Starting phenix.real_space_refine on Tue Sep 15 10:22:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uws_26841/09_2026/7uws_26841.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uws_26841/09_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_26841/09_2026/7uws_26841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uws_26841/09_2026/7uws_26841.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uws_26841/09_2026/7uws_26841.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uws_26841/09_2026/7uws_26841.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uws_26841/09_2026/7uws_26841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uws_26841/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 8.40, per 1000 atoms: 0.21 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: 3.13 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: 3.97 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: 7.13 Time building geometry restraints manager: 4.24 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: 53594 1.93 - 3.86: 1249 3.86 - 5.79: 176 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 - 35.06: 23545 35.06 - 70.12: 486 70.12 - 105.18: 40 105.18 - 140.24: 2 140.24 - 175.30: 13 Dihedral angle restraints: 24086 sinusoidal: 10222 harmonic: 13864 Sorted by residual: dihedral pdb=" C4' U H 107 " pdb=" C3' U H 107 " pdb=" C2' U H 107 " pdb=" C1' U H 107 " ideal model delta sinusoidal sigma weight residual 36.34 -35.12 71.46 1 3.10e+00 1.04e-01 6.81e+02 dihedral pdb=" C4' U H 133 " pdb=" C3' U H 133 " pdb=" C2' U H 133 " pdb=" C1' U H 133 " ideal model delta sinusoidal sigma weight residual 36.34 -35.00 71.35 1 3.10e+00 1.04e-01 6.79e+02 dihedral pdb=" C4' U H 458 " pdb=" C3' U H 458 " pdb=" C2' U H 458 " pdb=" C1' U H 458 " ideal model delta sinusoidal sigma weight residual 36.35 -34.79 71.14 1 3.10e+00 1.04e-01 6.76e+02 ... (remaining 24083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5382 0.068 - 0.135: 545 0.135 - 0.203: 19 0.203 - 0.270: 67 0.270 - 0.338: 21 Chirality restraints: 6034 Sorted by residual: chirality pdb=" P U H 130 " pdb=" OP1 U H 130 " pdb=" OP2 U H 130 " pdb=" O5' U H 130 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" P U H 478 " pdb=" OP1 U H 478 " pdb=" OP2 U H 478 " pdb=" O5' U H 478 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" P U H 463 " pdb=" OP1 U H 463 " pdb=" OP2 U H 463 " pdb=" O5' U H 463 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (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: 0.260 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: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.720 Find NCS groups from input model: 0.940 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: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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= 0.140 Angle : 0.678 9.645 55039 Z= 0.379 Chirality : 0.050 0.338 6034 Planarity : 0.005 0.091 6770 Dihedral : 15.345 175.300 15192 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/Z covalent geometry : bond 0.00275 / 0.14 (40492) covalent geometry : angle 0.67788 / 0.38 (55039) hydrogen bonds : bond 0.19666 / 12.79 ( 1381) hydrogen bonds : angle 6.98350 / 4.89 ( 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 : 1.216 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: 0.2355 time to fit residues: 426.0217 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 : 1.335 ------------------------------------------------------------------------------- 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: 5.9990 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: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 302 GLN ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.179256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141512 restraints weight = 51788.083| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.99 r_work: 0.3575 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 40492 Z= 0.239 Angle : 0.790 17.961 55039 Z= 0.374 Chirality : 0.060 0.946 6034 Planarity : 0.005 0.064 6770 Dihedral : 11.566 178.794 6008 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.55 % Allowed : 11.32 % Favored : 87.13 % 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: -1.32 (0.12), residues: 4672 helix: 0.32 (0.13), residues: 1786 sheet: -1.73 (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 0.032 0.002 TYR C 74 PHE 0.031 0.002 PHE R 228 TRP 0.043 0.002 TRP G 88 HIS 0.005 0.001 HIS U 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (40492) covalent geometry : angle 0.79009 / 0.37 (55039) hydrogen bonds : bond 0.04219 / 2.82 ( 1381) hydrogen bonds : angle 4.99329 / 3.45 ( 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 1068 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1004 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8202 (mm-40) REVERT: A 240 MET cc_start: 0.8461 (mtp) cc_final: 0.8063 (ttp) REVERT: A 253 GLU cc_start: 0.7144 (pm20) cc_final: 0.6936 (pm20) REVERT: A 258 MET cc_start: 0.7834 (tpp) cc_final: 0.7318 (tpp) REVERT: A 354 LYS cc_start: 0.7181 (mttt) cc_final: 0.6942 (ttmt) REVERT: B 1 MET cc_start: 0.4409 (mmp) cc_final: 0.3756 (mmp) REVERT: B 47 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8799 (t) REVERT: B 149 MET cc_start: 0.7887 (mtp) cc_final: 0.7648 (mtp) REVERT: B 154 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8251 (tptp) REVERT: B 158 ASP cc_start: 0.8507 (m-30) cc_final: 0.7768 (m-30) REVERT: B 165 LYS cc_start: 0.8928 (mttm) cc_final: 0.8688 (mttt) REVERT: B 297 PHE cc_start: 0.8824 (t80) cc_final: 0.8392 (t80) REVERT: B 324 TYR cc_start: 0.7853 (m-10) cc_final: 0.7494 (m-10) REVERT: C 8 ILE cc_start: 0.7608 (pt) cc_final: 0.7259 (pt) REVERT: C 394 MET cc_start: 0.7121 (mmm) cc_final: 0.6747 (mpp) REVERT: C 419 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8338 (tm-30) REVERT: D 26 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8011 (mt-10) REVERT: D 54 TYR cc_start: 0.8910 (m-80) cc_final: 0.8675 (m-80) REVERT: D 154 LYS cc_start: 0.9093 (tptm) cc_final: 0.8839 (tppp) REVERT: D 158 ASP cc_start: 0.8555 (m-30) cc_final: 0.8265 (m-30) REVERT: D 257 GLU cc_start: 0.8243 (tp30) cc_final: 0.7977 (tp30) REVERT: D 394 MET cc_start: 0.6966 (mmp) cc_final: 0.6666 (mmp) REVERT: E 253 GLU cc_start: 0.8238 (pm20) cc_final: 0.8032 (pm20) REVERT: F 1 MET cc_start: 0.6074 (mmm) cc_final: 0.4982 (mmm) REVERT: F 94 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8637 (t0) REVERT: F 204 MET cc_start: 0.9230 (tpt) cc_final: 0.8968 (tpt) REVERT: F 258 MET cc_start: 0.8039 (mmm) cc_final: 0.7448 (tpp) REVERT: F 377 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7992 (tt0) REVERT: F 402 MET cc_start: 0.8487 (ptm) cc_final: 0.8151 (ptp) REVERT: G 151 GLU cc_start: 0.7831 (tp30) cc_final: 0.7381 (tp30) REVERT: G 236 LYS cc_start: 0.8603 (tttm) cc_final: 0.8203 (tmtt) REVERT: G 272 ASP cc_start: 0.8797 (p0) cc_final: 0.8435 (p0) REVERT: G 317 ARG cc_start: 0.8102 (mpt180) cc_final: 0.7866 (mpt180) REVERT: G 336 TYR cc_start: 0.7468 (t80) cc_final: 0.7083 (t80) REVERT: J 81 TYR cc_start: 0.8375 (t80) cc_final: 0.8130 (t80) REVERT: L 79 ARG cc_start: 0.8253 (mmp-170) cc_final: 0.8022 (mmp-170) REVERT: L 106 LYS cc_start: 0.8723 (mttm) cc_final: 0.8490 (mttm) REVERT: L 193 MET cc_start: 0.8343 (mpp) cc_final: 0.7485 (mpp) REVERT: L 206 LEU cc_start: 0.8758 (tp) cc_final: 0.8504 (tp) REVERT: M 67 MET cc_start: 0.7864 (tmm) cc_final: 0.7469 (tmm) REVERT: N 184 GLU cc_start: 0.7595 (tp30) cc_final: 0.7056 (tp30) REVERT: O 98 MET cc_start: 0.8711 (tpp) cc_final: 0.8441 (tpp) REVERT: O 144 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8501 (mtm-85) REVERT: P 74 SER cc_start: 0.6518 (t) cc_final: 0.6233 (t) REVERT: P 179 ASP cc_start: 0.8158 (m-30) cc_final: 0.7820 (m-30) REVERT: P 224 GLN cc_start: 0.7557 (pm20) cc_final: 0.7170 (pm20) REVERT: Q 70 MET cc_start: 0.7532 (tpp) cc_final: 0.7100 (ttt) REVERT: Q 167 TYR cc_start: 0.7490 (m-80) cc_final: 0.7280 (m-80) REVERT: S 140 PHE cc_start: 0.7566 (p90) cc_final: 0.6768 (p90) REVERT: S 167 TYR cc_start: 0.6900 (m-10) cc_final: 0.6654 (m-10) REVERT: S 192 TYR cc_start: 0.7415 (m-80) cc_final: 0.6663 (m-80) REVERT: S 193 MET cc_start: 0.5126 (mmt) cc_final: 0.4896 (mmt) REVERT: T 192 TYR cc_start: 0.7925 (m-80) cc_final: 0.7547 (m-80) REVERT: U 151 MET cc_start: 0.8200 (mpp) cc_final: 0.7328 (mpp) REVERT: U 167 TYR cc_start: 0.6526 (m-80) cc_final: 0.6193 (m-80) outliers start: 64 outliers final: 43 residues processed: 1035 average