \ gh 180 or resid 186 through 194 or resid 201 through 212 or resid 220 through 22 \ 5)) selection = (chain 'U' and (resid 62 through 143 or resid 148 through 162 or resid 169 throu \ gh 180 or resid 186 through 225)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'Q' and (resid 66 through 178 or resid 192 through 195 or resid 200 throu \ gh 211 or resid 224 through 229)) selection = (chain 'R' and (resid 66 through 137 or resid 153 through 229)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 38.730 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.003 0.099 40492 Z= 0.138 Angle : 0.651 9.645 55039 Z= 0.374 Chirality : 0.040 0.263 6034 Planarity : 0.005 0.091 6770 Dihedral : 15.935 178.669 15464 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.12 % Allowed : 0.27 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.19 (0.12), residues: 4672 helix: 0.57 (0.13), residues: 1714 sheet: -1.96 (0.23), residues: 516 loop : -1.53 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 33 TYR 0.037 0.001 TYR D 54 PHE 0.025 0.001 PHE R 228 TRP 0.015 0.001 TRP G 248 HIS 0.005 0.001 HIS U 115 Details of bonding type rmsd covalent geometry : bond 0.00271 (40492) covalent geometry : angle 0.65113 (55039) hydrogen bonds : bond 0.19666 ( 1381) hydrogen bonds : angle 6.98350 ( 3915) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1108 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.8476 (t80) cc_final: 0.8140 (t80) REVERT: A 170 GLN cc_start: 0.7964 (mp10) cc_final: 0.7739 (mp10) REVERT: A 257 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6807 (mt-10) REVERT: A 312 ARG cc_start: 0.8897 (tmt-80) cc_final: 0.8667 (tmt-80) REVERT: A 324 TYR cc_start: 0.7865 (m-10) cc_final: 0.7646 (m-10) REVERT: B 1 MET cc_start: 0.4238 (mmp) cc_final: 0.3678 (mmp) REVERT: B 33 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7155 (ttt180) REVERT: B 154 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8284 (tptp) REVERT: B 158 ASP cc_start: 0.7913 (m-30) cc_final: 0.7307 (m-30) REVERT: B 165 LYS cc_start: 0.8756 (mttm) cc_final: 0.8476 (mttt) REVERT: C 1 MET cc_start: 0.5568 (mmm) cc_final: 0.5191 (mmm) REVERT: C 4 THR cc_start: 0.9218 (t) cc_final: 0.8985 (m) REVERT: C 7 ARG cc_start: 0.7701 (ttt90) cc_final: 0.7280 (ttt180) REVERT: C 394 MET cc_start: 0.7303 (mmm) cc_final: 0.7051 (mpp) REVERT: D 154 LYS cc_start: 0.8893 (tptm) cc_final: 0.8643 (tppp) REVERT: D 394 MET cc_start: 0.6194 (mmp) cc_final: 0.5937 (mmp) REVERT: D 411 THR cc_start: 0.8609 (p) cc_final: 0.8399 (p) REVERT: F 1 MET cc_start: 0.5855 (mmm) cc_final: 0.4699 (mmm) REVERT: F 74 TYR cc_start: 0.8949 (t80) cc_final: 0.8735 (t80) REVERT: F 102 ILE cc_start: 0.8092 (tt) cc_final: 0.7892 (pt) REVERT: F 258 MET cc_start: 0.7939 (mmm) cc_final: 0.7411 (tpp) REVERT: F 377 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7805 (tt0) REVERT: F 402 MET cc_start: 0.8198 (ptm) cc_final: 0.7938 (ptp) REVERT: G 236 LYS cc_start: 0.8162 (tttm) cc_final: 0.7716 (tmtt) REVERT: G 324 TYR cc_start: 0.7413 (m-80) cc_final: 0.7088 (m-80) REVERT: J 81 TYR cc_start: 0.8126 (t80) cc_final: 0.7625 (t80) REVERT: J 168 LYS cc_start: 0.8453 (mmtm) cc_final: 0.8046 (mptt) REVERT: L 206 LEU cc_start: 0.8658 (tp) cc_final: 0.8406 (tp) REVERT: N 162 PHE cc_start: 0.9003 (p90) cc_final: 0.8768 (p90) REVERT: N 217 THR cc_start: 0.8131 (m) cc_final: 0.7929 (m) REVERT: P 74 SER cc_start: 0.6466 (t) cc_final: 0.6240 (t) REVERT: P 106 LYS cc_start: 0.8546 (mttt) cc_final: 0.8325 (mttp) REVERT: P 179 ASP cc_start: 0.7736 (m-30) cc_final: 0.7386 (m-30) REVERT: Q 101 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7610 (mtpt) REVERT: S 140 PHE cc_start: 0.7592 (p90) cc_final: 0.6980 (p90) REVERT: S 207 LYS cc_start: 0.7700 (pttm) cc_final: 0.7386 (pttm) REVERT: T 76 LYS cc_start: 0.8045 (pttp) cc_final: 0.7592 (ptpt) REVERT: T 192 TYR cc_start: 0.7866 (m-80) cc_final: 0.7563 (m-80) REVERT: U 151 MET cc_start: 0.8038 (mpp) cc_final: 0.7082 (mpp) outliers start: 5 outliers final: 2 residues processed: 1109 average time/residue: 0.2351 time to fit residues: 423.5171 Evaluate side-chains 968 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 966 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 LYS Chi-restraints excluded: chain L residue 183 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 470 optimal weight: 20.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN B 190 ASN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN E 294 ASN E 302 GLN F 94 ASN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 GLN M 115 HIS M 163 ASN N 90 GLN O 115 HIS P 115 HIS R 153 ASN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.179879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.141953 restraints weight = 51831.164| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.00 r_work: 0.3581 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 40492 Z= 0.229 Angle : 0.676 9.010 55039 Z= 0.353 Chirality : 0.044 0.258 6034 Planarity : 0.005 0.064 6770 Dihedral : 14.211 179.680 6280 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 1.58 % Allowed : 11.12 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.31 (0.12), residues: 4672 helix: 0.34 (0.13), residues: 1786 sheet: -1.72 (0.22), residues: 577 loop : -1.61 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 52 TYR 0.030 0.002 TYR T 81 PHE 0.030 0.002 PHE R 228 TRP 0.020 0.001 TRP G 88 HIS 0.005 0.001 HIS U 115 Details of bonding type rmsd covalent geometry : bond 0.00538 (40492) covalent geometry : angle 0.67621 (55039) hydrogen bonds : bond 0.04296 ( 1381) hydrogen bonds : angle 4.98389 ( 3915) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1005 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8103 (mm-40) REVERT: A 240 MET cc_start: 0.8461 (mtp) cc_final: 0.8109 (ttp) REVERT: A 258 MET cc_start: 0.7836 (tpp) cc_final: 0.7221 (tpp) REVERT: A 354 LYS cc_start: 0.7169 (mttt) cc_final: 0.6933 (ttmt) REVERT: B 1 MET cc_start: 0.4425 (mmp) cc_final: 0.3797 (mmp) REVERT: B 33 ARG cc_start: 0.8482 (mtm110) cc_final: 0.7479 (ttt180) REVERT: B 47 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8782 (t) REVERT: B 149 MET cc_start: 0.7880 (mtp) cc_final: 0.7640 (mtp) REVERT: B 154 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8263 (tptp) REVERT: B 158 ASP cc_start: 0.8484 (m-30) cc_final: 0.7748 (m-30) REVERT: B 165 LYS cc_start: 0.8966 (mttm) cc_final: 0.8727 (mttt) REVERT: B 236 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8607 (tmmt) REVERT: B 297 PHE cc_start: 0.8831 (t80) cc_final: 0.8395 (t80) REVERT: C 8 ILE cc_start: 0.7587 (pt) cc_final: 0.7248 (pt) REVERT: C 163 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7787 (tp40) REVERT: C 192 THR cc_start: 0.8741 (p) cc_final: 0.8377 (p) REVERT: C 394 MET cc_start: 0.7146 (mmm) cc_final: 0.6780 (mpp) REVERT: C 419 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8334 (tm-30) REVERT: D 26 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8017 (mt-10) REVERT: D 54 TYR cc_start: 0.8906 (m-80) cc_final: 0.8681 (m-80) REVERT: D 154 LYS cc_start: 0.9086 (tptm) cc_final: 0.8850 (tppp) REVERT: D 158 ASP cc_start: 0.8545 (m-30) cc_final: 0.8263 (m-30) REVERT: D 257 GLU cc_start: 0.8232 (tp30) cc_final: 0.7980 (tp30) REVERT: D 394 MET cc_start: 0.6932 (mmp) cc_final: 0.6629 (mmp) REVERT: F 1 MET cc_start: 0.6089 (mmm) cc_final: 0.4992 (mmm) REVERT: F 94 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8616 (t0) REVERT: F 204 MET cc_start: 0.9229 (tpt) cc_final: 0.8969 (tpt) REVERT: F 258 MET cc_start: 0.8029 (mmm) cc_final: 0.7434 (tpp) REVERT: F 377 