Starting phenix.real_space_refine on Sat Mar 7 07:34:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nt5_12581/03_2026/7nt5_12581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nt5_12581/03_2026/7nt5_12581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nt5_12581/03_2026/7nt5_12581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nt5_12581/03_2026/7nt5_12581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nt5_12581/03_2026/7nt5_12581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nt5_12581/03_2026/7nt5_12581.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 77 5.49 5 S 195 5.16 5 C 25275 2.51 5 N 6795 2.21 5 O 7858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 178 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40200 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2974 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2974 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "F" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "G" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "H" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "I" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "J" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "K" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2979 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "L" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2969 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 15, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "M" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2916 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "N" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1556 Classifications: {'RNA': 78} Modifications used: {'5*END': 1, 'rna2p_pyr': 14, 'rna3p_pyr': 63} Link IDs: {'rna2p': 14, 'rna3p': 63} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 9.17, per 1000 atoms: 0.23 Number of scatterers: 40200 At special positions: 0 Unit cell: (213.792, 215.888, 127.856, 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 195 16.00 P 77 15.00 O 7858 8.00 N 6795 7.00 C 25275 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: 3.69 Conformation dependent library (CDL) restraints added in 1.9 seconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9538 Finding SS restraints... Secondary structure from input PDB file: 298 helices and 13 sheets defined 69.1% alpha, 3.0% beta 0 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 4.97 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 removed outlier: 3.804A pdb=" N ALA A 8 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.777A pdb=" N ARG A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.995A pdb=" N GLY A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 105 through 108 removed outlier: 4.323A pdb=" N VAL A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 123 through 139 Processing helix chain 'A' and resid 147 through 153 removed outlier: 4.113A pdb=" N TYR A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 180 removed outlier: 4.328A pdb=" N LEU A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 210 through 224 Processing helix chain 'A' and resid 224 through 240 removed outlier: 3.716A pdb=" N ARG A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.679A pdb=" N ASN A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 279 through 286 removed outlier: 5.755A pdb=" N ASN A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU A 286 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 Processing helix chain 'A' and resid 306 through 311 Proline residue: A 309 - end of helix No H-bonds generated for 'chain 'A' and resid 306 through 311' Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.546A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'B' and resid 5 through 18 removed outlier: 3.898A pdb=" N SER B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 44 through 61 Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.623A pdb=" N ALA B 121 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 139 Processing helix chain 'B' and resid 147 through 153 removed outlier: 4.065A pdb=" N TYR B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 180 removed outlier: 4.764A pdb=" N THR B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU B 175 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA B 177 " --> pdb=" O TRP B 173 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 removed outlier: 4.674A pdb=" N SER B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 210 through 224 Processing helix chain 'B' and resid 224 through 240 removed outlier: 4.040A pdb=" N ARG B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 260 removed outlier: 3.656A pdb=" N ASN B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.657A pdb=" N ALA B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 305 removed outlier: 4.272A pdb=" N SER B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Proline residue: B 309 - end of helix No H-bonds generated for 'chain 'B' and resid 306 through 311' Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.589A pdb=" N PHE B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 327 through 342 Processing helix chain 'B' and resid 356 through 369 Processing helix chain 'B' and resid 385 through 397 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 83 through 92 removed outlier: 3.525A pdb=" N LEU C 87 " --> pdb=" O ARG C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 139 Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 157 through 180 removed outlier: 4.169A pdb=" N LEU C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA C 177 " --> pdb=" O TRP C 173 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 