time/residue: 0.2388 time to fit residues: 402.8365 Evaluate side-chains 984 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 939 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 D residue 350 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 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: 0.6980 chunk 404 optimal weight: 9.9990 chunk 149 optimal weight: 0.0570 chunk 63 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 423 optimal weight: 0.0770 overall best weight: 1.0858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 294 ASN B 302 GLN ** 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** D 315 ASN E 251 ASN E 294 ASN E 395 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN N 90 GLN ** U 93 ASN ** 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 = 0.4230 r_free = 0.4230 target = 0.184317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147210 restraints weight = 51254.968| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.99 r_work: 0.3647 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1753 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= 0.123 Angle : 0.660 12.979 55039 Z= 0.318 Chirality : 0.051 0.716 6034 Planarity : 0.005 0.057 6770 Dihedral : 11.565 179.644 6008 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.75 % Allowed : 14.45 % Favored : 83.80 % 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: -1.03 (0.12), residues: 4672 helix: 0.60 (0.13), residues: 1759 sheet: -1.39 (0.23), residues: 529 loop : -1.52 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 144 TYR 0.028 0.001 TYR A 56 PHE 0.031 0.002 PHE B 171 TRP 0.011 0.001 TRP F 378 HIS 0.004 0.001 HIS L 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (40492) covalent geometry : angle 0.66043 / 0.32 (55039) hydrogen bonds : bond 0.03626 / 2.42 ( 1381) hydrogen bonds : angle 4.58477 / 3.16 ( 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 1079 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1007 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9264 (tptt) cc_final: 0.8921 (tptp) REVERT: A 163 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8148 (mm-40) REVERT: A 187 ASN cc_start: 0.8252 (m-40) cc_final: 0.7826 (t0) REVERT: A 253 GLU cc_start: 0.7102 (pm20) cc_final: 0.6856 (pm20) REVERT: A 258 MET cc_start: 0.7660 (tpp) cc_final: 0.7028 (tpp) REVERT: B 1 MET cc_start: 0.4212 (mmp) cc_final: 0.3616 (mmp) REVERT: B 33 ARG cc_start: 0.8323 (mtm110) cc_final: 0.7603 (ttt90) REVERT: B 47 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8687 (t) REVERT: B 154 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8292 (tptp) REVERT: B 158 ASP cc_start: 0.8463 (m-30) cc_final: 0.7773 (m-30) REVERT: B 165 LYS cc_start: 0.8935 (mttm) cc_final: 0.8702 (mttt) REVERT: B 297 PHE cc_start: 0.8748 (t80) cc_final: 0.8302 (t80) REVERT: B 324 TYR cc_start: 0.7827 (m-10) cc_final: 0.7470 (m-10) REVERT: C 51 LEU cc_start: 0.8478 (mt) cc_final: 0.8080 (mt) REVERT: C 187 ASN cc_start: 0.8708 (t0) cc_final: 0.8507 (t0) REVERT: C 263 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8510 (tp) REVERT: C 394 MET cc_start: 0.7027 (mmm) cc_final: 0.6254 (mpp) REVERT: C 419 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8219 (tm-30) REVERT: D 26 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7945 (mt-10) REVERT: D 72 TYR cc_start: 0.9324 (t80) cc_final: 0.9078 (t80) REVERT: D 154 LYS cc_start: 0.9091 (tptm) cc_final: 0.8822 (tppp) REVERT: D 158 ASP cc_start: 0.8546 (m-30) cc_final: 0.8265 (m-30) REVERT: D 236 LYS cc_start: 0.8971 (tttm) cc_final: 0.8679 (tttm) REVERT: D 257 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7517 (tp30) REVERT: D 394 MET cc_start: 0.6862 (mmp) cc_final: 0.6576 (mmp) REVERT: E 83 LYS cc_start: 0.9050 (ttmm) cc_final: 0.8820 (ttmm) REVERT: F 1 MET cc_start: 0.6163 (mmm) cc_final: 0.4719 (mmm) REVERT: F 204 MET cc_start: 0.9171 (tpt) cc_final: 0.8933 (tpt) REVERT: F 240 MET cc_start: 0.8825 (mtp) cc_final: 0.8303 (ttm) REVERT: F 258 MET cc_start: 0.7943 (mmm) cc_final: 0.7412 (tpp) REVERT: F 377 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7948 (tt0) REVERT: F 402 MET cc_start: 0.8422 (ptm) cc_final: 0.8097 (ptp) REVERT: G 63 ASN cc_start: 0.8340 (t0) cc_final: 0.7888 (t0) REVERT: G 200 MET cc_start: 0.8652 (ttp) cc_final: 0.8414 (ttp) REVERT: G 236 LYS cc_start: 0.8578 (tttm) cc_final: 0.8170 (tmtt) REVERT: G 272 ASP cc_start: 0.8759 (p0) cc_final: 0.8389 (p0) REVERT: G 275 MET cc_start: 0.8356 (tmm) cc_final: 0.7952 (tmm) REVERT: G 317 ARG cc_start: 0.8029 (mpt180) cc_final: 0.7758 (mpt180) REVERT: G 336 TYR cc_start: 0.7315 (t80) cc_final: 0.6889 (t80) REVERT: J 68 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6721 (mp) REVERT: J 224 GLN cc_start: 0.8052 (pm20) cc_final: 0.7817 (pm20) REVERT: L 70 MET cc_start: 0.8610 (tpp) cc_final: 0.8210 (ttt) REVERT: L 168 LYS cc_start: 0.8985 (mmtm) cc_final: 0.8541 (mmpt) REVERT: L 190 TRP cc_start: 0.8597 (m100) cc_final: 0.8249 (m100) REVERT: L 193 MET cc_start: 0.8339 (mpp) cc_final: 0.7955 (mpp) REVERT: L 206 LEU cc_start: 0.8641 (tp) cc_final: 0.8389 (tp) REVERT: N 184 GLU cc_start: 0.7573 (tp30) cc_final: 0.7003 (tp30) REVERT: N 193 MET cc_start: 0.8426 (mpp) cc_final: 0.7280 (mpp) REVERT: O 98 MET cc_start: 0.8584 (tpp) cc_final: 0.8351 (tpp) REVERT: P 60 ARG cc_start: 0.8489 (ptp-110) cc_final: 0.8204 (ptp-110) REVERT: P 74 SER cc_start: 0.6411 (t) cc_final: 0.6100 (t) REVERT: P 151 MET cc_start: 0.8839 (mtt) cc_final: 0.8134 (mtt) REVERT: P 179 ASP cc_start: 0.8101 (m-30) cc_final: 0.7747 (m-30) REVERT: P 202 GLN cc_start: 0.8365 (tt0) cc_final: 0.7877 (tm-30) REVERT: P 224 GLN cc_start: 0.7586 (pm20) cc_final: 0.7315 (pm20) REVERT: Q 70 MET cc_start: 0.7527 (tpp) cc_final: 0.7102 (ttt) REVERT: Q 167 TYR cc_start: 0.7449 (m-80) cc_final: 0.7166 (m-80) REVERT: S 98 MET cc_start: 0.8098 (mmm) cc_final: 0.7814 (mtp) REVERT: S 140 PHE cc_start: 0.7500 (p90) cc_final: 0.6607 (p90) REVERT: T 76 LYS cc_start: 0.7986 (pttp) cc_final: 0.7472 (ptpt) REVERT: T 81 TYR cc_start: 0.7657 (t80) cc_final: 0.7452 (t80) REVERT: T 173 PHE cc_start: 0.7983 (m-80) cc_final: 0.7781 (m-10) REVERT: T 192 TYR cc_start: 0.7913 (m-80) cc_final: 0.7551 (m-80) REVERT: U 151 MET cc_start: 0.8108 (mpp) cc_final: 0.7242 (mpp) REVERT: U 167 TYR cc_start: 0.6459 (m-80) cc_final: 0.6242 (m-80) outliers start: 72 outliers final: 37 residues processed: 1036 average time/residue: 0.2293 time to fit residues: 388.6194 Evaluate side-chains 979 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 938 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 162 ASN 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 247 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 89 SER 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 94 ASN Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain K residue 148 ILE 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 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 R residue 93 ASN Chi-restraints excluded: chain S residue 189 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 55 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 326 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 373 optimal weight: 8.9990 chunk 445 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 260 GLN A 294 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** B 94 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 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN D 162 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 GLN F 94 ASN F 347 GLN G 94 ASN M 90 GLN N 90 GLN N 198 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.176101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138344 restraints weight = 51649.303| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.84 r_work: 0.3551 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 40492 Z= 0.227 Angle : 0.717 15.208 55039 Z= 0.347 Chirality : 0.053 0.873 6034 Planarity : 0.005 0.057 6770 Dihedral : 11.557 179.568 6004 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.82 % Allowed : 15.54 % Favored : 81.64 % 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: -1.22 (0.12), residues: 4672 helix: 0.38 (0.13), residues: 1772 sheet: -1.39 (0.22), residues: 558 loop : -1.60 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 399 TYR 0.026 0.002 TYR D 54 PHE 0.031 0.002 PHE U 175 TRP 0.012 0.001 TRP D 300 HIS 0.004 0.001 HIS N 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (40492) covalent geometry : angle 0.71736 / 