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7994 (tt0) REVERT: F 402 MET cc_start: 0.8486 (ptm) cc_final: 0.8154 (ptp) REVERT: G 151 GLU cc_start: 0.7816 (tp30) cc_final: 0.7380 (tp30) REVERT: G 236 LYS cc_start: 0.8583 (tttm) cc_final: 0.8195 (tmtt) REVERT: G 272 ASP cc_start: 0.8757 (p0) cc_final: 0.8415 (p0) REVERT: G 336 TYR cc_start: 0.7458 (t80) cc_final: 0.7070 (t80) REVERT: G 408 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.8081 (ttm-80) REVERT: L 79 ARG cc_start: 0.8253 (mmp-170) cc_final: 0.8021 (mmp-170) REVERT: L 106 LYS cc_start: 0.8761 (mttm) cc_final: 0.8536 (mttm) REVERT: L 193 MET cc_start: 0.8335 (mpp) cc_final: 0.7488 (mpp) REVERT: L 206 LEU cc_start: 0.8766 (tp) cc_final: 0.8512 (tp) REVERT: M 67 MET cc_start: 0.7848 (tmm) cc_final: 0.7459 (tmm) REVERT: N 184 GLU cc_start: 0.7591 (tp30) cc_final: 0.7058 (tp30) REVERT: O 98 MET cc_start: 0.8716 (tpp) cc_final: 0.8457 (tpp) REVERT: O 144 ARG cc_start: 0.8840 (mtm-85) cc_final: 0.8492 (mtm-85) REVERT: P 74 SER cc_start: 0.6519 (t) cc_final: 0.6236 (t) REVERT: P 179 ASP cc_start: 0.8150 (m-30) cc_final: 0.7815 (m-30) REVERT: P 224 GLN cc_start: 0.7534 (pm20) cc_final: 0.7171 (pm20) REVERT: Q 70 MET cc_start: 0.7531 (tpp) cc_final: 0.7082 (ttt) REVERT: S 140 PHE cc_start: 0.7556 (p90) cc_final: 0.6746 (p90) REVERT: S 167 TYR cc_start: 0.6894 (m-10) cc_final: 0.6670 (m-10) REVERT: S 192 TYR cc_start: 0.7409 (m-80) cc_final: 0.6667 (m-80) REVERT: S 193 MET cc_start: 0.5124 (mmt) cc_final: 0.4893 (mmt) REVERT: T 192 TYR cc_start: 0.7923 (m-80) cc_final: 0.7553 (m-80) REVERT: U 151 MET cc_start: 0.8195 (mpp) cc_final: 0.7331 (mpp) REVERT: U 167 TYR cc_start: 0.6511 (m-80) cc_final: 0.6206 (m-80) outliers start: 65 outliers final: 42 residues processed: 1037 average time/residue: 0.2560 time to fit residues: 429.7724 Evaluate side-chains 988 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 944 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 388 LYS Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 210 CYS Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 221 VAL Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain U residue 88 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 401 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 439 optimal weight: 4.9990 chunk 404 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 423 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 294 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN D 294 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 ASN E 251 ASN F 302 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN N 90 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.175861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138450 restraints weight = 51497.680| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.94 r_work: 0.3544 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 40492 Z= 0.231 Angle : 0.662 9.324 55039 Z= 0.344 Chirality : 0.044 0.282 6034 Planarity : 0.005 0.061 6770 Dihedral : 14.206 179.765 6280 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.50 % Allowed : 14.40 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.38 (0.12), residues: 4672 helix: 0.28 (0.13), residues: 1802 sheet: -1.53 (0.22), residues: 585 loop : -1.73 (0.12), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 144 TYR 0.027 0.002 TYR A 56 PHE 0.032 0.002 PHE B 171 TRP 0.010 0.001 TRP D 300 HIS 0.004 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00547 (40492) covalent geometry : angle 0.66222 (55039) hydrogen bonds : bond 0.04017 ( 1381) hydrogen bonds : angle 4.76360 ( 3915) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 983 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.9108 (tpp) cc_final: 0.8757 (tpt) REVERT: A 240 MET cc_start: 0.8415 (mtp) cc_final: 0.8179 (ttm) REVERT: A 258 MET cc_start: 0.7742 (tpp) cc_final: 0.7203 (tpp) REVERT: B 1 MET cc_start: 0.4067 (mmp) cc_final: 0.3436 (mmp) REVERT: B 47 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8764 (t) REVERT: B 154 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8288 (tptp) REVERT: B 158 ASP cc_start: 0.8496 (m-30) cc_final: 0.7744 (m-30) REVERT: B 165 LYS cc_start: 0.8886 (mttm) cc_final: 0.8668 (mttt) REVERT: B 324 TYR cc_start: 0.7879 (m-10) cc_final: 0.7617 (m-10) REVERT: C 8 ILE cc_start: 0.7487 (pt) cc_final: 0.7156 (pt) REVERT: C 236 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8222 (ttpt) REVERT: C 263 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8683 (tp) REVERT: C 394 MET cc_start: 0.7070 (mmm) cc_final: 0.6228 (mpp) REVERT: C 419 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8216 (tm-30) REVERT: D 26 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8022 (mt-10) REVERT: D 54 TYR cc_start: 0.8885 (m-80) cc_final: 0.8676 (m-80) REVERT: D 154 LYS cc_start: 0.9130 (tptm) cc_final: 0.8882 (tppp) REVERT: D 158 ASP cc_start: 0.8571 (m-30) cc_final: 0.8301 (m-30) REVERT: D 257 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: D 260 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: D 394 MET cc_start: 0.7076 (mmp) cc_final: 0.6749 (mmp) REVERT: E 83 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8949 (ttmm) REVERT: E 240 MET cc_start: 0.8602 (ttm) cc_final: 0.8394 (ttm) REVERT: E 253 GLU cc_start: 0.8177 (pm20) cc_final: 0.7976 (pm20) REVERT: E 262 MET cc_start: 0.8779 (mtt) cc_final: 0.8294 (mtt) REVERT: F 1 MET cc_start: 0.6091 (mmm) cc_final: 0.4564 (mmm) REVERT: F 151 GLU cc_start: 0.8355 (tp30) cc_final: 0.8135 (tp30) REVERT: F 240 MET cc_start: 0.8876 (mtp) cc_final: 0.8213 (ttm) REVERT: G 119 ASP cc_start: 0.5460 (m-30) cc_final: 0.5111 (m-30) REVERT: G 236 LYS cc_start: 0.8642 (tttm) cc_final: 0.8197 (tmtt) REVERT: G 247 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7599 (t) REVERT: G 272 ASP cc_start: 0.8818 (p0) cc_final: 0.8405 (p0) REVERT: G 336 TYR cc_start: 0.7414 (t80) cc_final: 0.7021 (t80) REVERT: J 68 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7120 (mp) REVERT: J 81 TYR cc_start: 0.8222 (t80) cc_final: 0.7888 (t80) REVERT: J 92 ASP cc_start: 0.8267 (p0) cc_final: 0.8032 (p0) REVERT: J 138 ARG cc_start: 0.7738 (mmt180) cc_final: 0.7431 (mmm160) REVERT: J 224 GLN cc_start: 0.8238 (pm20) cc_final: 0.7998 (pm20) REVERT: K 70 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8426 (tpp) REVERT: L 193 MET cc_start: 0.8395 (mpp) cc_final: 0.7905 (mpp) REVERT: L 206 LEU cc_start: 0.8719 (tp) cc_final: 0.8481 (tp) REVERT: M 67 MET cc_start: 0.7964 (tmm) cc_final: 0.7576 (tmm) REVERT: M 81 TYR cc_start: 0.8445 (t80) cc_final: 0.8212 (t80) REVERT: M 128 GLN cc_start: 0.8149 (mt0) cc_final: 0.7760 (pm20) REVERT: N 184 GLU cc_start: 0.7639 (tp30) cc_final: 0.7044 (tp30) REVERT: N 185 LYS cc_start: 0.7627 (tppt) cc_final: 0.6917 (tptm) REVERT: N 193 MET cc_start: 0.8691 (mpp) cc_final: 0.7445 (mpp) REVERT: O 168 LYS cc_start: 0.8902 (mmtm) cc_final: 0.8610 (mmtt) REVERT: P 74 SER cc_start: 0.6565 (t) cc_final: 0.6244 (t) REVERT: P 179 ASP cc_start: 0.8152 (m-30) cc_final: 0.7855 (m-30) REVERT: P 224 GLN cc_start: 0.7681 (pm20) cc_final: 0.7400 (pm20) REVERT: Q 70 MET cc_start: 0.7814 (tpp) cc_final: 0.7600 (ttt) REVERT: Q 167 TYR cc_start: 0.7123 (m-80) cc_final: 0.6910 (m-80) REVERT: Q 193 MET cc_start: 0.6247 (mmm) cc_final: 0.5794 (mmm) REVERT: R 173 PHE cc_start: 0.7823 (m-10) cc_final: 0.7586 (m-80) REVERT: S 192 TYR cc_start: 0.7715 (m-80) cc_final: 0.6810 (m-80) REVERT: T 81 TYR cc_start: 0.7626 (t80) cc_final: 0.7366 (t80) REVERT: T 192 TYR cc_start: 0.7954 (m-80) cc_final: 0.7605 (m-80) REVERT: U 151 MET cc_start: 0.8180 (mpp) cc_final: 0.7300 (mpp) REVERT: U 167 TYR cc_start: 0.6706 (m-80) cc_final: 0.6352 (m-80) outliers start: 103 outliers final: 67 residues processed: 1034 average time/residue: 0.2469 time to fit residues: 415.6233 Evaluate side-chains 996 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 922 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 210 CYS Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 210 CYS Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain K residue 70 MET Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain U residue 156 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 0.0070 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 16 optimal weight: 0.0670 chunk 94 optimal weight: 2.9990 chunk 376 optimal weight: 7.9990 chunk 373 optimal weight: 8.9990 chunk 445 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN A 294 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN B 294 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN E 294 ASN F 94 ASN F 347 GLN M 90 GLN N 90 GLN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 198 GLN ** U 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.182187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.144542 restraints weight = 51122.711| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.02 r_work: 0.3611 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40492 Z= 0.123 Angle : 0.599 8.566 55039 Z= 0.311 Chirality : 0.041 0.257 6034 Planarity : 0.004 0.056 6770 Dihedral : 14.136 179.208 6276 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.06 % Allowed : 16.49 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.03 (0.12), residues: 4672 helix: 0.59 (0.13), residues: 1752 sheet: -1.38 (0.23), residues: 528 loop : -1.50 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 399 TYR 0.024 0.001 TYR C 74 PHE 0.030 0.002 PHE U 140 TRP 0.012 0.001 TRP F 378 HIS 0.004 0.001 HIS U 115 Details of bonding type rmsd covalent geometry : bond 0.00280 (40492) covalent geometry : angle 0.59893 (55039) hydrogen bonds : bond 0.03396 ( 1381) hydrogen bonds : angle 4.43015 ( 3915) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 992 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9211 (tptt) cc_final: 0.8914 (tptp) REVERT: A 157 MET cc_start: 0.9103 (tpp) cc_final: 0.8851 (tpt) REVERT: A 187 ASN cc_start: 0.8334 (m-40) cc_final: 0.7883 (t0) REVERT: A 258 MET cc_start: 0.7735 (tpp) cc_final: 0.7181 (tpp) REVERT: A 324 TYR cc_start: 0.8059 (m-10) cc_final: 0.7797 (m-10) REVERT: B 1 MET cc_start: 0.3822 (mmp) cc_final: 0.3565 (mmp) REVERT: B 33 ARG cc_start: 0.8509 (mtm110) cc_final: 0.7735 (ttt90) REVERT: B 47 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8729 (t) REVERT: B 154 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8256 (tptp) REVERT: B 158 ASP cc_start: 0.8510 (m-30) cc_final: 0.7738 (m-30) REVERT: B 165 LYS cc_start: 0.8893 (mttm) cc_final: 0.8658 (mttt) REVERT: B 240 MET cc_start: 0.8738 (ttm) cc_final: 0.8235 (ttm) REVERT: B 324 TYR cc_start: 0.7828 (m-10) cc_final: 0.7579 (m-10) REVERT: C 51 LEU cc_start: 0.8531 (mt) cc_final: 0.8228 (mt) REVERT: C 187 ASN cc_start: 0.8871 (t0) cc_final: 0.8410 (t0) REVERT: C 263 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8509 (tp) REVERT: C 394 MET cc_start: 0.7047 (mmm) cc_final: 0.6265 (mpp) REVERT: C 419 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8110 (tm-30) REVERT: D 26 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7937 (mt-10) REVERT: D 97 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8548 (mmtt) REVERT: D 154 LYS cc_start: 0.9145 (tptm) cc_final: 0.8857 (tppp) REVERT: D 158 ASP cc_start: 0.8595 (m-30) cc_final: 0.8317 (m-30) REVERT: D 236 LYS cc_start: 0.9010 (tttm) cc_final: 0.8635 (tttp) REVERT: D 257 GLU cc_start: 0.8120 (tp30) cc_final: 0.7692 (tt0) REVERT: D 394 MET cc_start: 0.7020 (mmp) cc_final: 0.6644 (mmt) REVERT: E 11 ASN cc_start: 0.8218 (t0) cc_final: 0.7952 (t0) REVERT: E 262 MET cc_start: 0.8817 (mtt) cc_final: 0.8593 (mtt) REVERT: F 1 MET cc_start: 0.5892 (mmm) cc_final: 0.4605 (mmm) REVERT: F 258 MET cc_start: 0.8066 (mmm) cc_final: 0.7420 (tpp) REVERT: F 377 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7945 (tt0) REVERT: F 409 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7910 (tm-30) REVERT: G 119 ASP cc_start: 0.5227 (m-30) cc_final: 0.4795 (m-30) REVERT: G 236 LYS cc_start: 0.8573 (tttm) cc_final: 0.8145 (tmtt) REVERT: G 272 ASP cc_start: 0.8767 (p0) cc_final: 0.8299 (p0) REVERT: G 336 TYR cc_start: 0.7373 (t80) cc_final: 0.7030 (t80) REVERT: J 68 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6766 (mp) REVERT: J 81 TYR cc_start: 0.8116 (t80) cc_final: 0.7845 (t80) REVERT: J 138 ARG cc_start: 0.7428 (mmt180) cc_final: 0.7144 (mmt180) REVERT: J 224 GLN cc_start: 0.8234 (pm20) cc_final: 0.8019 (pm20) REVERT: K 70 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8355 (tpp) REVERT: L 190 TRP cc_start: 0.8587 (m100) cc_final: 0.8233 (m100) REVERT: L 193 MET cc_start: 0.8368 (mpp) cc_final: 0.7955 (mpp) REVERT: L 206 LEU cc_start: 0.8626 (tp) cc_final: 0.8378 (tp) REVERT: M 128 GLN cc_start: 0.8096 (mt0) cc_final: 0.7745 (pm20) REVERT: N 70 MET cc_start: 0.8153 (ttt) cc_final: 0.7725 (tpp) REVERT: N 184 GLU cc_start: 0.7615 (tp30) cc_final: 0.7086 (tp30) REVERT: N 193 MET cc_start: 0.8781 (mpp) cc_final: 0.7786 (mpp) REVERT: O 144 ARG cc_start: 0.8904 (mtm-85) cc_final: 0.8517 (mtm-85) REVERT: O 168 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8534 (mmtt) REVERT: O 192 TYR cc_start: 0.8259 (m-80) cc_final: 0.7199 (m-80) REVERT: P 74 SER cc_start: 0.6199 (t) cc_final: 0.5979 (t) REVERT: P 151 MET cc_start: 0.8856 (mtt) cc_final: 0.8292 (mtm) REVERT: P 179 ASP cc_start: 0.8124 (m-30) cc_final: 0.7828 (m-30) REVERT: P 202 GLN cc_start: 0.8395 (tt0) cc_final: 0.7868 (tm-30) REVERT: P 224 GLN cc_start: 0.7710 (pm20) cc_final: 0.7390 (pm20) REVERT: Q 70 MET cc_start: 0.7672 (tpp) cc_final: 0.7433 (ttt) REVERT: Q 156 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6882 (mt-10) REVERT: Q 167 TYR cc_start: 0.7275 (m-80) cc_final: 0.7005 (m-80) REVERT: Q 193 MET cc_start: 0.6086 (mmm) cc_final: 0.5620 (mmm) REVERT: R 176 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7713 (p) REVERT: S 76 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6418 (pttp) REVERT: S 98 MET cc_start: 0.8384 (mmm) cc_final: 0.7952 (mtp) REVERT: T 70 MET cc_start: 0.7580 (tpp) cc_final: 0.7173 (ttt) REVERT: T 76 LYS cc_start: 0.8043 (pttp) cc_final: 0.7402 (ptpt) REVERT: T 173 PHE cc_start: 0.7942 (m-80) cc_final: 0.7655 (m-10) REVERT: T 192 TYR cc_start: 0.7930 (m-80) cc_final: 0.7582 (m-80) REVERT: T 208 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7003 (t80) REVERT: U 101 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8147 (mtmm) REVERT: U 151 MET cc_start: 0.8035 (mpp) cc_final: 0.7163 (mpp) REVERT: U 167 TYR cc_start: 0.6574 (m-80) cc_final: 0.6235 (m-80) outliers start: 85 outliers final: 46 residues processed: 1035 average time/residue: 0.2448 time to fit residues: 411.4219 Evaluate side-chains 986 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 933 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 70 MET Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 208 PHE Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 55 optimal weight: 6.9990 chunk 320 optimal weight: 20.0000 chunk 448 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 230 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 420 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 260 GLN A 294 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN F 347 GLN