210 through 224 Processing helix chain 'C' and resid 224 through 240 removed outlier: 3.683A pdb=" N ARG C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 260 removed outlier: 3.662A pdb=" N ASN C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 274 Processing helix chain 'C' and resid 279 through 286 removed outlier: 5.862A pdb=" N ASN C 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU C 286 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 305 Processing helix chain 'C' and resid 306 through 309 Proline residue: C 309 - end of helix No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.556A pdb=" N PHE C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 327 through 342 removed outlier: 3.563A pdb=" N THR C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 356 through 368 Processing helix chain 'C' and resid 385 through 396 Processing helix chain 'D' and resid 5 through 18 removed outlier: 3.581A pdb=" N ALA D 9 " --> pdb=" O PHE D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 44 through 61 Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.853A pdb=" N GLY D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 122 through 139 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 157 through 180 removed outlier: 4.163A pdb=" N LEU D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 176 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA D 177 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 200 removed outlier: 4.610A pdb=" N SER D 189 " --> pdb=" O THR D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 210 through 224 Processing helix chain 'D' and resid 224 through 240 removed outlier: 3.752A pdb=" N ARG D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 260 removed outlier: 3.660A pdb=" N ASN D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 274 Processing helix chain 'D' and resid 279 through 285 removed outlier: 5.779A pdb=" N ASN D 285 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.071A pdb=" N ASP D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 311 Proline residue: D 309 - end of helix No H-bonds generated for 'chain 'D' and resid 306 through 311' Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.561A pdb=" N PHE D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 327 through 342 removed outlier: 3.546A pdb=" N THR D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 368 removed outlier: 3.773A pdb=" N PHE D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 396 Processing helix chain 'E' and resid 5 through 18 Processing helix chain 'E' and resid 25 through 29 Processing helix chain 'E' and resid 44 through 61 removed outlier: 3.552A pdb=" N GLU E 50 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 Processing helix chain 'E' and resid 79 through 81 No H-bonds generated for 'chain 'E' and resid 79 through 81' Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 123 through 139 removed outlier: 3.732A pdb=" N SER E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 157 through 177 removed outlier: 3.963A pdb=" N LEU E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA E 177 " --> pdb=" O TRP E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.560A pdb=" N VAL E 198 " --> pdb=" O TRP E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 208 Processing helix chain 'E' and resid 210 through 223 removed outlier: 3.622A pdb=" N GLU E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 240 removed outlier: 4.036A pdb=" N ARG E 228 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 260 removed outlier: 4.086A pdb=" N TYR E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 279 through 286 removed outlier: 6.016A pdb=" N ASN E 285 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLU E 286 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 305 Processing helix chain 'E' and resid 306 through 311 Proline residue: E 309 - end of helix No H-bonds generated for 'chain 'E' and resid 306 through 311' Processing helix chain 'E' and resid 318 through 323 removed outlier: 3.557A pdb=" N PHE E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.532A pdb=" N THR E 340 " --> pdb=" O GLY E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 368 Processing helix chain 'E' and resid 385 through 397 removed outlier: 3.779A pdb=" N VAL E 389 " --> pdb=" O SER E 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 18 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 44 through 61 Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.515A pdb=" N GLY F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'F' and resid 123 through 139 Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 157 through 180 removed outlier: 3.643A pdb=" N LEU F 175 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA F 177 " --> pdb=" O TRP F 173 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS F 178 " --> pdb=" O ILE F 174 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL F 180 " --> pdb=" O ILE F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 200 removed outlier: 3.959A pdb=" N ARG F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 208 Processing helix chain 'F' and resid 210 through 224 removed outlier: 3.817A pdb=" N GLU F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 238 removed outlier: 3.500A pdb=" N ARG F 228 " --> pdb=" O SER F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 260 removed outlier: 3.643A pdb=" N ASN F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR F 258 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'F' and resid 284 through 286 No H-bonds generated for 'chain 'F' and resid 284 through 286' Processing helix chain 'F' and resid 287 through 305 