0.35 (55039) hydrogen bonds : bond 0.03773 / 2.51 ( 1381) hydrogen bonds : angle 4.56345 / 3.14 ( 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 1079 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 963 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9279 (tptt) cc_final: 0.8914 (tptp) REVERT: A 184 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.9024 (t) REVERT: A 253 GLU cc_start: 0.7179 (pm20) cc_final: 0.6914 (pm20) REVERT: A 260 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: A 324 TYR cc_start: 0.7999 (m-10) cc_final: 0.7743 (m-10) REVERT: A 354 LYS cc_start: 0.7163 (mttt) cc_final: 0.6947 (ttmt) REVERT: B 1 MET cc_start: 0.3947 (mmp) cc_final: 0.3634 (mmp) REVERT: B 47 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8723 (t) REVERT: B 154 LYS cc_start: 0.8840 (ttpt) cc_final: 0.8267 (tptp) REVERT: B 158 ASP cc_start: 0.8508 (m-30) cc_final: 0.7711 (m-30) REVERT: B 165 LYS cc_start: 0.8790 (mttm) cc_final: 0.8529 (mttt) REVERT: B 240 MET cc_start: 0.8787 (ttm) cc_final: 0.8350 (ttm) REVERT: B 324 TYR cc_start: 0.7902 (m-10) cc_final: 0.7671 (m-10) REVERT: B 388 LYS cc_start: 0.8569 (ptpp) cc_final: 0.8267 (ptpp) REVERT: C 158 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: C 236 LYS cc_start: 0.8458 (ttpp) cc_final: 0.8188 (ttpt) REVERT: C 263 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8627 (tp) REVERT: C 394 MET cc_start: 0.7109 (mmm) cc_final: 0.6333 (mpp) REVERT: C 419 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8111 (tm-30) REVERT: D 26 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7995 (mt-10) REVERT: D 54 TYR cc_start: 0.8929 (m-80) cc_final: 0.8505 (m-80) REVERT: D 154 LYS cc_start: 0.9125 (tptm) cc_final: 0.8860 (tppp) REVERT: D 158 ASP cc_start: 0.8605 (m-30) cc_final: 0.8328 (m-30) REVERT: D 180 ASP cc_start: 0.8059 (p0) cc_final: 0.7614 (p0) REVERT: D 257 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: D 394 MET cc_start: 0.7056 (mmp) cc_final: 0.6743 (mmp) REVERT: D 402 MET cc_start: 0.7517 (ptt) cc_final: 0.7315 (ptp) REVERT: E 11 ASN cc_start: 0.8210 (t0) cc_final: 0.7937 (t0) REVERT: E 262 MET cc_start: 0.8839 (mtt) cc_final: 0.8364 (mtt) REVERT: F 1 MET cc_start: 0.6183 (mmm) cc_final: 0.4821 (mmm) REVERT: F 151 GLU cc_start: 0.8390 (tp30) cc_final: 0.8155 (tp30) REVERT: F 258 MET cc_start: 0.8093 (mmm) cc_final: 0.7326 (tpt) REVERT: F 402 MET cc_start: 0.8501 (ptm) cc_final: 0.8159 (ptp) REVERT: F 409 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8065 (tm-30) REVERT: G 119 ASP cc_start: 0.5483 (m-30) cc_final: 0.5132 (m-30) REVERT: G 200 MET cc_start: 0.8711 (ttp) cc_final: 0.8477 (ttp) REVERT: G 236 LYS cc_start: 0.8525 (tttm) cc_final: 0.8189 (tmtt) REVERT: G 247 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7570 (t) REVERT: G 272 ASP cc_start: 0.8821 (p0) cc_final: 0.8374 (p0) REVERT: G 317 ARG cc_start: 0.8256 (mpt180) cc_final: 0.7886 (mpt180) REVERT: G 336 TYR cc_start: 0.7372 (t80) cc_final: 0.6996 (t80) REVERT: J 68 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6982 (mp) REVERT: J 81 TYR cc_start: 0.8149 (t80) cc_final: 0.7805 (t80) REVERT: J 92 ASP cc_start: 0.8227 (p0) cc_final: 0.7988 (p0) REVERT: J 138 ARG cc_start: 0.7720 (mmt180) cc_final: 0.7383 (mmt180) REVERT: K 131 TYR cc_start: 0.8910 (m-80) cc_final: 0.8708 (m-80) REVERT: L 184 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: L 193 MET cc_start: 0.8681 (mpp) cc_final: 0.8319 (mpp) REVERT: L 206 LEU cc_start: 0.8636 (tp) cc_final: 0.8433 (tp) REVERT: M 67 MET cc_start: 0.7901 (tmm) cc_final: 0.7523 (tmm) REVERT: N 184 GLU cc_start: 0.7648 (tp30) cc_final: 0.7017 (tp30) REVERT: N 193 MET cc_start: 0.8857 (mpp) cc_final: 0.7796 (mpp) REVERT: O 144 ARG cc_start: 0.8844 (mtm-85) cc_final: 0.8454 (mtm-85) REVERT: O 192 TYR cc_start: 0.8416 (m-80) cc_final: 0.7508 (m-80) REVERT: P 74 SER cc_start: 0.6474 (t) cc_final: 0.6157 (t) REVERT: P 179 ASP cc_start: 0.8108 (m-30) cc_final: 0.7802 (m-30) REVERT: P 224 GLN cc_start: 0.7737 (pm20) cc_final: 0.7382 (pm20) REVERT: Q 70 MET cc_start: 0.7901 (tpp) cc_final: 0.7614 (ttp) REVERT: Q 98 MET cc_start: 0.8338 (pmm) cc_final: 0.8016 (pmm) REVERT: Q 167 TYR cc_start: 0.7458 (m-80) cc_final: 0.7137 (m-80) REVERT: R 176 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7723 (p) REVERT: S 98 MET cc_start: 0.8149 (mmm) cc_final: 0.7853 (mtp) REVERT: S 167 TYR cc_start: 0.6911 (m-10) cc_final: 0.6662 (m-10) REVERT: S 192 TYR cc_start: 0.7634 (m-80) cc_final: 0.6800 (m-80) REVERT: T 70 MET cc_start: 0.7595 (tpp) cc_final: 0.7343 (ttt) REVERT: T 173 PHE cc_start: 0.8086 (m-80) cc_final: 0.7781 (m-10) REVERT: T 192 TYR cc_start: 0.7931 (m-80) cc_final: 0.7592 (m-80) REVERT: T 208 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7068 (t80) REVERT: U 63 LYS cc_start: 0.6941 (mmtt) cc_final: 0.5863 (mmmt) REVERT: U 151 MET cc_start: 0.8121 (mpp) cc_final: 0.7232 (mpp) REVERT: U 167 TYR cc_start: 0.6575 (m-80) cc_final: 0.6229 (m-80) outliers start: 116 outliers final: 72 residues processed: 1022 average time/residue: 0.2348 time to fit residues: 392.6436 Evaluate side-chains 1008 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 925 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 350 VAL 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 8 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 212 SER 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 64 VAL 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 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 284 SER 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 263 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 35 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 G residue 8 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 204 MET Chi-restraints excluded: chain G residue 230 THR 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 84 VAL Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 130 GLU 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 174 THR Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 184 GLU 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 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 176 THR Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 88 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 55 optimal weight: 2.9990 chunk 320 optimal weight: 20.0000 chunk 448 optimal weight: 40.0000 chunk 219 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 420 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 148 GLN ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 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 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN D 260 GLN D 294 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN F 94 ASN F 347 GLN G 302 GLN M 90 GLN N 90 GLN N 115 HIS ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.175220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137705 restraints weight = 51324.876| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.81 r_work: 0.3546 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 40492 Z= 0.217 Angle : 0.708 16.418 55039 Z= 0.342 Chirality : 0.053 0.968 6034 Planarity : 0.005 0.056 6770 Dihedral : 11.531 179.999 6004 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.96 % Allowed : 17.10 % Favored : 79.94 % 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: -1.21 (0.12), residues: 4672 helix: 0.39 (0.13), residues: 1771 sheet: -1.29 (0.22), residues: 575 loop : -1.62 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 399 TYR 0.019 0.001 TYR C 74 PHE 0.031 0.002 PHE U 140 TRP 0.011 0.001 TRP D 300 HIS 0.003 0.001 HIS N 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (40492) covalent geometry : angle 0.70805 / 0.34 (55039) hydrogen bonds : bond 0.03657 / 2.43 ( 1381) hydrogen bonds : angle 4.51815 / 3.11 ( 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 1065 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 943 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9285 (tptt) cc_final: 0.8886 (tptp) REVERT: A 184 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.9003 (t) REVERT: A 253 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: A 324 TYR cc_start: 0.7975 (m-10) cc_final: 0.7753 (m-10) REVERT: A 354 LYS cc_start: 0.7259 (mttt) cc_final: 0.7000 (ttmt) REVERT: B 1 MET cc_start: 0.3949 (mmp) cc_final: 0.3641 (mmp) REVERT: B 47 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8712 (t) REVERT: B 154 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8241 (tptp) REVERT: B 158 ASP cc_start: 0.8501 (m-30) cc_final: 0.7715 (m-30) REVERT: B 165 LYS cc_start: 0.8787 (mttm) cc_final: 0.8521 (mttt) REVERT: B 240 MET cc_start: 0.8775 (ttm) cc_final: 0.8359 (ttm) REVERT: B 324 TYR cc_start: 0.7921 (m-10) cc_final: 0.7721 (m-10) REVERT: B 388 LYS cc_start: 0.8573 (ptpp) cc_final: 0.8296 (ptpp) REVERT: C 158 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: C 187 ASN cc_start: 0.8904 (t0) cc_final: 0.8500 (t0) REVERT: C 236 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8171 (ttpt) REVERT: C 263 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8672 (tp) REVERT: C 394 MET cc_start: 0.7121 (mmm) cc_final: 0.6359 (mpp) REVERT: C 419 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 26 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8099 (mt-10) REVERT: D 34 LYS cc_start: 0.5164 (mtpt) cc_final: 0.4678 (mtpt) REVERT: D 54 TYR cc_start: 0.8999 (m-80) cc_final: 0.8536 (m-80) REVERT: D 149 MET cc_start: 0.8458 (mpp) cc_final: 0.8219 (mpp) REVERT: D 154 LYS cc_start: 0.9132 (tptm) cc_final: 0.8855 (tppp) REVERT: D 158 ASP cc_start: 0.8610 (m-30) cc_final: 0.8337 (m-30) REVERT: D 180 ASP cc_start: 0.8158 (p0) cc_final: 0.7591 (p0) REVERT: D 257 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: D 260 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: D 394 MET cc_start: 0.7154 (mmp) cc_final: 0.6809 (mmp) REVERT: E 262 MET cc_start: 0.8764 (mtt) cc_final: 0.8387 (mtt) REVERT: F 1 MET cc_start: 0.5961 (mmm) cc_final: 0.4631 (mmm) REVERT: F 63 ASN cc_start: 0.8144 (t0) cc_final: 0.7690 (t0) REVERT: F 258 MET cc_start: 0.8078 (mmm) cc_final: 0.7500 (tpp) REVERT: G 119 ASP cc_start: 0.5407 (m-30) cc_final: 0.5089 (m-30) REVERT: G 200 MET cc_start: 0.8700 (ttp) cc_final: 0.8427 (ttp) REVERT: G 236 LYS cc_start: 0.8519 (tttm) cc_final: 0.8185 (tmtt) REVERT: G 247 THR cc_start: 0.7871 (OUTLIER) cc_final: 0.7618 (t) REVERT: G 272 ASP cc_start: 0.8827 (p0) cc_final: 0.8370 (p0) REVERT: G 317 ARG cc_start: 0.8269 (mpt180) cc_final: 0.7812 (mpt180) REVERT: G 336 TYR cc_start: 0.7383 (t80) cc_final: 0.7020 (t80) REVERT: J 68 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7043 (mp) REVERT: J 81 TYR cc_start: 0.8205 (t80) cc_final: 0.7859 (t80) REVERT: J 92 ASP cc_start: 0.8314 (p0) cc_final: 0.8072 (p0) REVERT: J 138 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7485 (mmm160) REVERT: J 168 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8269 (mptt) REVERT: K 79 ARG cc_start: 0.8758 (mmp80) cc_final: 0.8442 (mmp80) REVERT: K 95 TYR cc_start: 0.8928 (t80) cc_final: 0.8718 (t80) REVERT: L 193 MET cc_start: 0.8688 (mpp) cc_final: 0.8324 (mpp) REVERT: L 206 LEU cc_start: 0.8629 (tp) cc_final: 0.8385 (tp) REVERT: M 67 MET cc_start: 0.7956 (tmm) cc_final: 0.7694 (tmm) REVERT: N 184 GLU cc_start: 0.7649 (tp30) cc_final: 0.7115 (tp30) REVERT: N 193 MET cc_start: 0.8852 (mpp) cc_final: 0.7796 (mpp) REVERT: O 192 TYR cc_start: 0.8408 (m-80) cc_final: 0.7468 (m-80) REVERT: P 74 SER cc_start: 0.6511 (t) cc_final: 0.6194 (t) REVERT: P 179 ASP cc_start: 0.8106 (m-30) cc_final: 0.7775 (m-30) REVERT: P 224 GLN cc_start: 0.7808 (pm20) cc_final: 0.7478 (pm20) REVERT: Q 167 TYR cc_start: 0.7441 (m-80) cc_final: 0.7086 (m-80) REVERT: Q 193 MET cc_start: 0.5858 (mmm) cc_final: 0.5445 (mmm) REVERT: S 76 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6483 (pttp) REVERT: S 98 MET cc_start: 0.8125 (mmm) cc_final: 0.7845 (mtp) REVERT: S 192 TYR cc_start: 0.7662 (m-80) cc_final: 0.6581 (m-80) REVERT: T 173 PHE cc_start: 0.7876 (m-80) cc_final: 0.7557 (m-10) REVERT: T 192 TYR cc_start: 0.7936 (m-80) cc_final: 0.7645 (m-80) REVERT: T 208 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.6968 (t80) REVERT: U 63 LYS cc_start: 0.7066 (mmtt) cc_final: 0.5998 (mmmt) REVERT: U 64 PHE cc_start: 0.7609 (p90) cc_final: 0.7118 (p90) REVERT: U 66 PHE cc_start: 0.7555 (p90) cc_final: 0.6544 (p90) REVERT: U 101 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8238 (mtmm) REVERT: U 151 MET cc_start: 0.8073 (mpp) cc_final: 0.7193 (mpp) REVERT: U 167 TYR cc_start: 0.6689 (m-80) cc_final: 0.6364 (m-80) outliers start: 122 outliers final: 78 residues processed: 1007 average time/residue: 0.2274 time to fit residues: 375.3912 Evaluate side-chains 1009 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 920 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 184 VAL 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 350 VAL 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 158 ASP 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 C residue 323 GLU Chi-restraints excluded: chain D residue 64 VAL 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 210 CYS Chi-restraints excluded: chain D residue 241 SER 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 278 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 94 ASN 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 376 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 204 MET 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 84 VAL 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 J residue 197 TYR Chi-restraints excluded: chain K residue 88 VAL 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 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 223 ASP 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 171 LEU Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 107 ILE 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 S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 208 PHE 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: 0.8980 chunk 388 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 369 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 469 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 459 optimal weight: 8.9990 chunk 422 optimal weight: 30.0000 chunk 434 optimal weight: 0.0060 chunk 343 optimal weight: 0.8980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN F 347 GLN G 11 ASN G 251 ASN M 90 GLN N 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.181940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.144426 restraints weight = 51117.794| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.01 r_work: 0.3619 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40492 Z= 0.117 Angle : 0.658 15.574 55039 Z= 0.318 Chirality : 0.050 0.895 6034 Planarity : 0.004 0.055 6770 Dihedral : 11.391 179.765 6004 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.16 % Allowed : 18.14 % Favored : 79.70 % 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: -0.91 (0.12), residues: 4672 helix: 0.66 (0.13), residues: 1759 sheet: -1.18 (0.23), residues: 546 loop : -1.45 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 399 TYR 0.024 0.001 TYR T 81 PHE 0.033 0.002 PHE U 140 TRP 0.012 0.001 TRP F 378 HIS 0.005 0.001 HIS S 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (40492) covalent geometry : angle 0.65814 / 0.32 (55039) hydrogen bonds : bond 0.03221 / 2.14 ( 1381) hydrogen bonds : angle 4.27271 / 2.93 ( 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 1055 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 966 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9355 (tptt) cc_final: 0.9118 (tptp) REVERT: A 184 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8934 (t) REVERT: A 187 ASN cc_start: 0.8429 (m-40) cc_final: 0.7959 (t0) REVERT: A 258 MET cc_start: 0.7405 (tpp) cc_final: 0.6817 (tpp) REVERT: A 324 TYR cc_start: 0.8029 (m-10) cc_final: 0.7775 (m-10) REVERT: B 1 MET cc_start: 0.3968 (mmp) cc_final: 0.3722 (mmp) REVERT: B 33 ARG cc_start: 0.8409 (mtm110) cc_final: 0.7620 (ttt90) REVERT: B 47 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8621 (t) REVERT: B 154 LYS cc_start: 0.8832 (ttpt) cc_final: 0.8223 (tptp) REVERT: B 158 ASP cc_start: 0.8471 (m-30) cc_final: 0.7698 (m-30) REVERT: B 165 LYS cc_start: 0.8755 (mttm) cc_final: 0.8467 (mttt) REVERT: B 240 MET cc_start: 0.8690 (ttm) cc_final: 0.8420 (ttm) REVERT: B 275 MET cc_start: 0.8917 (tmm) cc_final: 0.8125 (tmm) REVERT: B 278 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8286 (pt) REVERT: B 324 TYR cc_start: 0.7942 (m-10) cc_final: 0.7734 (m-10) REVERT: B 344 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7267 (mt) REVERT: B 388 LYS cc_start: 0.8608 (ptpp) cc_final: 0.8330 (ptpp) REVERT: C 158 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: C 187 ASN cc_start: 0.8904 (t0) cc_final: 0.8464 (t0) REVERT: C 236 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8125 (ttpt) REVERT: C 