G 11 ASN G 302 GLN M 90 GLN N 90 GLN N 115 HIS ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.175133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137765 restraints weight = 51230.214| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.79 r_work: 0.3543 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 40492 Z= 0.228 Angle : 0.658 9.116 55039 Z= 0.341 Chirality : 0.044 0.288 6034 Planarity : 0.005 0.055 6770 Dihedral : 14.121 179.956 6276 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.94 % Allowed : 17.10 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.19 (0.12), residues: 4672 helix: 0.40 (0.13), residues: 1770 sheet: -1.32 (0.22), residues: 579 loop : -1.60 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 7 TYR 0.027 0.002 TYR D 54 PHE 0.032 0.002 PHE U 140 TRP 0.012 0.001 TRP D 300 HIS 0.003 0.001 HIS F 203 Details of bonding type rmsd covalent geometry : bond 0.00538 (40492) covalent geometry : angle 0.65845 (55039) hydrogen bonds : bond 0.03665 ( 1381) hydrogen bonds : angle 4.50403 ( 3915) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 952 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9236 (tptt) cc_final: 0.8924 (tptp) REVERT: A 157 MET cc_start: 0.9047 (tpp) cc_final: 0.8482 (tpt) REVERT: A 324 TYR cc_start: 0.8088 (m-10) cc_final: 0.7858 (m-10) REVERT: B 1 MET cc_start: 0.3924 (mmp) cc_final: 0.3622 (mmp) REVERT: B 47 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8733 (t) REVERT: B 154 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8329 (tptp) REVERT: B 158 ASP cc_start: 0.8489 (m-30) cc_final: 0.7738 (m-30) REVERT: B 165 LYS cc_start: 0.8781 (mttm) cc_final: 0.8523 (mttt) REVERT: B 240 MET cc_start: 0.8813 (ttm) cc_final: 0.8357 (ttm) REVERT: B 388 LYS cc_start: 0.8572 (ptpp) cc_final: 0.8287 (ptpp) REVERT: C 236 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8183 (ttpt) REVERT: C 263 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8612 (tp) REVERT: C 394 MET cc_start: 0.7120 (mmm) cc_final: 0.6764 (mpp) REVERT: C 419 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8136 (tm-30) REVERT: D 26 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8010 (mt-10) REVERT: D 34 LYS cc_start: 0.5149 (tttt) cc_final: 0.4369 (mtpt) REVERT: D 54 TYR cc_start: 0.8886 (m-80) cc_final: 0.8436 (m-80) REVERT: D 149 MET cc_start: 0.8364 (mpp) cc_final: 0.8091 (mpp) REVERT: D 154 LYS cc_start: 0.9178 (tptm) cc_final: 0.8883 (tppp) REVERT: D 158 ASP cc_start: 0.8580 (m-30) cc_final: 0.8299 (m-30) REVERT: D 236 LYS cc_start: 0.9031 (tttm) cc_final: 0.8683 (tttp) REVERT: D 257 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: D 394 MET cc_start: 0.7119 (mmp) cc_final: 0.6656 (mmp) REVERT: E 11 ASN cc_start: 0.8191 (t0) cc_final: 0.7917 (t0) REVERT: E 262 MET cc_start: 0.8842 (mtt) cc_final: 0.8565 (mtt) REVERT: F 1 MET cc_start: 0.5997 (mmm) cc_final: 0.4677 (mmm) REVERT: F 26 GLU cc_start: 0.7989 (tt0) cc_final: 0.7629 (tt0) REVERT: F 63 ASN cc_start: 0.8217 (t0) cc_final: 0.7770 (t0) REVERT: F 151 GLU cc_start: 0.8362 (tp30) cc_final: 0.8134 (tp30) REVERT: F 258 MET cc_start: 0.8041 (mmm) cc_final: 0.7296 (tpt) REVERT: F 408 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7764 (ttm-80) REVERT: G 119 ASP cc_start: 0.5482 (m-30) cc_final: 0.5138 (m-30) REVERT: G 151 GLU cc_start: 0.7881 (tp30) cc_final: 0.7635 (tp30) REVERT: G 200 MET cc_start: 0.8730 (ttp) cc_final: 0.8474 (ttp) REVERT: G 236 LYS cc_start: 0.8520 (tttm) cc_final: 0.8185 (tmtt) REVERT: G 247 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7525 (t) REVERT: G 272 ASP cc_start: 0.8835 (p0) cc_final: 0.8364 (p0) REVERT: G 336 TYR cc_start: 0.7414 (t80) cc_final: 0.7062 (t80) REVERT: G 394 MET cc_start: 0.7457 (mpp) cc_final: 0.6614 (mpp) REVERT: J 68 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7069 (mp) REVERT: J 81 TYR cc_start: 0.8263 (t80) cc_final: 0.7926 (t80) REVERT: J 92 ASP cc_start: 0.8289 (p0) cc_final: 0.8038 (p0) REVERT: J 138 ARG cc_start: 0.7813 (mmt180) cc_final: 0.7347 (mmt180) REVERT: J 168 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8189 (mptt) REVERT: K 69 LYS cc_start: 0.8146 (mmpt) cc_final: 0.7764 (mtpp) REVERT: L 193 MET cc_start: 0.8685 (mpp) cc_final: 0.8307 (mpp) REVERT: L 206 LEU cc_start: 0.8611 (tp) cc_final: 0.8376 (tp) REVERT: M 67 MET cc_start: 0.8079 (tmm) cc_final: 0.7732 (tmm) REVERT: M 184 GLU cc_start: 0.6899 (mp0) cc_final: 0.6286 (mp0) REVERT: N 70 MET cc_start: 0.8224 (ttt) cc_final: 0.7814 (ttt) REVERT: N 184 GLU cc_start: 0.7646 (tp30) cc_final: 0.7098 (tp30) REVERT: N 193 MET cc_start: 0.8882 (mpp) cc_final: 0.7935 (mpp) REVERT: O 192 TYR cc_start: 0.8447 (m-80) cc_final: 0.7522 (m-80) REVERT: P 74 SER cc_start: 0.6222 (t) cc_final: 0.6006 (t) REVERT: P 179 ASP cc_start: 0.8105 (m-30) cc_final: 0.7806 (m-30) REVERT: P 224 GLN cc_start: 0.7867 (pm20) cc_final: 0.7583 (pm20) REVERT: Q 156 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6970 (mt-10) REVERT: Q 167 TYR cc_start: 0.7376 (m-80) cc_final: 0.7081 (m-80) REVERT: Q 193 MET cc_start: 0.5995 (mmm) cc_final: 0.5550 (mmm) REVERT: R 176 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7776 (p) REVERT: S 98 MET cc_start: 0.8450 (mmm) cc_final: 0.8005 (mtp) REVERT: S 192 TYR cc_start: 0.7672 (m-80) cc_final: 0.6595 (m-80) REVERT: T 70 MET cc_start: 0.7696 (tpp) cc_final: 0.7451 (ttt) REVERT: T 173 PHE cc_start: 0.7907 (m-80) cc_final: 0.7638 (m-10) REVERT: T 192 TYR cc_start: 0.7940 (m-80) cc_final: 0.7641 (m-80) REVERT: T 207 LYS cc_start: 0.7804 (pptt) cc_final: 0.7559 (pptt) REVERT: T 208 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.6900 (t80) REVERT: U 63 LYS cc_start: 0.7234 (mmtt) cc_final: 0.6124 (mmmt) REVERT: U 151 MET cc_start: 0.8049 (mpp) cc_final: 0.7171 (mpp) REVERT: U 167 TYR cc_start: 0.6687 (m-80) cc_final: 0.6382 (m-80) outliers start: 121 outliers final: 84 residues processed: 1014 average time/residue: 0.2464 time to fit residues: 404.8254 Evaluate side-chains 1009 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 918 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 210 CYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 211 ILE Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 208 PHE Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 218 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 369 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 469 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 459 optimal weight: 0.6980 chunk 422 optimal weight: 30.0000 chunk 434 optimal weight: 7.9990 chunk 343 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 260 GLN A 294 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN D 294 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN F 347 GLN G 11 ASN G 251 ASN M 90 GLN N 90 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.179105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.141729 restraints weight = 51084.539| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.83 r_work: 0.3588 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40492 Z= 0.141 Angle : 0.610 9.261 55039 Z= 0.316 Chirality : 0.042 0.259 6034 Planarity : 0.004 0.055 6770 Dihedral : 14.077 179.616 6276 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.70 % Allowed : 17.70 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.01 (0.12), residues: 4672 helix: 0.59 (0.13), residues: 1759 sheet: -1.20 (0.22), residues: 562 loop : -1.52 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 7 TYR 0.025 0.001 TYR T 81 PHE 0.035 0.002 PHE U 140 TRP 0.011 0.001 TRP S 190 HIS 0.003 0.001 HIS S 188 Details of bonding type