Processing helix chain 'F' and resid 306 through 311 Proline residue: F 309 - end of helix No H-bonds generated for 'chain 'F' and resid 306 through 311' Processing helix chain 'F' and resid 318 through 323 removed outlier: 3.578A pdb=" N PHE F 322 " --> pdb=" O ILE F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 342 Processing helix chain 'F' and resid 356 through 369 removed outlier: 3.515A pdb=" N ALA F 367 " --> pdb=" O GLY F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 396 Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 25 through 29 Processing helix chain 'G' and resid 44 through 61 removed outlier: 4.009A pdb=" N GLU G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 78 removed outlier: 3.534A pdb=" N SER G 78 " --> pdb=" O PHE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 81 No H-bonds generated for 'chain 'G' and resid 79 through 81' Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 122 through 139 removed outlier: 3.680A pdb=" N GLU G 126 " --> pdb=" O GLN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 153 Processing helix chain 'G' and resid 157 through 180 removed outlier: 3.562A pdb=" N THR G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU G 175 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G 176 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA G 177 " --> pdb=" O TRP G 173 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS G 178 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL G 180 " --> pdb=" O ILE G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 200 removed outlier: 4.737A pdb=" N SER G 189 " --> pdb=" O THR G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 210 through 224 Processing helix chain 'G' and resid 224 through 240 removed outlier: 3.655A pdb=" N ARG G 228 " --> pdb=" O SER G 224 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS G 240 " --> pdb=" O ILE G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 260 removed outlier: 3.569A pdb=" N ASN G 257 " --> pdb=" O SER G 253 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR G 258 " --> pdb=" O ASP G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'G' and resid 279 through 285 removed outlier: 5.959A pdb=" N ASN G 285 " --> pdb=" O LEU G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 305 removed outlier: 4.550A pdb=" N ASP G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 311 Proline residue: G 309 - end of helix No H-bonds generated for 'chain 'G' and resid 306 through 311' Processing helix chain 'G' and resid 318 through 323 removed outlier: 3.559A pdb=" N PHE G 322 " --> pdb=" O ILE G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 326 No H-bonds generated for 'chain 'G' and resid 324 through 326' Processing helix chain 'G' and resid 327 through 342 removed outlier: 3.551A pdb=" N THR G 340 " --> pdb=" O GLY G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 368 Processing helix chain 'G' and resid 385 through 396 Processing helix chain 'H' and resid 5 through 18 Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 44 through 61 Processing helix chain 'H' and resid 65 through 79 removed outlier: 3.570A pdb=" N MET H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 Processing helix chain 'H' and resid 122 through 139 removed outlier: 3.691A pdb=" N GLU H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 153 Processing helix chain 'H' and resid 157 through 180 removed outlier: 4.107A pdb=" N LEU H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA H 177 " --> pdb=" O TRP H 173 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS H 178 " --> pdb=" O ILE H 174 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL H 180 " --> pdb=" O ILE H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 200 removed outlier: 3.708A pdb=" N ARG H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 210 through 224 Processing helix chain 'H' and resid 224 through 240 removed outlier: 3.698A pdb=" N ARG H 228 " --> pdb=" O SER H 224 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS H 240 " --> pdb=" O ILE H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 260 removed outlier: 3.612A pdb=" N ASN H 257 " --> pdb=" O SER H 253 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR H 258 " --> pdb=" O ASP H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'H' and resid 279 through 286 removed outlier: 5.413A pdb=" N ASN H 285 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU H 286 " --> pdb=" O ALA H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 305 Processing helix chain 'H' and resid 306 through 311 Proline residue: H 309 - end of helix No H-bonds generated for 'chain 'H' and resid 306 through 311' Processing helix chain 'H' and resid 318 through 323 removed outlier: 3.542A pdb=" N PHE H 322 " --> pdb=" O ILE H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 326 No H-bonds generated for 'chain 'H' and resid 324 through 326' Processing helix chain 'H' and resid 327 through 342 removed outlier: 3.652A pdb=" N THR H 340 " --> pdb=" O GLY H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 370 removed outlier: 4.180A pdb=" N HIS H 370 " --> pdb=" O SER H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 397 Processing helix chain 'I' and resid 5 through 16 removed outlier: 3.616A pdb=" N ALA I 9 " --> pdb=" O PHE I 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR I 14 " --> pdb=" O SER I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 44 through 61 Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 83 through 92 Processing helix chain 'I' and resid 122 through 139 Processing helix chain 'I' and resid 147 through 153 removed outlier: 4.102A pdb=" N TYR I 151 " --> pdb=" O ASP