394 MET cc_start: 0.6951 (mmm) cc_final: 0.6170 (mpp) REVERT: C 419 GLU cc_start: 0.8577 (tm-30) cc_final: 0.7928 (tm-30) REVERT: D 26 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8083 (mt-10) REVERT: D 54 TYR cc_start: 0.8848 (m-80) cc_final: 0.8424 (m-80) REVERT: D 97 LYS cc_start: 0.9026 (mmmt) cc_final: 0.8539 (mmtt) REVERT: D 154 LYS cc_start: 0.9106 (tptm) cc_final: 0.8793 (tppp) REVERT: D 158 ASP cc_start: 0.8623 (m-30) cc_final: 0.8419 (m-30) REVERT: D 236 LYS cc_start: 0.8980 (tttm) cc_final: 0.8604 (tttp) REVERT: D 257 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: D 394 MET cc_start: 0.6998 (mmp) cc_final: 0.6692 (mmt) REVERT: E 253 GLU cc_start: 0.8116 (pm20) cc_final: 0.7906 (pm20) REVERT: E 257 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7029 (mt-10) REVERT: F 1 MET cc_start: 0.6020 (mmm) cc_final: 0.4848 (mmm) REVERT: F 94 ASN cc_start: 0.8718 (t0) cc_final: 0.8447 (t0) REVERT: F 258 MET cc_start: 0.8060 (mmm) cc_final: 0.7596 (tpp) REVERT: F 377 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7911 (tt0) REVERT: G 119 ASP cc_start: 0.5228 (m-30) cc_final: 0.4809 (m-30) REVERT: G 200 MET cc_start: 0.8686 (ttp) cc_final: 0.8344 (ttp) REVERT: G 236 LYS cc_start: 0.8598 (tttm) cc_final: 0.8157 (tmtt) REVERT: G 247 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7402 (t) REVERT: G 272 ASP cc_start: 0.8729 (p0) cc_final: 0.8261 (p0) REVERT: G 317 ARG cc_start: 0.8182 (mpt180) cc_final: 0.7814 (mpt180) REVERT: G 336 TYR cc_start: 0.7355 (t80) cc_final: 0.7022 (t80) REVERT: J 68 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6691 (mp) REVERT: J 138 ARG cc_start: 0.7480 (mmt180) cc_final: 0.7094 (mmt180) REVERT: J 168 LYS cc_start: 0.8594 (mmtm) cc_final: 0.8203 (mptt) REVERT: K 98 MET cc_start: 0.8082 (mtp) cc_final: 0.7831 (mtt) REVERT: L 190 TRP cc_start: 0.8567 (m100) cc_final: 0.8270 (m100) REVERT: L 193 MET cc_start: 0.8553 (mpp) cc_final: 0.8273 (mpp) REVERT: M 184 GLU cc_start: 0.6622 (mp0) cc_final: 0.5941 (mp0) REVERT: M 208 PHE cc_start: 0.7940 (m-80) cc_final: 0.7555 (m-10) REVERT: N 70 MET cc_start: 0.8218 (ttt) cc_final: 0.7903 (ttt) REVERT: N 184 GLU cc_start: 0.7621 (tp30) cc_final: 0.7078 (tp30) REVERT: N 193 MET cc_start: 0.8780 (mpp) cc_final: 0.7834 (mpp) REVERT: O 144 ARG cc_start: 0.8856 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: O 192 TYR cc_start: 0.8245 (m-80) cc_final: 0.7302 (m-80) REVERT: P 74 SER cc_start: 0.6242 (t) cc_final: 0.6018 (t) REVERT: P 179 ASP cc_start: 0.8032 (m-30) cc_final: 0.7699 (m-30) REVERT: P 202 GLN cc_start: 0.8424 (tt0) cc_final: 0.7904 (tm-30) REVERT: P 224 GLN cc_start: 0.7835 (pm20) cc_final: 0.7558 (pm20) REVERT: Q 101 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8075 (mtmt) REVERT: Q 167 TYR cc_start: 0.7392 (m-80) cc_final: 0.7043 (m-80) REVERT: Q 193 MET cc_start: 0.6030 (mmm) cc_final: 0.5641 (mmm) REVERT: R 176 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7725 (p) REVERT: S 76 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6408 (pttp) REVERT: S 98 MET cc_start: 0.8065 (mmm) cc_final: 0.7807 (mtp) REVERT: T 76 LYS cc_start: 0.7899 (pttp) cc_final: 0.7371 (ptpt) REVERT: T 173 PHE cc_start: 0.8186 (m-80) cc_final: 0.7817 (m-10) REVERT: T 192 TYR cc_start: 0.7929 (m-80) cc_final: 0.7628 (m-80) REVERT: U 63 LYS cc_start: 0.7071 (mmtt) cc_final: 0.5996 (mmmt) REVERT: U 101 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8160 (mtmm) REVERT: U 151 MET cc_start: 0.7919 (mpp) cc_final: 0.7049 (mpp) REVERT: U 167 TYR cc_start: 0.6631 (m-80) cc_final: 0.6345 (m-80) outliers start: 89 outliers final: 58 residues processed: 1012 average time/residue: 0.2339 time to fit residues: 386.2617 Evaluate side-chains 979 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 911 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 184 VAL 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 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 344 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 8 ILE 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 164 CYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain D residue 64 VAL 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 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET 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 89 SER Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 347 GLN Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 204 MET 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 123 LEU Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 170 THR 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 O residue 221 VAL Chi-restraints excluded: chain P residue 89 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 61 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 365 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 455 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 398 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 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 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN M 90 GLN N 90 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.180722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143333 restraints weight = 51378.290| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.97 r_work: 0.3602 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2459 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= 0.139 Angle : 0.666 15.231 55039 Z= 0.321 Chirality : 0.050 0.882 6034 Planarity : 0.004 0.055 6770 Dihedral : 11.365 179.609 6004 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.23 % Allowed : 19.16 % Favored : 78.61 % 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: -0.85 (0.12), residues: 4672 helix: 0.68 (0.13), residues: 1747 sheet: -1.07 (0.23), residues: 547 loop : -1.40 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 399 TYR 0.024 0.001 TYR C 324 PHE 0.032 0.002 PHE U 140 TRP 0.012 0.001 TRP D 300 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (40492) covalent geometry : angle 0.66629 / 0.32 (55039) hydrogen bonds : bond 0.03231 / 2.15 ( 1381) hydrogen bonds : angle 4.23828 / 2.91 ( 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 1013 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 921 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9390 (tptt) cc_final: 0.9150 (tptp) REVERT: A 184 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8916 (t) REVERT: A 187 ASN cc_start: 0.8449 (m-40) cc_final: 0.7988 (t0) REVERT: A 324 TYR cc_start: 0.8030 (m-10) cc_final: 0.7745 (m-10) REVERT: B 154 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8221 (tptp) REVERT: B 158 ASP cc_start: 0.8386 (m-30) cc_final: 0.7574 (m-30) REVERT: B 165 LYS cc_start: 0.8738 (mttm) cc_final: 0.8427 (mttt) REVERT: B 170 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7319 (mp-120) REVERT: B 236 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8461 (tttm) REVERT: B 240 MET cc_start: 0.8726 (ttm) cc_final: 0.8390 (ttm) REVERT: B 278 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8313 (pt) REVERT: B 388 LYS cc_start: 0.8616 (ptpp) cc_final: 0.8337 (ptpp) REVERT: C 187 ASN cc_start: 0.8912 (t0) cc_final: 0.8474 (t0) REVERT: C 236 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8130 (ttpt) REVERT: C 394 MET cc_start: 0.6951 (mmm) cc_final: 0.6122 (mpp) REVERT: C 419 GLU cc_start: 0.8606 (tm-30) cc_final: 0.7924 (tm-30) REVERT: D 26 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8098 (mt-10) REVERT: D 54 TYR cc_start: 0.8937 (m-80) cc_final: 0.8093 (m-80) REVERT: D 149 MET cc_start: 0.8334 (mpp) cc_final: 0.8110 (mpp) REVERT: D 154 LYS cc_start: 0.9114 (tptm) cc_final: 0.8795 (tppp) REVERT: D 236 LYS cc_start: 0.8991 (tttm) cc_final: 0.8626 (tttp) REVERT: D 257 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7718 (tp30) REVERT: D 394 MET cc_start: 0.6950 (mmp) cc_final: 0.6480 (mmt) REVERT: F 1 MET cc_start: 0.5775 (mmm) cc_final: 0.4614 (mmm) REVERT: F 240 MET cc_start: 0.8895 (mtp) cc_final: 0.8614 (ttm) REVERT: F 258 MET cc_start: 0.8127 (mmm) cc_final: 0.7607 (tpp) REVERT: F 377 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7975 (tt0) REVERT: G 119 ASP cc_start: 0.5412 (m-30) cc_final: 0.5057 (m-30) REVERT: G 200 MET cc_start: 0.8687 (ttp) cc_final: 0.8331 (ttp) REVERT: G 236 LYS cc_start: 0.8611 (tttm) cc_final: 0.8168 (tmtt) REVERT: G 247 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7395 (t) REVERT: G 272 ASP cc_start: 0.8741 (p0) cc_final: 0.8275 (p0) REVERT: G 317 ARG cc_start: 