rmsd covalent geometry : bond 0.00333 (40492) covalent geometry : angle 0.61032 (55039) hydrogen bonds : bond 0.03324 ( 1381) hydrogen bonds : angle 4.32895 ( 3915) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 955 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9223 (tptt) cc_final: 0.8896 (tptp) REVERT: A 157 MET cc_start: 0.9045 (tpp) cc_final: 0.8390 (tpt) REVERT: A 324 TYR cc_start: 0.8083 (m-10) cc_final: 0.7843 (m-10) REVERT: B 33 ARG cc_start: 0.8439 (mtm110) cc_final: 0.7681 (ttt90) REVERT: B 47 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8672 (t) REVERT: B 154 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8235 (tptp) REVERT: B 158 ASP cc_start: 0.8468 (m-30) cc_final: 0.7712 (m-30) REVERT: B 165 LYS cc_start: 0.8751 (mttm) cc_final: 0.8470 (mttt) REVERT: B 240 MET cc_start: 0.8755 (ttm) cc_final: 0.8297 (ttm) REVERT: B 278 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8376 (pt) REVERT: B 388 LYS cc_start: 0.8551 (ptpp) cc_final: 0.8327 (ptpp) REVERT: C 97 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8477 (mmmt) REVERT: C 187 ASN cc_start: 0.8903 (t0) cc_final: 0.8489 (t0) REVERT: C 394 MET cc_start: 0.6983 (mmm) cc_final: 0.6163 (mpp) REVERT: C 419 GLU cc_start: 0.8585 (tm-30) cc_final: 0.7923 (tm-30) REVERT: D 26 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8176 (mt-10) REVERT: D 34 LYS cc_start: 0.4877 (tttt) cc_final: 0.4093 (mtpt) REVERT: D 54 TYR cc_start: 0.8888 (m-80) cc_final: 0.8389 (m-80) REVERT: D 154 LYS cc_start: 0.9162 (tptm) cc_final: 0.8852 (tppp) REVERT: D 224 ASP cc_start: 0.7902 (t0) cc_final: 0.7015 (t0) REVERT: D 236 LYS cc_start: 0.9009 (tttm) cc_final: 0.8656 (tttp) REVERT: D 257 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: D 260 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: D 394 MET cc_start: 0.7039 (mmp) cc_final: 0.6557 (mmt) REVERT: E 11 ASN cc_start: 0.8171 (t0) cc_final: 0.7894 (t0) REVERT: F 1 MET cc_start: 0.5958 (mmm) cc_final: 0.4570 (mmm) REVERT: F 258 MET cc_start: 0.8110 (mmm) cc_final: 0.7608 (tpp) REVERT: G 119 ASP cc_start: 0.5429 (m-30) cc_final: 0.5016 (m-30) REVERT: G 151 GLU cc_start: 0.7844 (tp30) cc_final: 0.7583 (tp30) REVERT: G 200 MET cc_start: 0.8688 (ttp) cc_final: 0.8445 (ttp) REVERT: G 236 LYS cc_start: 0.8472 (tttm) cc_final: 0.8147 (tmtt) REVERT: G 247 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7488 (t) REVERT: G 272 ASP cc_start: 0.8770 (p0) cc_final: 0.8302 (p0) REVERT: G 336 TYR cc_start: 0.7331 (t80) cc_final: 0.7028 (t80) REVERT: G 394 MET cc_start: 0.7521 (mpp) cc_final: 0.6716 (mpp) REVERT: J 81 TYR cc_start: 0.8170 (t80) cc_final: 0.7943 (t80) REVERT: J 138 ARG cc_start: 0.7590 (mmt180) cc_final: 0.7334 (mmt-90) REVERT: J 168 LYS cc_start: 0.8621 (mmtm) cc_final: 0.8239 (mptt) REVERT: K 95 TYR cc_start: 0.8745 (t80) cc_final: 0.8511 (t80) REVERT: L 193 MET cc_start: 0.8613 (mpp) cc_final: 0.8292 (mpp) REVERT: M 184 GLU cc_start: 0.6776 (mp0) cc_final: 0.6161 (mp0) REVERT: N 184 GLU cc_start: 0.7643 (tp30) cc_final: 0.7079 (tp30) REVERT: N 193 MET cc_start: 0.8851 (mpp) cc_final: 0.8052 (mpp) REVERT: O 144 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8457 (mtm-85) REVERT: O 192 TYR cc_start: 0.8308 (m-80) cc_final: 0.7361 (m-80) REVERT: P 74 SER cc_start: 0.6187 (t) cc_final: 0.5962 (t) REVERT: P 179 ASP cc_start: 0.7950 (m-30) cc_final: 0.7626 (m-30) REVERT: P 224 GLN cc_start: 0.7849 (pm20) cc_final: 0.7577 (pm20) REVERT: Q 156 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6903 (mt-10) REVERT: Q 167 TYR cc_start: 0.7232 (m-80) cc_final: 0.6918 (m-80) REVERT: R 176 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7737 (p) REVERT: S 76 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6424 (pttp) REVERT: S 98 MET cc_start: 0.8404 (mmm) cc_final: 0.7970 (mtp) REVERT: S 192 TYR cc_start: 0.7727 (m-80) cc_final: 0.6780 (m-80) REVERT: T 192 TYR cc_start: 0.7950 (m-80) cc_final: 0.7639 (m-80) REVERT: U 63 LYS cc_start: 0.7453 (mmtt) cc_final: 0.6399 (mmmt) REVERT: U 68 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.5212 (mm) REVERT: U 101 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8188 (mtmm) REVERT: U 151 MET cc_start: 0.7918 (mpp) cc_final: 0.7059 (mpp) REVERT: U 167 TYR cc_start: 0.6643 (m-80) cc_final: 0.6259 (m-80) REVERT: U 173 PHE cc_start: 0.7124 (m-80) cc_final: 0.6891 (t80) outliers start: 111 outliers final: 74 residues processed: 1010 average time/residue: 0.2478 time to fit residues: 406.6053 Evaluate side-chains 1013 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 931 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 347 GLN Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain T residue 211 ILE Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 61 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 365 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 228 optimal weight: 0.9990 chunk 455 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 398 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN F 94 ASN G 11 ASN G 302 GLN M 90 GLN N 90 GLN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.177584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.141613 restraints weight = 51503.056| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.76 r_work: 0.3559 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 40492 Z= 0.202 Angle : 0.644 8.940 55039 Z= 0.333 Chirality : 0.043 0.283 6034 Planarity : 0.005 0.054 6770 Dihedral : 14.063 179.541 6276 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.01 % Allowed : 18.48 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.10 (0.12), residues: 4672 helix: 0.47 (0.13), residues: 1770 sheet: -1.15 (0.22), residues: 578 loop : -1.57 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 399 TYR 0.022 0.001 TYR D 54 PHE 0.032 0.002 PHE U 140 TRP 0.012 0.001 TRP D 300 HIS 0.003 0.001 HIS F 203 Details of bonding type rmsd covalent geometry : bond 0.00479 (40492) covalent geometry : angle 0.64403 (55039) hydrogen bonds : bond 0.03493 ( 1381) hydrogen bonds : angle 4.37647 ( 3915) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 939 time to evaluate : 1.282 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 154 LYS cc_start: 0.9255 (tptt) cc_final: 0.8918 (tptp) REVERT: A 168 ASN cc_start: 0.8705 (t0) cc_final: 0.8383 (t0) REVERT: A 253 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: A 324 TYR cc_start: 0.8074 (m-10) cc_final: 0.7830 (m-10) REVERT: B 47 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8704 (t) REVERT: B 154 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8292 (tptp) REVERT: B 158 ASP cc_start: 0.8359 (m-30) cc_final: 0.7562 (m-30) REVERT: B 165 LYS cc_start: 0.8743 (mttm) cc_final: 0.8466 (mttt) REVERT: B 170 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7371 (mp-120) REVERT: B 240 MET cc_start: 0.8809 (ttm) cc_final: 0.8333 (ttm) REVERT: B 278 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8466 (pt) REVERT: B 388 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8380 (ptpp) REVERT: C 7 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7909 (ttt180) REVERT: C 187 ASN cc_start: 0.8929 (t0) cc_final: 0.8519 (t0) REVERT: C 263 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8561 (tp) REVERT: C 394 MET cc_start: 0.7052 (mmm) cc_final: 0.6252 (mpp) REVERT: D 34 LYS cc_start: 0.4923 (tttt) cc_final: 0.4093 (mtpt) REVERT: D 54 TYR cc_start: 0.8873 (m-80) cc_final: 0.8201 (m-80) REVERT: D 143 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7640 (ttp80) REVERT: D 154 LYS cc_start: 0.9206 (tptm) cc_final: 0.8962 (tppp) REVERT: D 158 