I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 180 removed outlier: 4.171A pdb=" N LEU I 175 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE I 176 " --> pdb=" O ILE I 172 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA I 177 " --> pdb=" O TRP I 173 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYS I 178 " --> pdb=" O ILE I 174 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL I 180 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 200 removed outlier: 3.905A pdb=" N ARG I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 208 Processing helix chain 'I' and resid 210 through 224 Processing helix chain 'I' and resid 224 through 240 removed outlier: 3.729A pdb=" N ARG I 228 " --> pdb=" O SER I 224 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS I 240 " --> pdb=" O ILE I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 260 removed outlier: 3.663A pdb=" N ASN I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR I 258 " --> pdb=" O ASP I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'I' and resid 279 through 286 removed outlier: 5.679A pdb=" N ASN I 285 " --> pdb=" O LEU I 282 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU I 286 " --> pdb=" O ALA I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 305 Processing helix chain 'I' and resid 306 through 311 Proline residue: I 309 - end of helix No H-bonds generated for 'chain 'I' and resid 306 through 311' Processing helix chain 'I' and resid 318 through 323 removed outlier: 3.616A pdb=" N PHE I 322 " --> pdb=" O ILE I 318 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 326 No H-bonds generated for 'chain 'I' and resid 324 through 326' Processing helix chain 'I' and resid 327 through 342 removed outlier: 3.520A pdb=" N THR I 340 " --> pdb=" O GLY I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 356 through 368 Processing helix chain 'I' and resid 370 through 374 Processing helix chain 'I' and resid 387 through 396 removed outlier: 3.746A pdb=" N VAL I 396 " --> pdb=" O LEU I 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 18 Processing helix chain 'J' and resid 25 through 29 Processing helix chain 'J' and resid 44 through 61 Processing helix chain 'J' and resid 65 through 79 Processing helix chain 'J' and resid 83 through 92 Processing helix chain 'J' and resid 123 through 139 Processing helix chain 'J' and resid 147 through 153 removed outlier: 4.097A pdb=" N TYR J 151 " --> pdb=" O ASP J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 177 removed outlier: 4.115A pdb=" N LEU J 175 " --> pdb=" O GLN J 171 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE J 176 " --> pdb=" O ILE J 172 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA J 177 " --> pdb=" O TRP J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 200 removed outlier: 4.616A pdb=" N SER J 189 " --> pdb=" O THR J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 208 Processing helix chain 'J' and resid 210 through 224 Processing helix chain 'J' and resid 224 through 240 removed outlier: 3.687A pdb=" N ARG J 228 " --> pdb=" O SER J 224 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS J 240 " --> pdb=" O ILE J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 260 removed outlier: 3.590A pdb=" N ASN J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR J 258 " --> pdb=" O ASP J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 274 Processing helix chain 'J' and resid 279 through 286 removed outlier: 6.141A pdb=" N ASN J 285 " --> pdb=" O LEU J 282 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU J 286 " --> pdb=" O ALA J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 305 Processing helix chain 'J' and resid 306 through 311 Proline residue: J 309 - end of helix No H-bonds generated for 'chain 'J' and resid 306 through 311' Processing helix chain 'J' and resid 318 through 323 removed outlier: 3.541A pdb=" N PHE J 322 " --> pdb=" O ILE J 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 326 No H-bonds generated for 'chain 'J' and resid 324 through 326' Processing helix chain 'J' and resid 327 through 342 removed outlier: 3.556A pdb=" N THR J 340 " --> pdb=" O GLY J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 367 removed outlier: 3.644A pdb=" N ALA J 367 " --> pdb=" O GLY J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 removed outlier: 6.354A pdb=" N ASP J 375 " --> pdb=" O GLY J 372 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN J 377 " --> pdb=" O ILE J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 396 Processing helix chain 'K' and resid 5 through 18 Processing helix chain 'K' and resid 25 through 29 Processing helix chain 'K' and resid 44 through 61 Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 83 through 91 Processing helix chain 'K' and resid 117 through 121 Processing helix chain 'K' and resid 123 through 139 Processing helix chain 'K' and resid 148 through 153 Processing helix chain 'K' and resid 157 through 177 removed outlier: 4.178A pdb=" N LEU K 175 " --> pdb=" O GLN K 171 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE K 176 " --> pdb=" O ILE K 172 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA K 177 " --> pdb=" O TRP K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 200 removed outlier: 4.495A pdb=" N ARG K 192 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 208 Processing helix chain 'K' and resid 210 through 224 Processing helix chain 'K' and resid 224 through 240 removed outlier: 3.767A pdb=" N ARG K 228 " --> pdb=" O SER K 224 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS K 240 " --> pdb=" O ILE K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 260 removed outlier: 3.595A