0.8156 (mpt180) cc_final: 0.7803 (mpt180) REVERT: G 336 TYR cc_start: 0.7347 (t80) cc_final: 0.7013 (t80) REVERT: J 68 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6729 (mp) REVERT: J 70 MET cc_start: 0.6826 (tpt) cc_final: 0.6534 (tpt) REVERT: J 138 ARG cc_start: 0.7548 (mmt180) cc_final: 0.7213 (mmt180) REVERT: L 193 MET cc_start: 0.8598 (mpp) cc_final: 0.8275 (mpp) REVERT: M 128 GLN cc_start: 0.7983 (mt0) cc_final: 0.7539 (pm20) REVERT: M 184 GLU cc_start: 0.6681 (mp0) cc_final: 0.5995 (mp0) REVERT: N 70 MET cc_start: 0.8056 (ttt) cc_final: 0.7676 (ttt) REVERT: N 184 GLU cc_start: 0.7604 (tp30) cc_final: 0.7051 (tp30) REVERT: N 193 MET cc_start: 0.8772 (mpp) cc_final: 0.8022 (mpp) REVERT: O 98 MET cc_start: 0.8599 (tpp) cc_final: 0.8349 (tpp) REVERT: O 192 TYR cc_start: 0.8343 (m-80) cc_final: 0.7408 (m-80) REVERT: P 74 SER cc_start: 0.6210 (t) cc_final: 0.5953 (t) REVERT: P 179 ASP cc_start: 0.7982 (m-30) cc_final: 0.7680 (m-30) REVERT: P 202 GLN cc_start: 0.8438 (tt0) cc_final: 0.7905 (tm-30) REVERT: P 224 GLN cc_start: 0.7813 (pm20) cc_final: 0.7574 (pm20) REVERT: Q 167 TYR cc_start: 0.7387 (m-80) cc_final: 0.7035 (m-80) REVERT: R 173 PHE cc_start: 0.7922 (m-80) cc_final: 0.7467 (t80) REVERT: R 193 MET cc_start: 0.5847 (mmt) cc_final: 0.4021 (tpt) REVERT: S 76 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6417 (pttp) REVERT: S 98 MET cc_start: 0.8118 (mmm) cc_final: 0.7857 (mtp) REVERT: T 173 PHE cc_start: 0.8084 (m-80) cc_final: 0.7784 (m-10) REVERT: T 192 TYR cc_start: 0.7933 (m-80) cc_final: 0.7634 (m-80) REVERT: T 208 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7071 (t80) REVERT: U 63 LYS cc_start: 0.7064 (mmtt) cc_final: 0.6001 (mmmt) REVERT: U 101 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8192 (mtmm) REVERT: U 151 MET cc_start: 0.7910 (mpp) cc_final: 0.7061 (mpp) REVERT: U 167 TYR cc_start: 0.6599 (m-80) cc_final: 0.6283 (m-80) outliers start: 92 outliers final: 71 residues processed: 969 average time/residue: 0.2347 time to fit residues: 372.1388 Evaluate side-chains 978 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 899 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 184 VAL 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 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 C residue 8 ILE 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 164 CYS 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 323 GLU 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 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 314 ARG 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 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 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 204 MET 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 123 LEU Chi-restraints excluded: chain J residue 130 GLU 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 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 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 O residue 221 VAL Chi-restraints excluded: chain P residue 89 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 96 ILE Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain T residue 208 PHE 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: 8.9990 chunk 98 optimal weight: 1.9990 chunk 392 optimal weight: 10.0000 chunk 362 optimal weight: 2.9990 chunk 350 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 295 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** 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** F 94 ASN G 11 ASN M 90 GLN N 90 GLN O 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.181072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143595 restraints weight = 51244.736| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.88 r_work: 0.3614 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2531 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= 0.136 Angle : 0.669 14.938 55039 Z= 0.322 Chirality : 0.050 0.849 6034 Planarity : 0.004 0.055 6770 Dihedral : 11.328 179.602 6004 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.53 % Allowed : 19.26 % Favored : 78.22 % 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: -0.84 (0.12), residues: 4672 helix: 0.66 (0.13), residues: 1758 sheet: -0.96 (0.23), residues: 557 loop : -1.41 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 399 TYR 0.026 0.001 TYR T 81 PHE 0.034 0.002 PHE U 140 TRP 0.014 0.001 TRP D 300 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (40492) covalent geometry : angle 0.66881 / 0.32 (55039) hydrogen bonds : bond 0.03186 / 2.12 ( 1381) hydrogen bonds : angle 4.21036 / 2.89 ( 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 1041 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 937 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9417 (tptt) cc_final: 0.9185 (tptp) REVERT: A 168 ASN cc_start: 0.8646 (t0) cc_final: 0.8320 (t0) REVERT: A 184 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8901 (t) REVERT: A 187 ASN cc_start: 0.8462 (m-40) cc_final: 0.8032 (t0) REVERT: A 324 TYR cc_start: 0.7998 (m-10) cc_final: 0.7719 (m-10) REVERT: B 154 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8343 (tptp) REVERT: B 155 LYS cc_start: 0.8892 (tptp) cc_final: 0.8674 (tptp) REVERT: B 158 ASP cc_start: 0.8354 (m-30) cc_final: 0.7672 (m-30) REVERT: B 165 LYS cc_start: 0.8760 (mttm) cc_final: 0.8461 (mttt) REVERT: B 170 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7183 (mp-120) REVERT: B 236 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8420 (tttm) REVERT: B 240 MET cc_start: 0.8724 (ttm) cc_final: 0.8383 (ttm) REVERT: B 278 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8294 (pt) REVERT: B 388 LYS cc_start: 0.8623 (ptpp) cc_final: 0.8341 (ptpp) REVERT: C 187 ASN cc_start: 0.8915 (t0) cc_final: 0.8463 (t0) REVERT: C 394 MET cc_start: 0.6919 (mmm) cc_final: 0.6106 (mpp) REVERT: C 419 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7811 (tm-30) REVERT: D 26 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8095 (mt-10) REVERT: D 34 LYS cc_start: 0.4792 (tttt) cc_final: 0.4248 (mtpt) REVERT: D 54 TYR cc_start: 0.8854 (m-80) cc_final: 0.8145 (m-80) REVERT: D 164 CYS cc_start: 0.6592 (m) cc_final: 0.6228 (m) REVERT: D 236 LYS cc_start: 0.8917 (tttm) cc_final: 0.8542 (tttp) REVERT: D 257 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: D 394 MET cc_start: 0.6783 (mmp) cc_final: 0.6396 (mmt) REVERT: F 1 MET cc_start: 0.5779 (mmm) cc_final: 0.4619 (mmm) REVERT: F 151 GLU cc_start: 0.8143 (tp30) cc_final: 0.7924 (tp30) REVERT: F 240 MET cc_start: 0.8838 (mtp) cc_final: 0.8617 (ttm) REVERT: F 258 MET cc_start: 0.8120 (mmm) cc_final: 0.7600 (tpp) REVERT: F 348 PHE cc_start: 0.5397 (m-80) cc_final: 0.5144 (m-80) REVERT: F 377 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7967 (tt0) REVERT: G 119 ASP cc_start: 0.5277 (m-30) cc_final: 0.4929 (m-30) REVERT: G 200 MET cc_start: 0.8718 (ttp) cc_final: 0.8484 (ttp) REVERT: G 236 LYS cc_start: 0.8621 (tttm) cc_final: 0.8152 (tmtt) REVERT: G 247 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7405 (t) REVERT: G 272 ASP cc_start: 0.8782 (p0) cc_final: 0.8293 (p0) REVERT: G 317 ARG cc_start: 0.8153 (mpt180) cc_final: 0.7803 (mpt180) REVERT: G 336 TYR cc_start: 0.7337 (t80) cc_final: 0.6996 (t80) REVERT: J 68 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6691 (mt) REVERT: K 115 HIS cc_start: 0.7949 (m90) cc_final: 0.7709 (m90) REVERT: K 144 ARG cc_start: 0.8981 (mtm-85) cc_final: 0.8672 (mtm-85) REVERT: L 193 MET cc_start: 0.8591 (mpp) cc_final: 0.8259 (mpp) REVERT: M 148 ILE cc_start: 0.8977 (tp) cc_final: 0.8750 (tp) REVERT: M 184 GLU cc_start: 0.6730 (mp0) cc_final: 0.6118 (mp0) REVERT: N 184 GLU cc_start: 0.7607 (tp30) cc_final: 0.7046 (tp30) REVERT: N 193 MET cc_start: 0.8730 (mpp) cc_final: 0.7841 (mpp) REVERT: O 192 TYR cc_start: 0.8346 (m-80) cc_final: 0.7396 (m-80) REVERT: P 74 SER cc_start: 0.6195 (t) cc_final: 0.5980 (t) REVERT: P 179 ASP cc_start: 0.8029 (m-30) cc_final: 0.7693 (m-30) REVERT: P 202 GLN cc_start: 0.8464 (tt0) cc_final: 0.7905 (tm-30) REVERT: P 224 GLN cc_start: 0.7844 (pm20) cc_final: 0.7585 (pm20) REVERT: Q 167 TYR cc_start: 0.7379 (m-80) cc_final: 0.7009 (m-80) REVERT: R 173 PHE cc_start: 0.8019 (m-80) cc_final: 0.7599 (t80) REVERT: R 193 MET cc_start: 0.6125 (mmt) cc_final: 0.4468 (tpt) REVERT: S 76 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6284 (pttp) REVERT: S 98 MET cc_start: 0.8041 (mmm) cc_final: 0.7828 (mtp) REVERT: T 76 LYS cc_start: 0.7874 (pttp) cc_final: 