ASP cc_start: 0.8475 (m-30) cc_final: 0.8214 (m-30) REVERT: D 224 ASP cc_start: 0.7954 (t0) cc_final: 0.7063 (t0) REVERT: D 236 LYS cc_start: 0.9033 (tttm) cc_final: 0.8683 (tttp) REVERT: D 257 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: D 394 MET cc_start: 0.6692 (mmp) cc_final: 0.6439 (mmt) REVERT: E 11 ASN cc_start: 0.8145 (t0) cc_final: 0.7873 (t0) REVERT: F 1 MET cc_start: 0.5775 (mmm) cc_final: 0.4619 (mmm) REVERT: F 63 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7625 (t0) REVERT: F 240 MET cc_start: 0.8839 (ttm) cc_final: 0.8579 (ttm) REVERT: F 258 MET cc_start: 0.8049 (mmm) cc_final: 0.7659 (tpt) REVERT: G 119 ASP cc_start: 0.5494 (m-30) cc_final: 0.5150 (m-30) REVERT: G 200 MET cc_start: 0.8718 (ttp) cc_final: 0.8444 (ttp) REVERT: G 236 LYS cc_start: 0.8496 (tttm) cc_final: 0.8166 (tmtt) REVERT: G 247 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7449 (t) REVERT: G 272 ASP cc_start: 0.8789 (p0) cc_final: 0.8318 (p0) REVERT: G 336 TYR cc_start: 0.7333 (t80) cc_final: 0.7049 (t80) REVERT: G 394 MET cc_start: 0.7521 (mpp) cc_final: 0.6686 (mpp) REVERT: J 81 TYR cc_start: 0.8186 (t80) cc_final: 0.7898 (t80) REVERT: J 138 ARG cc_start: 0.7778 (mmt180) cc_final: 0.7506 (mmt-90) REVERT: K 79 ARG cc_start: 0.9059 (tpm170) cc_final: 0.8658 (tpm170) REVERT: K 95 TYR cc_start: 0.8772 (t80) cc_final: 0.8527 (t80) REVERT: L 193 MET cc_start: 0.8699 (mpp) cc_final: 0.8301 (mpp) REVERT: M 184 GLU cc_start: 0.6847 (mp0) cc_final: 0.6214 (mp0) REVERT: N 184 GLU cc_start: 0.7638 (tp30) cc_final: 0.7064 (tp30) REVERT: N 193 MET cc_start: 0.8866 (mpp) cc_final: 0.7896 (mpp) REVERT: O 192 TYR cc_start: 0.8430 (m-80) cc_final: 0.7455 (m-80) REVERT: O 193 MET cc_start: 0.8244 (mpp) cc_final: 0.7883 (mtm) REVERT: P 179 ASP cc_start: 0.7928 (m-30) cc_final: 0.7625 (m-30) REVERT: P 224 GLN cc_start: 0.7938 (pm20) cc_final: 0.7677 (pm20) REVERT: Q 156 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7007 (mt-10) REVERT: Q 167 TYR cc_start: 0.7248 (m-80) cc_final: 0.6920 (m-80) REVERT: R 173 PHE cc_start: 0.8011 (m-80) cc_final: 0.7740 (t80) REVERT: S 76 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6446 (pttp) REVERT: S 98 MET cc_start: 0.8455 (mmm) cc_final: 0.8008 (mtp) REVERT: T 76 LYS cc_start: 0.7942 (pttp) cc_final: 0.7258 (ptpt) REVERT: T 81 TYR cc_start: 0.7449 (t80) cc_final: 0.7189 (t80) REVERT: T 167 TYR cc_start: 0.8079 (m-80) cc_final: 0.7814 (m-80) REVERT: T 192 TYR cc_start: 0.7952 (m-80) cc_final: 0.7654 (m-80) REVERT: T 207 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7667 (tptt) REVERT: T 208 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.6952 (t80) REVERT: U 63 LYS cc_start: 0.7187 (mmtt) cc_final: 0.6176 (mmmt) REVERT: U 101 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8190 (mtmm) REVERT: U 151 MET cc_start: 0.7984 (mpp) cc_final: 0.7129 (mpp) REVERT: U 167 TYR cc_start: 0.6653 (m-80) cc_final: 0.6336 (m-80) outliers start: 124 outliers final: 85 residues processed: 1001 average time/residue: 0.2446 time to fit residues: 397.2320 Evaluate side-chains 1014 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 917 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain T residue 207 LYS Chi-restraints excluded: chain T residue 208 PHE Chi-restraints excluded: chain U residue 98 MET Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 270 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 392 optimal weight: 0.9980 chunk 362 optimal weight: 4.9990 chunk 350 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 295 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN G 11 ASN M 90 GLN N 90 GLN O 90 GLN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.179074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141482 restraints weight = 51144.535| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.86 r_work: 0.3587 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40492 Z= 0.144 Angle : 0.621 9.221 55039 Z= 0.322 Chirality : 0.042 0.264 6034 Planarity : 0.004 0.055 6770 Dihedral : 14.052 179.241 6276 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.94 % Allowed : 19.21 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.97 (0.12), residues: 4672 helix: 0.58 (0.13), residues: 1764 sheet: -1.04 (0.22), residues: 570 loop : -1.51 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 399 TYR 0.024 0.001 TYR G 324 PHE 0.034 0.002 PHE U 140 TRP 0.014 0.001 TRP D 300 HIS 0.003 0.001 HIS N 188 Details of bonding type rmsd covalent geometry : bond 0.00342 (40492) covalent geometry : angle 0.62050 (55039) hydrogen bonds : bond 0.03301 ( 1381) hydrogen bonds : angle 4.27070 ( 3915) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 950 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9283 (tptt) cc_final: 0.8932 (tptp) REVERT: A 168 ASN cc_start: 0.8700 (t0) cc_final: 0.8375 (t0) REVERT: A 253 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: A 258 MET cc_start: 0.7500 (tpp) cc_final: 0.6987 (tpp) REVERT: A 324 TYR cc_start: 0.8113 (m-10) cc_final: 0.7829 (m-10) REVERT: B 47 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8676 (t) REVERT: B 154 LYS cc_start: 0.8877 (ttpt) cc_final: 0.8357 (tptp) REVERT: B 158 ASP cc_start: 0.8371 (m-30) cc_final: 0.7692 (m-30) REVERT: B 165 LYS cc_start: 0.8761 (mttm) cc_final: 0.8532 (mttt) REVERT: B 240 MET cc_start: 0.8742 (ttm) cc_final: 0.8333 (ttm) REVERT: B 278 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8354 (pt) REVERT: B 388 LYS cc_start: 0.8654 (ptpp) cc_final: 0.8393 (ptpp) REVERT: C 7 ARG cc_start: 0.8041 (ttt180) cc_final: 0.7808 (ttt180) REVERT: C 187 ASN cc_start: 0.8936 (t0) cc_final: 0.8517 (t0) REVERT: C 263 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8499 (tp) REVERT: C 394 MET cc_start: 0.6973 (mmm) cc_final: 0.6159 (mpp) REVERT: C 419 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8304 (tm-30) REVERT: D 34 LYS cc_start: 0.4960 (tttt) cc_final: 0.4063 (mtpt) REVERT: D 54 TYR cc_start: 0.8847 (m-80) cc_final: 0.8484 (m-80) REVERT: D 158 ASP cc_start: 0.8462 (m-30) cc_final: 0.8202 (m-30) REVERT: D 236 LYS cc_start: 0.9004 (tttm) cc_final: 0.8627 (tttp) REVERT: D 257 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: D 394 MET cc_start: 0.6711 (mmp) cc_final: 0.6438 (mmt) REVERT: E 11 ASN cc_start: 0.8158 (t0) cc_final: 0.7885 (t0) REVERT: F 1 MET cc_start: 0.5761 (mmm) cc_final: 0.4435 (mmm) REVERT: F 240 MET cc_start: 0.8815 (ttm) cc_final: 0.8267 (ttm) REVERT: F 258 MET cc_start: 0.8140 (mmm) cc_final: 0.7618 (tpp) REVERT: F 263 LEU cc_start: 0.9129 (mt) cc_final: 0.8918 (mt) REVERT: G 119 ASP cc_start: 0.5454 (m-30) cc_final: 0.5058 (m-30) REVERT: G 151 GLU cc_start: 0.7879 (tp30) cc_final: 0.7503 (tp30) REVERT: G 200 MET cc_start: 0.8712 (ttp) cc_final: 0.8382 (ttp) REVERT: G 236 LYS cc_start: 0.8612 (tttm) cc_final: 0.8168 (tmtt) REVERT: G 247 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7426 (t) REVERT: G 272 ASP cc_start: 0.8766 (p0) cc_final: 0.8280 (p0) REVERT: G 336 TYR cc_start: 0.7377 (t80) cc_final: 0.7046 (t80) REVERT: G 394 MET cc_start: 0.7471 (mpp) cc_final: 0.6559 (mpp) REVERT: J 138 ARG cc_start: 0.7655 (mmt180) cc_final: 0.7404 (mmt-90) REVERT: K 79 ARG cc_start: 0.9030 (tpm170) cc_final: 0.8639 (tpm170) REVERT: K 95 TYR cc_start: 0.8756 (t80) cc_final: 0.8455 (t80) REVERT: L 193 MET cc_start: 0.8653 (mpp) cc_final: 0.8277 (mpp) REVERT: M 184 GLU cc_start: 0.6799 (mp0) cc_final: 0.6176 (mp0) REVERT: N 184 GLU cc_start: 0.7630 (tp30) cc_final: 0.7028 (tp30) REVERT: N 193 MET cc_start: 0.8771 (mpp) cc_final: 0.7887 (mpp) REVERT: O 98 MET cc_start: 0.8591 (tpp) cc_final: 