pdb=" N ASN K 257 " --> pdb=" O SER K 253 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR K 258 " --> pdb=" O ASP K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 273 Processing helix chain 'K' and resid 279 through 286 removed outlier: 5.955A pdb=" N ASN K 285 " --> pdb=" O LEU K 282 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLU K 286 " --> pdb=" O ALA K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 305 Processing helix chain 'K' and resid 306 through 311 Proline residue: K 309 - end of helix No H-bonds generated for 'chain 'K' and resid 306 through 311' Processing helix chain 'K' and resid 318 through 323 removed outlier: 3.571A pdb=" N PHE K 322 " --> pdb=" O ILE K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 326 No H-bonds generated for 'chain 'K' and resid 324 through 326' Processing helix chain 'K' and resid 327 through 342 removed outlier: 3.547A pdb=" N THR K 340 " --> pdb=" O GLY K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 368 Processing helix chain 'K' and resid 373 through 377 Processing helix chain 'K' and resid 385 through 397 Processing helix chain 'L' and resid 5 through 18 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 44 through 61 Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.839A pdb=" N GLY L 71 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 91 Processing helix chain 'L' and resid 122 through 139 removed outlier: 3.621A pdb=" N LEU L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 153 removed outlier: 4.117A pdb=" N TYR L 151 " --> pdb=" O ASP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 180 removed outlier: 4.314A pdb=" N LEU L 175 " --> pdb=" O GLN L 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE L 176 " --> pdb=" O ILE L 172 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA L 177 " --> pdb=" O TRP L 173 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LYS L 178 " --> pdb=" O ILE L 174 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL L 180 " --> pdb=" O ILE L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 200 removed outlier: 3.671A pdb=" N TYR L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 208 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 224 through 240 removed outlier: 3.728A pdb=" N ARG L 228 " --> pdb=" O SER L 224 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS L 240 " --> pdb=" O ILE L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 260 removed outlier: 3.619A pdb=" N ASN L 257 " --> pdb=" O SER L 253 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR L 258 " --> pdb=" O ASP L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 273 Processing helix chain 'L' and resid 279 through 286 removed outlier: 5.641A pdb=" N ASN L 285 " --> pdb=" O LEU L 282 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU L 286 " --> pdb=" O ALA L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 305 Processing helix chain 'L' and resid 306 through 311 Proline residue: L 309 - end of helix No H-bonds generated for 'chain 'L' and resid 306 through 311' Processing helix chain 'L' and resid 318 through 323 removed outlier: 3.537A pdb=" N PHE L 322 " --> pdb=" O ILE L 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 342 removed outlier: 3.552A pdb=" N THR L 340 " --> pdb=" O GLY L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 368 Processing helix chain 'L' and resid 370 through 374 Processing helix chain 'L' and resid 385 through 397 Processing helix chain 'M' and resid 5 through 18 Processing helix chain 'M' and resid 25 through 29 Processing helix chain 'M' and resid 44 through 61 Processing helix chain 'M' and resid 65 through 79 removed outlier: 3.566A pdb=" N MET M 79 " --> pdb=" O THR M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 92 Processing helix chain 'M' and resid 122 through 139 Processing helix chain 'M' and resid 148 through 153 Processing helix chain 'M' and resid 157 through 180 removed outlier: 4.213A pdb=" N LEU M 175 " --> pdb=" O GLN M 171 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE M 176 " --> pdb=" O ILE M 172 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA M 177 " --> pdb=" O TRP M 173 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS M 178 " --> pdb=" O ILE M 174 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL M 180 " --> pdb=" O ILE M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 200 removed outlier: 3.704A pdb=" N LYS M 196 " --> pdb=" O ARG M 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR M 197 " --> pdb=" O ARG M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 208 Processing helix chain 'M' and resid 210 through 224 removed outlier: 3.606A pdb=" N GLU M 216 " --> pdb=" O GLN M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 240 removed outlier: 3.832A pdb=" N ARG M 228 " --> pdb=" O SER M 224 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS M 240 " --> pdb=" O ILE M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 260 removed outlier: 3.591A pdb=" N ASN M 257 " --> pdb=" O SER M 253 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR M 258 " --> pdb=" O ASP M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 274 Processing helix chain 'M' and resid 279 through 286 removed outlier: 5.585A pdb=" N ASN M 285 " --> pdb=" O LEU M 282 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU M 286 " --> pdb=" O ALA M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 305 Processing helix chain 'M' and resid 306 through 311 Proline residue: M 309 - end of helix No H-bonds generated for 'chain 'M' and resid 306 through 311' Processing helix chain 'M' and resid 318 through 323 removed outlier: 3.619A pdb=" N PHE M 322 " --> pdb=" O ILE M 318 