0.7401 (ptpt) REVERT: T 173 PHE cc_start: 0.8084 (m-80) cc_final: 0.7691 (m-10) REVERT: T 192 TYR cc_start: 0.7899 (m-80) cc_final: 0.7598 (m-80) REVERT: T 208 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7023 (t80) REVERT: U 63 LYS cc_start: 0.7018 (mmtt) cc_final: 0.5920 (mmmt) REVERT: U 151 MET cc_start: 0.7869 (mpp) cc_final: 0.7023 (mpp) REVERT: U 167 TYR cc_start: 0.6589 (m-80) cc_final: 0.6259 (m-80) outliers start: 104 outliers final: 79 residues processed: 991 average time/residue: 0.2321 time to fit residues: 377.0952 Evaluate side-chains 991 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 904 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 184 VAL 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 B residue 47 SER Chi-restraints excluded: chain B residue 164 CYS 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 8 ILE 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 164 CYS 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 121 VAL 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 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 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 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 204 MET 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 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 98 MET 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 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 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 O residue 221 VAL 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 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 208 PHE 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: 7.9990 chunk 263 optimal weight: 6.9990 chunk 443 optimal weight: 7.9990 chunk 423 optimal weight: 40.0000 chunk 309 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 323 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 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 260 GLN F 94 ASN G 11 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.177843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141864 restraints weight = 51488.015| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.78 r_work: 0.3562 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40492 Z= 0.206 Angle : 0.717 15.363 55039 Z= 0.347 Chirality : 0.052 0.892 6034 Planarity : 0.005 0.054 6770 Dihedral : 11.367 178.984 6004 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.67 % Allowed : 19.31 % Favored : 78.02 % 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: -0.95 (0.12), residues: 4672 helix: 0.53 (0.13), residues: 1762 sheet: -0.96 (0.23), residues: 571 loop : -1.46 (0.12), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 399 TYR 0.028 0.001 TYR G 324 PHE 0.032 0.002 PHE U 140 TRP 0.018 0.001 TRP G 300 HIS 0.003 0.001 HIS F 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (40492) covalent geometry : angle 0.71743 / 0.35 (55039) hydrogen bonds : bond 0.03447 / 2.30 ( 1381) hydrogen bonds : angle 4.31632 / 2.97 ( 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 1030 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 920 time to evaluate : 1.307 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: 0.9404 (tptt) cc_final: 0.9175 (tptp) REVERT: A 168 ASN cc_start: 0.8706 (t0) cc_final: 0.8389 (t0) REVERT: A 184 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8910 (t) REVERT: A 187 ASN cc_start: 0.8550 (m-40) cc_final: 0.8138 (t0) REVERT: A 324 TYR cc_start: 0.8087 (m-10) cc_final: 0.7806 (m-10) REVERT: A 419 GLU cc_start: 0.8168 (tt0) cc_final: 0.7766 (tt0) REVERT: B 47 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8707 (t) REVERT: B 154 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8367 (tptp) REVERT: B 158 ASP cc_start: 0.8414 (m-30) cc_final: 0.7746 (m-30) REVERT: B 165 LYS cc_start: 0.8642 (mttm) cc_final: 0.8383 (mttt) REVERT: B 170 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7209 (mp-120) REVERT: B 236 LYS cc_start: 0.8955 (ttpt) cc_final: 0.8471 (tttm) REVERT: B 240 MET cc_start: 0.8762 (ttm) cc_final: 0.8499 (ttm) REVERT: B 278 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8431 (pt) REVERT: B 388 LYS cc_start: 0.8639 (ptpp) cc_final: 0.8360 (ptpp) REVERT: C 154 LYS cc_start: 0.9213 (tptt) cc_final: 0.8997 (tptt) REVERT: C 187 ASN cc_start: 0.8936 (t0) cc_final: 0.8504 (t0) REVERT: C 236 LYS cc_start: 0.8459 (ttpp) cc_final: 0.8157 (ttpt) REVERT: C 394 MET cc_start: 0.7045 (mmm) cc_final: 0.6243 (mpp) REVERT: C 409 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: D 34 LYS cc_start: 0.4975 (tttt) cc_final: 0.4308 (mtpt) REVERT: D 54 TYR cc_start: 0.8873 (m-80) cc_final: 0.8430 (m-80) REVERT: D 164 CYS cc_start: 0.6822 (m) cc_final: 0.6471 (m) REVERT: D 236 LYS cc_start: 0.8929 (tttm) cc_final: 0.8561 (tttp) REVERT: D 257 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7744 (tp30) REVERT: D 394 MET cc_start: 0.6835 (mmp) cc_final: 0.6550 (mmt) REVERT: E 11 ASN cc_start: 0.8146 (t0) cc_final: 0.7876 (t0) REVERT: E 324 TYR cc_start: 0.7969 (m-10) cc_final: 0.7448 (m-80) REVERT: F 1 MET cc_start: 0.5776 (mmm) cc_final: 0.4610 (mmm) REVERT: F 63 ASN cc_start: 0.8207 (t0) cc_final: 0.7709 (t0) REVERT: F 151 GLU cc_start: 0.8175 (tp30) cc_final: 0.7943 (tp30) REVERT: F 258 MET cc_start: 0.8224 (mmm) cc_final: 0.7360 (tpt) REVERT: G 119 ASP cc_start: 0.5460 (m-30) cc_final: 0.5061 (m-30) REVERT: G 200 MET cc_start: 0.8701 (ttp) cc_final: 0.8494 (ttp) REVERT: G 236 LYS cc_start: 0.8620 (tttm) cc_final: 0.8176 (tmtt) REVERT: G 247 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7476 (t) REVERT: G 272 ASP cc_start: 0.8814 (p0) cc_final: 0.8335 (p0) REVERT: G 317 ARG cc_start: 0.8173 (mpt180) cc_final: 0.7727 (mpt180) REVERT: G 336 TYR cc_start: 0.7338 (t80) cc_final: 0.7004 (t80) REVERT: J 68 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6924 (mp) REVERT: J 138 ARG cc_start: 0.7830 (mmt180) cc_final: 0.7346 (mmt-90) REVERT: L 193 MET cc_start: 0.8701 (mpp) cc_final: 0.8307 (mpp) REVERT: M 184 GLU cc_start: 0.6898 (mp0) cc_final: 0.6242 (mp0) REVERT: M 208 PHE cc_start: 0.8102 (m-80) cc_final: 0.7604 (m-10) REVERT: N 70 MET cc_start: 0.8251 (tpp) cc_final: 0.8007 (mtp) REVERT: N 184 GLU cc_start: 0.7588 (tp30) cc_final: 0.7205 (tp30) REVERT: N 193 MET cc_start: 0.8795 (mpp) cc_final: 0.7864 (mpp) REVERT: O 192 TYR cc_start: 0.8400 (m-80) cc_final: 0.7479 (m-80) REVERT: P 74 SER cc_start: 0.6184 (t) cc_final: 0.5946 (t) REVERT: P 179 ASP cc_start: 0.8066 (m-30) cc_final: 0.7721 (m-30) REVERT: P 224 GLN cc_start: 0.8060 (pm20) cc_final: 0.7766 (pm20) REVERT: Q 167 TYR cc_start: 0.7256 (m-80) cc_final: 0.6879 (m-80) REVERT: Q 173 PHE cc_start: 0.7942 (m-80) cc_final: 0.7576 (t80) REVERT: R 173 PHE cc_start: 0.8065 (m-80) cc_final: 0.7655 (t80) REVERT: R 193 MET cc_start: 0.6171 (mmt) cc_final: 0.4547 (tpt) REVERT: S 76 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6404 (pttp) REVERT: S 98 MET cc_start: 0.8174 (mmm) cc_final: 0.7907 (mtp) REVERT: T 173 PHE cc_start: 0.8101 (m-80) cc_final: 0.7681 (m-10) REVERT: T 192 TYR cc_start: 0.7933 (m-80) cc_final: 0.7652 (m-80) REVERT: U 63 LYS cc_start: 0.7048 (mmtt) cc_final: 0.5953 (mmmt) REVERT: U 151 MET cc_start: 0.7869 (mpp) cc_final: 0.7047 (mpp) REVERT: U 167 TYR cc_start: 0.6633 (m-80) cc_final: 0.6384 (m-80) outliers start: 110 outliers final: 79 residues processed: 979 average time/residue: 0.2279 time to fit residues: 365.6175 Evaluate side-chains 990 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 902 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 350 VAL 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 8 ILE 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 323 GLU 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 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 376 VAL Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 35 SER 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 89 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 181 ILE 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 204 MET 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 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 89 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 170 THR 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 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 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: 0.7980 chunk 171 optimal weight: 0.5980 chunk 406 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 394 