0.8368 (tpp) REVERT: O 192 TYR cc_start: 0.8251 (m-80) cc_final: 0.7306 (m-80) REVERT: O 193 MET cc_start: 0.8221 (mpp) cc_final: 0.7846 (mtm) REVERT: P 179 ASP cc_start: 0.7893 (m-30) cc_final: 0.7590 (m-30) REVERT: P 202 GLN cc_start: 0.8474 (tt0) cc_final: 0.7878 (tm-30) REVERT: P 224 GLN cc_start: 0.8068 (pm20) cc_final: 0.7743 (pm20) REVERT: Q 156 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6976 (mt-10) REVERT: Q 167 TYR cc_start: 0.7225 (m-80) cc_final: 0.6876 (m-80) REVERT: R 193 MET cc_start: 0.5910 (mmt) cc_final: 0.4100 (tpt) REVERT: S 76 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6482 (pttp) REVERT: S 98 MET cc_start: 0.8413 (mmm) cc_final: 0.8003 (mtp) REVERT: T 76 LYS cc_start: 0.7926 (pttp) cc_final: 0.7243 (ptpt) REVERT: T 167 TYR cc_start: 0.8064 (m-80) cc_final: 0.7786 (m-80) REVERT: T 192 TYR cc_start: 0.7943 (m-80) cc_final: 0.7658 (m-80) REVERT: T 207 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7635 (tptt) REVERT: U 63 LYS cc_start: 0.6998 (mmtt) cc_final: 0.5990 (mmmt) REVERT: U 93 ASN cc_start: 0.7402 (t0) cc_final: 0.7196 (t0) REVERT: U 151 MET cc_start: 0.7916 (mpp) cc_final: 0.7072 (mpp) REVERT: U 167 TYR cc_start: 0.6627 (m-80) cc_final: 0.6309 (m-80) outliers start: 121 outliers final: 86 residues processed: 1016 average time/residue: 0.2496 time to fit residues: 412.1818 Evaluate side-chains 1017 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 923 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain T residue 207 LYS Chi-restraints excluded: chain T residue 211 ILE Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 257 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 443 optimal weight: 8.9990 chunk 423 optimal weight: 0.0770 chunk 309 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 323 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN G 11 ASN G 302 GLN M 90 GLN N 90 GLN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.178789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141360 restraints weight = 51334.066| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.97 r_work: 0.3580 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40492 Z= 0.152 Angle : 0.626 9.277 55039 Z= 0.324 Chirality : 0.042 0.260 6034 Planarity : 0.004 0.054 6770 Dihedral : 14.031 178.929 6276 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.77 % Allowed : 19.45 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.92 (0.12), residues: 4672 helix: 0.62 (0.13), residues: 1751 sheet: -1.02 (0.22), residues: 575 loop : -1.47 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 399 TYR 0.024 0.001 TYR T 81 PHE 0.035 0.002 PHE R 173 TRP 0.013 0.001 TRP D 300 HIS 0.003 0.001 HIS N 188 Details of bonding type rmsd covalent geometry : bond 0.00364 (40492) covalent geometry : angle 0.62630 (55039) hydrogen bonds : bond 0.03281 ( 1381) hydrogen bonds : angle 4.25960 ( 3915) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 940 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9268 (tptt) cc_final: 0.8901 (tptp) REVERT: A 168 ASN cc_start: 0.8718 (t0) cc_final: 0.8388 (t0) REVERT: A 187 ASN cc_start: 0.8489 (m-40) cc_final: 0.8103 (t0) REVERT: A 253 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: A 324 TYR cc_start: 0.8075 (m-10) cc_final: 0.7798 (m-10) REVERT: B 47 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8679 (t) REVERT: B 154 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8353 (tptp) REVERT: B 158 ASP cc_start: 0.8443 (m-30) cc_final: 0.7763 (m-30) REVERT: B 165 LYS cc_start: 0.8763 (mttm) cc_final: 0.8524 (mttt) REVERT: B 170 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7145 (mp-120) REVERT: B 240 MET cc_start: 0.8744 (ttm) cc_final: 0.8335 (ttm) REVERT: B 278 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8375 (pt) REVERT: B 388 LYS cc_start: 0.8673 (ptpp) cc_final: 0.8409 (ptpp) REVERT: C 187 ASN cc_start: 0.8936 (t0) cc_final: 0.8523 (t0) REVERT: C 263 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8450 (tp) REVERT: C 394 MET cc_start: 0.6973 (mmm) cc_final: 0.6160 (mpp) REVERT: C 419 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8289 (tm-30) REVERT: D 34 LYS cc_start: 0.4973 (tttt) cc_final: 0.4117 (mtpt) REVERT: D 54 TYR cc_start: 0.8832 (m-80) cc_final: 0.8471 (m-80) REVERT: D 158 ASP cc_start: 0.8469 (m-30) cc_final: 0.8221 (m-30) REVERT: D 224 ASP cc_start: 0.7876 (t70) cc_final: 0.6974 (t0) REVERT: D 236 LYS cc_start: 0.8943 (tttm) cc_final: 0.8553 (tttp) REVERT: D 257 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: D 394 MET cc_start: 0.6752 (mmp) cc_final: 0.6470 (mmt) REVERT: E 11 ASN cc_start: 0.8165 (t0) cc_final: 0.7897 (t0) REVERT: F 1 MET cc_start: 0.5464 (mmm) cc_final: 0.4372 (mmm) REVERT: F 240 MET cc_start: 0.8889 (ttm) cc_final: 0.8471 (ttm) REVERT: F 258 MET cc_start: 0.8155 (mmm) cc_final: 0.7625 (tpp) REVERT: G 119 ASP cc_start: 0.5484 (m-30) cc_final: 0.5122 (m-30) REVERT: G 236 LYS cc_start: 0.8607 (tttm) cc_final: 0.8167 (tmtt) REVERT: G 247 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7398 (t) REVERT: G 272 ASP cc_start: 0.8783 (p0) cc_final: 0.8287 (p0) REVERT: G 336 TYR cc_start: 0.7404 (t80) cc_final: 0.7074 (t80) REVERT: G 394 MET cc_start: 0.7458 (mpp) cc_final: 0.6599 (mpp) REVERT: J 70 MET cc_start: 0.7062 (tpt) cc_final: 0.6734 (tpt) REVERT: J 138 ARG cc_start: 0.7765 (mmt180) cc_final: 0.7550 (mmt-90) REVERT: K 79 ARG cc_start: 0.9039 (tpm170) cc_final: 0.8798 (tpm170) REVERT: K 95 TYR cc_start: 0.8756 (t80) cc_final: 0.8474 (t80) REVERT: L 62 GLU cc_start: 0.7974 (tp30) cc_final: 0.7757 (tp30) REVERT: L 193 MET cc_start: 0.8659 (mpp) cc_final: 0.8270 (mpp) REVERT: M 184 GLU cc_start: 0.6799 (mp0) cc_final: 0.6178 (mp0) REVERT: N 184 GLU cc_start: 0.7609 (tp30) cc_final: 0.7009 (tp30) REVERT: N 193 MET cc_start: 0.8749 (mpp) cc_final: 0.7893 (mpp) REVERT: O 98 MET cc_start: 0.8565 (tpp) cc_final: 0.8295 (tpp) REVERT: O 192 TYR cc_start: 0.8321 (m-80) cc_final: 0.7380 (m-80) REVERT: O 193 MET cc_start: 0.8246 (mpp) cc_final: 0.7879 (mtm) REVERT: P 179 ASP cc_start: 0.7929 (m-30) cc_final: 0.7588 (m-30) REVERT: P 202 GLN cc_start: 0.8511 (tt0) cc_final: 0.7932 (tm-30) REVERT: P 224 GLN cc_start: 0.8083 (pm20) cc_final: 0.7771 (pm20) REVERT: Q 156 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6965 (mt-10) REVERT: Q 167 TYR cc_start: 0.7189 (m-80) cc_final: 0.6848 (m-80) REVERT: Q 173 PHE cc_start: 0.8037 (m-80) cc_final: 0.7689 (t80) REVERT: R 176 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7526 (p) REVERT: R 193 MET cc_start: 0.5792 (mmt) cc_final: 0.4086 (tpt) REVERT: S 76 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6329 (pttp) REVERT: S 98 MET cc_start: 0.8470 (mmm) cc_final: 0.8038 (mtp) REVERT: T 76 LYS cc_start: 0.7935 (pttp) cc_final: 0.7251 (ptpt) REVERT: T 167 TYR cc_start: 0.8063 (m-80) cc_final: 0.7793 (m-80) REVERT: T 192 TYR cc_start: 0.7947 (m-80) cc_final: 0.7671 (m-80) REVERT: T 207 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7634 (tptt) REVERT: U 63 LYS cc_start: 0.7023 (mmtt) cc_final: 0.6000 (mmmt) REVERT: U 151 MET cc_start: 0.7874 (mpp) cc_final: 0.6999 (mpp) REVERT: U 167 TYR cc_start: 0.6585 (m-80) cc_final: 0.6262 (m-80) outliers start: 114 outliers final: 89 residues processed: 1000 average time/residue: 0.2509 time to fit residues: 408.0610 Evaluate side-chains 1015 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 916 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain T residue 207 LYS Chi-restraints excluded: chain T residue 211 ILE Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 137 