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 326 No H-bonds generated for 'chain 'M' and resid 324 through 326' Processing helix chain 'M' and resid 327 through 342 Processing helix chain 'M' and resid 356 through 368 Processing helix chain 'M' and resid 384 through 386 No H-bonds generated for 'chain 'M' and resid 384 through 386' Processing helix chain 'M' and resid 387 through 397 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 39 removed outlier: 5.848A pdb=" N THR A 33 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL A 100 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 35 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE A 102 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A 37 " --> pdb=" O ILE A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 39 Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 39 removed outlier: 5.824A pdb=" N THR C 33 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C 100 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE C 35 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE C 102 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE C 37 " --> pdb=" O ILE C 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 33 through 40 removed outlier: 5.938A pdb=" N THR D 33 " --> pdb=" O GLU D 98 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL D 100 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE D 35 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE D 102 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE D 37 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL D 104 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL D 39 " --> pdb=" O VAL D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 33 through 39 removed outlier: 6.219A pdb=" N THR E 33 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL E 100 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 35 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE E 102 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 37 " --> pdb=" O ILE E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 33 through 39 Processing sheet with id=AA7, first strand: chain 'G' and resid 33 through 39 removed outlier: 6.131A pdb=" N THR G 33 " --> pdb=" O GLU G 98 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL G 100 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE G 35 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE G 102 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE G 37 " --> pdb=" O ILE G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 36 through 39 Processing sheet with id=AA9, first strand: chain 'I' and resid 33 through 39 removed outlier: 6.447A pdb=" N THR I 33 " --> pdb=" O GLU I 98 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL I 100 " --> pdb=" O THR I 33 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE I 35 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE I 102 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE I 37 " --> pdb=" O ILE I 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 33 through 39 Processing sheet with id=AB2, first strand: chain 'K' and resid 33 through 39 removed outlier: 5.923A pdb=" N THR K 33 " --> pdb=" O GLU K 98 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL K 100 " --> pdb=" O THR K 33 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE K 35 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE K 102 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE K 37 " --> pdb=" O ILE K 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 33 through 39 removed outlier: 5.388A pdb=" N THR L 33 " --> pdb=" O GLU L 98 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL L 100 " --> pdb=" O THR L 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE L 35 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE L 102 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE L 37 " --> pdb=" O ILE L 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 33 through 39 2201 hydrogen bonds defined for protein. 6300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 8.63 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 7127 1.32 - 1.48: 16108 1.48 - 1.64: 17381 1.64 - 1.80: 217 1.80 - 1.96: 183 Bond restraints: 41016 Sorted by residual: bond pdb=" NE ARG M 343 " pdb=" CZ ARG M 343 " ideal model delta sigma weight residual 1.326 1.475 -0.149 1.10e-02 8.26e+03 1.83e+02 bond pdb=" NE ARG M 302 " pdb=" CZ ARG M 302 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.38e+01 bond pdb=" CA ALA F 323 " pdb=" CB ALA F 323 " ideal model delta sigma weight residual 1.530 1.438 0.092 1.46e-02 4.69e+03 3.93e+01 bond pdb=" CG MET E 345 " pdb=" SD MET E 345 " ideal model delta sigma weight residual 1.803 1.958 -0.155 2.50e-02 1.60e+03 3.87e+01 bond pdb=" CG MET H 345 " pdb=" SD MET H 345 " ideal model delta sigma weight residual 1.803 1.957 -0.154 2.50e-02 1.60e+03 3.78e+01 ... (remaining 41011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 50980 3.72 - 7.44: 4428 7.44 - 11.15: 386 11.15 - 14.87: 59 14.87 - 18.59: 8 Bond angle restraints: 55861 Sorted by residual: angle pdb=" NE ARG M 343 " pdb=" CZ ARG M 343 " pdb=" NH2 ARG M 343 " ideal model delta sigma weight residual 119.20 107.85 11.35 9.00e-01 1.23e+00 1.59e+02 angle pdb=" CD ARG M 302 " pdb=" NE ARG M 302 " pdb=" CZ ARG M 302 " ideal model delta sigma weight residual 124.40 138.39 -13.99 1.40e+00 5.10e-01 9.98e+01 angle pdb=" CD ARG M 343 " pdb=" NE ARG M 343 " pdb=" CZ ARG M 343 " ideal model delta sigma weight residual 124.40 137.99 -13.59 1.40e+00 5.10e-01 9.43e+01 angle pdb=" C4' U N 44 " pdb=" C3' U N 44 " pdb=" O3' U N 44 " ideal model delta sigma weight residual 113.00 99.71 13.29 1.50e+00 