optimal weight: 8.9990 chunk 304 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 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** E 260 GLN F 94 ASN G 11 ASN ** G 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.180395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144468 restraints weight = 51194.400| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.78 r_work: 0.3594 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40492 Z= 0.155 Angle : 0.693 15.207 55039 Z= 0.335 Chirality : 0.051 0.874 6034 Planarity : 0.005 0.054 6770 Dihedral : 11.338 178.907 6004 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.23 % Allowed : 19.89 % Favored : 77.88 % 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: -0.91 (0.12), residues: 4672 helix: 0.56 (0.13), residues: 1769 sheet: -0.83 (0.23), residues: 562 loop : -1.47 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 73 TYR 0.029 0.001 TYR T 81 PHE 0.033 0.002 PHE U 140 TRP 0.020 0.001 TRP G 300 HIS 0.003 0.001 HIS N 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (40492) covalent geometry : angle 0.69292 / 0.34 (55039) hydrogen bonds : bond 0.03274 / 2.18 ( 1381) hydrogen bonds : angle 4.23220 / 2.91 ( 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 1021 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 929 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.9411 (tptt) cc_final: 0.9182 (tptp) REVERT: A 168 ASN cc_start: 0.8701 (t0) cc_final: 0.8380 (t0) REVERT: A 184 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8881 (t) REVERT: A 187 ASN cc_start: 0.8539 (m-40) cc_final: 0.8148 (t0) REVERT: A 324 TYR cc_start: 0.8067 (m-10) cc_final: 0.7803 (m-10) REVERT: A 419 GLU cc_start: 0.8148 (tt0) cc_final: 0.7735 (tt0) REVERT: B 154 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8343 (tptp) REVERT: B 155 LYS cc_start: 0.8832 (tptp) cc_final: 0.8623 (tptp) REVERT: B 158 ASP cc_start: 0.8408 (m-30) cc_final: 0.7743 (m-30) REVERT: B 165 LYS cc_start: 0.8590 (mttm) cc_final: 0.8299 (mttt) REVERT: B 170 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7202 (mp-120) REVERT: B 236 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8453 (tttm) REVERT: B 240 MET cc_start: 0.8665 (ttm) cc_final: 0.8318 (ttm) REVERT: B 278 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8350 (pt) REVERT: B 388 LYS cc_start: 0.8687 (ptpp) cc_final: 0.8412 (ptpp) REVERT: C 154 LYS cc_start: 0.9211 (tptt) cc_final: 0.8947 (tptt) REVERT: C 158 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: C 187 ASN cc_start: 0.8941 (t0) cc_final: 0.8509 (t0) REVERT: C 236 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8153 (ttpt) REVERT: C 394 MET cc_start: 0.6994 (mmm) cc_final: 0.6184 (mpp) REVERT: C 409 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: D 34 LYS cc_start: 0.4925 (tttt) cc_final: 0.4296 (mtpt) REVERT: D 54 TYR cc_start: 0.8792 (m-80) cc_final: 0.8413 (m-80) REVERT: D 164 CYS cc_start: 0.6652 (m) cc_final: 0.6311 (m) REVERT: D 236 LYS cc_start: 0.8899 (tttm) cc_final: 0.8514 (tttp) REVERT: D 257 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7724 (tp30) REVERT: D 394 MET cc_start: 0.6699 (mmp) cc_final: 0.6432 (mmt) REVERT: E 324 TYR cc_start: 0.7917 (m-10) cc_final: 0.7456 (m-80) REVERT: E 332 LEU cc_start: 0.8294 (tp) cc_final: 0.7968 (mt) REVERT: F 1 MET cc_start: 0.5787 (mmm) cc_final: 0.4495 (mmm) REVERT: F 63 ASN cc_start: 0.8194 (t0) cc_final: 0.7709 (t0) REVERT: F 94 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8316 (t0) REVERT: F 151 GLU cc_start: 0.8124 (tp30) cc_final: 0.7887 (tp30) REVERT: F 240 MET cc_start: 0.8787 (ttm) cc_final: 0.8405 (ttm) REVERT: F 258 MET cc_start: 0.8159 (mmm) cc_final: 0.7636 (tpp) REVERT: G 83 LYS cc_start: 0.8775 (tptt) cc_final: 0.8562 (tptm) REVERT: G 119 ASP cc_start: 0.5463 (m-30) cc_final: 0.5108 (m-30) REVERT: G 200 MET cc_start: 0.8714 (ttp) cc_final: 0.8500 (ttp) REVERT: G 236 LYS cc_start: 0.8601 (tttm) cc_final: 0.8132 (tmtt) REVERT: G 247 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7438 (t) REVERT: G 272 ASP cc_start: 0.8787 (p0) cc_final: 0.8298 (p0) REVERT: G 317 ARG cc_start: 0.8147 (mpt180) cc_final: 0.7677 (mpt180) REVERT: G 336 TYR cc_start: 0.7364 (t80) cc_final: 0.6985 (t80) REVERT: J 138 ARG cc_start: 0.7707 (mmt180) cc_final: 0.7280 (mmm160) REVERT: K 144 ARG cc_start: 0.9007 (mtm-85) cc_final: 0.8743 (mtm-85) REVERT: L 193 MET cc_start: 0.8655 (mpp) cc_final: 0.8282 (mpp) REVERT: M 184 GLU cc_start: 0.6772 (mp0) cc_final: 0.6117 (mp0) REVERT: M 208 PHE cc_start: 0.7999 (m-80) cc_final: 0.7525 (m-10) REVERT: N 184 GLU cc_start: 0.7598 (tp30) cc_final: 0.7005 (tp30) REVERT: N 193 MET cc_start: 0.8730 (mpp) cc_final: 0.7873 (mpp) REVERT: O 192 TYR cc_start: 0.8268 (m-80) cc_final: 0.7342 (m-80) REVERT: O 193 MET cc_start: 0.8236 (mpp) cc_final: 0.7840 (mtm) REVERT: P 74 SER cc_start: 0.6161 (t) cc_final: 0.5933 (t) REVERT: P 179 ASP cc_start: 0.8038 (m-30) cc_final: 0.7666 (m-30) REVERT: P 202 GLN cc_start: 0.8517 (tt0) cc_final: 0.7936 (tm-30) REVERT: P 224 GLN cc_start: 0.8092 (pm20) cc_final: 0.7793 (pm20) REVERT: Q 167 TYR cc_start: 0.7206 (m-80) cc_final: 0.6845 (m-80) REVERT: Q 173 PHE cc_start: 0.7809 (m-80) cc_final: 0.7540 (t80) REVERT: R 193 MET cc_start: 0.6015 (mmt) cc_final: 0.4489 (tpt) REVERT: S 76 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6286 (pttp) REVERT: S 98 MET cc_start: 0.8090 (mmm) cc_final: 0.7859 (mtp) REVERT: T 76 LYS cc_start: 0.7851 (pttp) cc_final: 0.7374 (ptpt) REVERT: T 173 PHE cc_start: 0.8036 (m-80) cc_final: 0.7637 (m-10) REVERT: T 192 TYR cc_start: 0.7927 (m-80) cc_final: 0.7659 (m-80) REVERT: U 63 LYS cc_start: 0.7034 (mmtt) cc_final: 0.5931 (mmmt) REVERT: U 151 MET cc_start: 0.7800 (mpp) cc_final: 0.6927 (mpp) REVERT: U 167 TYR cc_start: 0.6587 (m-80) cc_final: 0.6258 (m-80) outliers start: 92 outliers final: 76 residues processed: 977 average time/residue: 0.2318 time to fit residues: 372.2180 Evaluate side-chains 1002 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 917 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 184 VAL 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 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 8 ILE 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 409 GLU 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 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 376 VAL Chi-restraints excluded: chain D residue 393 MET Chi-restraints excluded: chain E residue 35 SER 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 94 ASN 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 204 MET 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 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 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 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 221 VAL 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 189 VAL 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: 0.8980 chunk 83 optimal weight: 5.9990 chunk 462 optimal weight: 8.9990 chunk 387 optimal weight: 9.9990 chunk 319 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 262 optimal weight: 10.0000 chunk 459 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 190 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 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 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 302 GLN M 90 GLN N 90 GLN ** R 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.182041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146211 restraints weight = 51267.586| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.79 r_work: 0.3609 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40492 Z= 0.137 Angle : 0.687 14.881 55039 Z= 0.332 Chirality : 0.050 0.846 6034 Planarity : 0.005 0.055 6770 Dihedral : 11.306 178.095 6004 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.43 % Allowed : 20.01 % Favored : 77.56 % 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: 0.63 (0.13), residues: 1763 sheet: -0.76 (0.23), residues: 550 loop : -1.41 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 399 TYR 0.027 0.001 TYR G 324 PHE 0.033 0.002 PHE U 175 TRP 0.040 0.001 TRP G 300 HIS 0.002 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (40492) covalent geometry : angle 0.68667 / 0.33 (55039) hydrogen bonds : bond 0.03179 / 2.12 ( 1381) hydrogen bonds : angle 4.17538 / 2.88 ( 3915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9567.42 seconds wall clock time: 165 minutes 3.89 seconds (9903.89 seconds total)