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 406 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 394 optimal weight: 4.9990 chunk 304 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 330 optimal weight: 0.0870 chunk 54 optimal weight: 0.7980 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN G 11 ASN M 90 GLN N 90 GLN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.181190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143897 restraints weight = 51008.070| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.85 r_work: 0.3615 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40492 Z= 0.129 Angle : 0.618 8.939 55039 Z= 0.319 Chirality : 0.041 0.239 6034 Planarity : 0.005 0.059 6770 Dihedral : 14.006 178.829 6276 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.53 % Allowed : 19.67 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.82 (0.12), residues: 4672 helix: 0.69 (0.13), residues: 1751 sheet: -0.94 (0.23), residues: 523 loop : -1.41 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 7 TYR 0.024 0.001 TYR T 81 PHE 0.033 0.002 PHE U 140 TRP 0.021 0.001 TRP G 300 HIS 0.003 0.001 HIS N 188 Details of bonding type rmsd covalent geometry : bond 0.00304 (40492) covalent geometry : angle 0.61821 (55039) hydrogen bonds : bond 0.03167 ( 1381) hydrogen bonds : angle 4.19094 ( 3915) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 951 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9230 (tptt) cc_final: 0.8862 (tptp) REVERT: A 168 ASN cc_start: 0.8692 (t0) cc_final: 0.8368 (t0) REVERT: A 187 ASN cc_start: 0.8443 (m-40) cc_final: 0.8068 (t0) REVERT: A 258 MET cc_start: 0.7406 (tpp) cc_final: 0.7098 (tpt) REVERT: B 154 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8336 (tptp) REVERT: B 158 ASP cc_start: 0.8368 (m-30) cc_final: 0.7658 (m-30) REVERT: B 165 LYS cc_start: 0.8734 (mttm) cc_final: 0.8506 (mttt) REVERT: B 240 MET cc_start: 0.8685 (ttm) cc_final: 0.8259 (ttm) REVERT: B 278 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8300 (pt) REVERT: B 388 LYS cc_start: 0.8679 (ptpp) cc_final: 0.8409 (ptpp) REVERT: C 187 ASN cc_start: 0.8921 (t0) cc_final: 0.8497 (t0) REVERT: C 409 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: D 34 LYS cc_start: 0.5264 (tttt) cc_final: 0.4490 (mtpt) REVERT: D 54 TYR cc_start: 0.8763 (m-80) cc_final: 0.8372 (m-80) REVERT: D 97 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8527 (mmtt) REVERT: D 158 ASP cc_start: 0.8466 (m-30) cc_final: 0.8199 (m-30) REVERT: D 224 ASP cc_start: 0.7831 (t70) cc_final: 0.6936 (t0) REVERT: D 236 LYS cc_start: 0.8934 (tttm) cc_final: 0.8533 (tttp) REVERT: D 257 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: D 394 MET cc_start: 0.6719 (mmp) cc_final: 0.6416 (mmt) REVERT: E 324 TYR cc_start: 0.7886 (m-10) cc_final: 0.7484 (m-10) REVERT: E 332 LEU cc_start: 0.8286 (tp) cc_final: 0.7974 (mt) REVERT: F 1 MET cc_start: 0.5615 (mmm) cc_final: 0.4529 (mmm) REVERT: F 240 MET cc_start: 0.8863 (ttm) cc_final: 0.8526 (ttm) REVERT: F 258 MET cc_start: 0.8116 (mmm) cc_final: 0.7589 (tpp) REVERT: G 236 LYS cc_start: 0.8599 (tttm) cc_final: 0.8132 (tmtt) REVERT: G 247 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7392 (t) REVERT: G 263 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8933 (mt) REVERT: G 272 ASP cc_start: 0.8768 (p0) cc_final: 0.8284 (p0) REVERT: G 336 TYR cc_start: 0.7358 (t80) cc_final: 0.7019 (t80) REVERT: G 394 MET cc_start: 0.7602 (mpp) cc_final: 0.6713 (mpp) REVERT: J 70 MET cc_start: 0.6970 (tpt) cc_final: 0.6687 (tpt) REVERT: J 138 ARG cc_start: 0.7664 (mmt180) cc_final: 0.7438 (mmt-90) REVERT: J 168 LYS cc_start: 0.8624 (mmtm) cc_final: 0.8189 (mptt) REVERT: K 95 TYR cc_start: 0.8721 (t80) cc_final: 0.8390 (t80) REVERT: K 192 TYR cc_start: 0.8400 (m-80) cc_final: 0.8015 (m-80) REVERT: L 193 MET cc_start: 0.8630 (mpp) cc_final: 0.8259 (mpp) REVERT: M 128 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7883 (mm-40) REVERT: M 184 GLU cc_start: 0.6684 (mp0) cc_final: 0.6067 (mp0) REVERT: M 208 PHE cc_start: 0.8033 (m-80) cc_final: 0.7660 (m-10) REVERT: N 184 GLU cc_start: 0.7603 (tp30) cc_final: 0.7202 (tp30) REVERT: N 193 MET cc_start: 0.8673 (mpp) cc_final: 0.7874 (mpp) REVERT: O 98 MET cc_start: 0.8460 (tpp) cc_final: 0.8203 (tpp) REVERT: O 192 TYR cc_start: 0.8276 (m-80) cc_final: 0.7270 (m-80) REVERT: O 193 MET cc_start: 0.8196 (mpp) cc_final: 0.7800 (mtm) REVERT: P 179 ASP cc_start: 0.7977 (m-30) cc_final: 0.7627 (m-30) REVERT: P 202 GLN cc_start: 0.8446 (tt0) cc_final: 0.7900 (tm-30) REVERT: P 224 GLN cc_start: 0.8118 (pm20) cc_final: 0.7805 (pm20) REVERT: Q 156 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6920 (mt-10) REVERT: Q 167 TYR cc_start: 0.7139 (m-80) cc_final: 0.6793 (m-80) REVERT: Q 173 PHE cc_start: 0.7933 (m-80) cc_final: 0.7628 (t80) REVERT: R 193 MET cc_start: 0.6046 (mmt) cc_final: 0.4509 (tpt) REVERT: S 76 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6232 (pttp) REVERT: S 98 MET cc_start: 0.8434 (mmm) cc_final: 0.8093 (mtp) REVERT: S 140 PHE cc_start: 0.6416 (p90) cc_final: 0.5870 (p90) REVERT: T 76 LYS cc_start: 0.7977 (pttp) cc_final: 0.7314 (ptpt) REVERT: T 98 MET cc_start: 0.8327 (mmt) cc_final: 0.8106 (mmm) REVERT: T 167 TYR cc_start: 0.8057 (m-80) cc_final: 0.7798 (m-80) REVERT: T 192 TYR cc_start: 0.7925 (m-80) cc_final: 0.7663 (m-80) REVERT: T 207 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7573 (tptt) REVERT: T 208 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.6897 (t80) REVERT: U 63 LYS cc_start: 0.7019 (mmtt) cc_final: 0.5997 (mmmt) REVERT: U 68 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5219 (mm) REVERT: U 151 MET cc_start: 0.7838 (mpp) cc_final: 0.6972 (mpp) REVERT: U 167 TYR cc_start: 0.6647 (m-80) cc_final: 0.6422 (m-80) outliers start: 104 outliers final: 85 residues processed: 1008 average time/residue: 0.2368 time to fit residues: 389.6216 Evaluate side-chains 1007 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 913 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain T residue 207 LYS Chi-restraints excluded: chain T residue 208 PHE Chi-restraints excluded: chain T residue 211 ILE Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 462 optimal weight: 2.9990 chunk 387 optimal weight: 8.9990 chunk 319 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 459 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 267 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 GLN F 94 ASN G 11 ASN G 302 GLN M 90 GLN ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.180607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.143037 restraints weight = 51162.059| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.88 r_work: 0.3599 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40492 Z= 0.144 Angle : 0.628 9.212 55039 Z= 0.324 Chirality : 0.042 0.242 6034 Planarity : 0.005 0.055 6770 Dihedral : 13.990 179.882 6276 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.55 % Allowed : 19.94 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.87 (0.12), residues: 4672 helix: 0.64 (0.13), residues: 1763 sheet: -0.91 (0.23), residues: 540 loop : -1.45 (0.12), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 7 TYR 0.026 0.001 TYR G 324 PHE 0.033 0.002 PHE U 140 TRP 0.039 0.001 TRP G 300 HIS 0.003 0.001 HIS N 188 Details of bonding type rmsd covalent geometry : bond 0.00342 (40492) covalent geometry : angle 0.62840 (55039) hydrogen bonds : bond 0.03196 ( 1381) hydrogen bonds : angle 4.18763 ( 3915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10076.83 seconds wall clock time: 173 minutes 45.19 seconds (10425.19 seconds total)