4.44e-01 7.86e+01 angle pdb=" C4' U N 68 " pdb=" C3' U N 68 " pdb=" O3' U N 68 " ideal model delta sigma weight residual 113.00 100.14 12.86 1.50e+00 4.44e-01 7.35e+01 ... (remaining 55856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.79: 22819 20.79 - 41.58: 1866 41.58 - 62.36: 351 62.36 - 83.15: 71 83.15 - 103.94: 18 Dihedral angle restraints: 25125 sinusoidal: 10341 harmonic: 14784 Sorted by residual: dihedral pdb=" N ILE I 350 " pdb=" C ILE I 350 " pdb=" CA ILE I 350 " pdb=" CB ILE I 350 " ideal model delta harmonic sigma weight residual 123.40 144.98 -21.58 0 2.50e+00 1.60e-01 7.45e+01 dihedral pdb=" CA ALA F 283 " pdb=" C ALA F 283 " pdb=" N LEU F 284 " pdb=" CA LEU F 284 " ideal model delta harmonic sigma weight residual 180.00 137.21 42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" C ILE I 350 " pdb=" N ILE I 350 " pdb=" CA ILE I 350 " pdb=" CB ILE I 350 " ideal model delta harmonic sigma weight residual -122.00 -140.94 18.94 0 2.50e+00 1.60e-01 5.74e+01 ... (remaining 25122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 4998 0.180 - 0.360: 1321 0.360 - 0.541: 192 0.541 - 0.721: 30 0.721 - 0.901: 8 Chirality restraints: 6549 Sorted by residual: chirality pdb=" CB VAL E 180 " pdb=" CA VAL E 180 " pdb=" CG1 VAL E 180 " pdb=" CG2 VAL E 180 " both_signs ideal model delta sigma weight residual False -2.63 -1.73 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CB THR G 293 " pdb=" CA THR G 293 " pdb=" OG1 THR G 293 " pdb=" CG2 THR G 293 " both_signs ideal model delta sigma weight residual False 2.55 1.66 0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" CB VAL I 165 " pdb=" CA VAL I 165 " pdb=" CG1 VAL I 165 " pdb=" CG2 VAL I 165 " both_signs ideal model delta sigma weight residual False -2.63 -1.76 -0.86 2.00e-01 2.50e+01 1.87e+01 ... (remaining 6546 not shown) Planarity restraints: 6897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U N 24 " 0.175 2.00e-02 2.50e+03 8.53e-02 1.64e+02 pdb=" N1 U N 24 " -0.050 2.00e-02 2.50e+03 pdb=" C2 U N 24 " -0.055 2.00e-02 2.50e+03 pdb=" O2 U N 24 " -0.029 2.00e-02 2.50e+03 pdb=" N3 U N 24 " -0.044 2.00e-02 2.50e+03 pdb=" C4 U N 24 " 0.023 2.00e-02 2.50e+03 pdb=" O4 U N 24 " 0.123 2.00e-02 2.50e+03 pdb=" C5 U N 24 " -0.056 2.00e-02 2.50e+03 pdb=" C6 U N 24 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U N 70 " -0.172 2.00e-02 2.50e+03 7.86e-02 1.39e+02 pdb=" N1 U N 70 " 0.102 2.00e-02 2.50e+03 pdb=" C2 U N 70 " 0.050 2.00e-02 2.50e+03 pdb=" O2 U N 70 " 0.035 2.00e-02 2.50e+03 pdb=" N3 U N 70 " -0.018 2.00e-02 2.50e+03 pdb=" C4 U N 70 " -0.025 2.00e-02 2.50e+03 pdb=" O4 U N 70 " -0.067 2.00e-02 2.50e+03 pdb=" C5 U N 70 " 0.015 2.00e-02 2.50e+03 pdb=" C6 U N 70 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U N 68 " 0.123 2.00e-02 2.50e+03 6.70e-02 1.01e+02 pdb=" N1 U N 68 " 0.007 2.00e-02 2.50e+03 pdb=" C2 U N 68 " -0.012 2.00e-02 2.50e+03 pdb=" O2 U N 68 " -0.091 2.00e-02 2.50e+03 pdb=" N3 U N 68 " 0.036 2.00e-02 2.50e+03 pdb=" C4 U N 68 " 0.011 2.00e-02 2.50e+03 pdb=" O4 U N 68 " 0.070 2.00e-02 2.50e+03 pdb=" C5 U N 68 " -0.064 2.00e-02 2.50e+03 pdb=" C6 U N 68 " -0.080 2.00e-02 2.50e+03 ... (remaining 6894 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 56 2.49 - 3.09: 29881 3.09 - 3.70: 65346 3.70 - 4.30: 96614 4.30 - 4.90: 151303 Nonbonded interactions: 343200 Sorted by model distance: nonbonded pdb=" NZ LYS F 295 " pdb=" O ILE G 4 " model vdw 1.889 3.120 nonbonded pdb=" O GLN E 376 " pdb=" OD1 ASN F 285 " model vdw 2.010 3.040 nonbonded pdb=" NE2 GLN C 199 " pdb=" O2 U N 20 " model vdw 2.092 3.120 nonbonded pdb=" NH2 ARG C 343 " pdb=" O GLY D 353 " model vdw 2.205 3.120 nonbonded pdb=" NH1 ARG J 352 " pdb=" OP2 U N 56 " model vdw 2.224 3.120 ... (remaining 343195 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 4 through 368 or resid 382 through 397)) selection = (chain 'B' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'C' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'D' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'E' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'F' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'G' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'H' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'I' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'J' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'K' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'L' and (resid 4 through 368 or resid 382 through 397)) selection = (chain 'M' and resid 4 through 397) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 41.080 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.013 0.158 41016 Z= 0.797 Angle : 2.204 18.592 55861 Z= 1.409 Chirality : 0.164 0.901 6549 Planarity : 0.014 0.102 6897 Dihedral : 15.964 103.941 15587 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.50 % Rotamer: Outliers : 1.47 % Allowed : 8.52 % Favored : 90.02 % Cbeta Deviations : 4.40 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.10), residues: 5088 helix: -1.47 (0.08), residues: 3117 sheet: -1.50 (0.32), residues: 184 loop : -1.45 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.098 0.005 ARG M 343 TYR 0.133 0.021 TYR K 359 PHE 0.085 0.015 PHE M 273 TRP 0.102 0.020 TRP I 173 Details of bonding type rmsd covalent geometry : bond 0.01300 (41016) covalent geometry : angle 2.20440 (55861) hydrogen bonds : bond 0.16282 ( 2201) hydrogen bonds : angle 6.77994 ( 6300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1317 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.3967 (tpt170) cc_final: 0.3525 (mmm160) REVERT: A 51 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6989 (tp) REVERT: A 83 ARG cc_start: 0.6990 (mmp-170) cc_final: 0.6677 (mpt180) REVERT: A 87 LEU cc_start: 0.6879 (tp) cc_final: 0.6601 (tp) REVERT: A 89 ARG cc_start: 0.7024 (ptp-170) cc_final: 0.6788 (ptm160) REVERT: A 100 VAL cc_start: 0.6529 (t) cc_final: 0.6273 (m) REVERT: A 147 ASP cc_start: 0.7823 (m-30) cc_final: 0.7610 (t0) REVERT: A 154 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7714 (mmp80) REVERT: A 190 GLU cc_start: 0.7707 (mt-10) cc_final: 0.6915 (pt0) REVERT: A 250 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7290 (tp30) REVERT: A 260 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7345 (pt0) REVERT: A 261 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7417 (mm-30) REVERT: A 273 PHE cc_start: 0.6160 (m-80) cc_final: 0.5588 (m-80) REVERT: A 278 ARG cc_start: 0.6511 (mtt180) cc_final: 0.5938 (mtm-85) REVERT: A 313 LEU cc_start: 0.7679 (tp) cc_final: 0.7412 (mt) REVERT: A 327 TYR cc_start: 0.6661 (p90) cc_final: 0.6449 (p90) REVERT: A 335 MET cc_start: 0.5605 (mmp) cc_final: 0.5343 (mmp) REVERT: B 34 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7362 (tmtt) REVERT: B 38 PHE cc_start: 0.7572 (m-80) cc_final: 0.7327 (m-80) REVERT: B 78 SER cc_start: 0.7930 (t) cc_final: 0.7264 (p) REVERT: B 82 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7748 (tp30) REVERT: B 96 ASP cc_start: 0.5446 (m-30) cc_final: 0.5151 (m-30) REVERT: B 114 MET cc_start: 0.7030 (tpt) cc_final: 0.6435 (tmm) REVERT: B 153 LEU cc_start: 0.7273 (tp) cc_final: 0.7019 (mt) REVERT: B 176 ILE cc_start: 0.8585 (tp) cc_final: 0.8308 (tt) REVERT: B 180 VAL cc_start: 0.8460 (t) cc_final: 0.7710 (m) REVERT: B 200 GLN cc_start: 0.8679 (mt0) cc_final: 0.8460 (mt0) REVERT: B 210 THR cc_start: 0.8146 (p) cc_final: 0.7685 (p) REVERT: B 225 LEU cc_start: 0.7918 (tp) cc_final: 0.7667 (tt) REVERT: B 272 ARG cc_start: 0.6895 (ttp-110) cc_final: 0.6357 (ttp-170) REVERT: B 284 LEU cc_start: 0.6220 (mt) cc_final: 0.5943 (mt) REVERT: B 286 GLU cc_start: 0.7596 (pm20) cc_final: 0.7384 (pm20) REVERT: B 301 TYR cc_start: 0.7778 (t80) cc_final: 0.7462 (t80) REVERT: B 311 MET cc_start: 0.8250 (ptp) cc_final: 0.8012 (ptm) REVERT: B 331 TRP cc_start: 0.7681 (t60) cc_final: 0.7439 (t60) REVERT: B 364 GLN cc_start: 0.4975 (mt0) cc_final: 0.4670 (mt0) REVERT: C 34 LYS cc_start: 0.7381 (tttt) cc_final: 0.6981 (mptt) REVERT: C 70 VAL cc_start: 0.6856 (t) cc_final: 0.6431 (p) REVERT: C 80 TYR cc_start: 0.7247 (m-10) cc_final: 0.6978 (m-80) REVERT: C 89 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7744 (mtm110) REVERT: C 129 MET cc_start: 0.8703 (tpp) cc_final: 0.8329 (ppp) REVERT: C 151 TYR cc_start: 0.5825 (t80) cc_final: 0.5371 (t80) REVERT: C 158 MET cc_start: 0.7204 (mtm) cc_final: 0.6627 (mmt) REVERT: C 166 ILE cc_start: 0.8163 (pt) cc_final: 0.7950 (mt) REVERT: C 180 VAL cc_start: 0.8482 (t) cc_final: 0.8034 (m) REVERT: C 184 ASP cc_start: 0.7543 (m-30) cc_final: 0.7327 (p0) REVERT: C 335 MET cc_start: 0.7223 (mmp) cc_final: 0.6898 (mmm) REVERT: C 343 ARG cc_start: 0.6801 (mtm110) cc_final: 0.6324 (mmt180) REVERT: C 358 MET cc_start: 0.6098 (mmm) cc_final: 0.5805 (tpp) REVERT: C 361 ARG cc_start: 0.7032 (mtm-85) cc_final: 0.6156 (tpt170) REVERT: D 67 SER cc_start: 0.8521 (p) cc_final: 0.8169 (t) REVERT: D 94 ASP cc_start: 0.4770 (t0) cc_final: 0.4519 (t0) REVERT: D 96 ASP cc_start: 0.7048 (m-30) cc_final: 0.6647 (m-30) REVERT: D 125 MET cc_start: 0.7480 (mtm) cc_final: 0.7217 (tpt) REVERT: D 217 MET cc_start: 0.7567 (tpt) cc_final: 0.7267 (tpt) REVERT: D 250 GLU cc_start: 0.8649 (tt0) cc_final: 0.8285 (tp30) REVERT: D 275 LEU cc_start: 0.6620 (tp) cc_final: 0.5955 (tt) REVERT: D 278 ARG cc_start: 0.7621 (mtt180) cc_final: 0.7019 (ttp-170) REVERT: D 287 PHE cc_start: 0.7810 (m-80) cc_final: 0.7501 (m-80) REVERT: D 288 GLN cc_start: 0.7859 (mm110) cc_final: 0.7546 (mp10) REVERT: D 311 MET cc_start: 0.7836 (ptp) cc_final: 0.7611 (ptm) REVERT: E 5 PHE cc_start: 0.7915 (m-80) cc_final: 0.7523 (m-80) REVERT: E 7 GLU cc_start: 0.7516 (tp30) cc_final: 0.7108 (tp30) REVERT: E 31 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6098 (mt) REVERT: E 50 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8495 (tp30) REVERT: E 96 ASP cc_start: 0.6562 (m-30) cc_final: 0.6244 (m-30) REVERT: E 103 ASP cc_start: 0.6883 (p0) cc_final: 0.6554 (p0) REVERT: E 114 MET cc_start: 0.6083 (tpt) cc_final: 0.5287 (tmm) REVERT: E 137 ASP cc_start: 0.7171 (m-30) cc_final: 0.6902 (m-30) REVERT: E 154 ARG cc_start: 0.8293 (mtt90) cc_final: 0.8064 (mmt-90) REVERT: E 193 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7638 (mmp80) REVERT: E 250 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8016 (mp0) REVERT: F 7 GLU cc_start: 0.8108 (tp30) cc_final: 0.7780 (mm-30) REVERT: F 12 ARG cc_start: 0.7703 (tpp80) cc_final: 0.7184 (mmt180) REVERT: F 36 ARG cc_start: 0.6347 (mtm180) cc_final: 0.6130 (ptp-110) REVERT: F 68 MET cc_start: 0.6811 (mmm) cc_final: 0.6573 (mtp) REVERT: F 79 MET cc_start: 0.8007 (mmt) cc_final: 0.7771 (mmp) REVERT: F 83 ARG cc_start: 0.7445 (mmm-85) cc_final: 0.7154 (tpp80) REVERT: F 103 ASP cc_start: 0.7420 (p0) cc_final: 0.7084 (p0) REVERT: F 125 MET cc_start: 0.7087 (mtm) cc_final: 0.6854 (mtp) REVERT: F 129 MET cc_start: 0.8717 (tpt) cc_final: 0.8448 (mmt) REVERT: F 147 ASP cc_start: 0.7990 (t0) cc_final: 0.7559 (t0) REVERT: F 158 MET cc_start: 0.7578 (ttm) cc_final: 0.7349 (ttm) REVERT: F 188 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7852 (tp30) REVERT: F 216 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7542 (mm-30) REVERT: F 219 ASN cc_start: 0.6535 (m-40) cc_final: 0.6314 (m110) REVERT: F 233 GLU cc_start: 0.8823 (tp30) cc_final: 0.8507 (mt-10) REVERT: F 307 ARG cc_start: 0.8388 (mtt-85) cc_final: 0.7724 (mpp-170) REVERT: F 345 MET cc_start: 0.7292 (mmm) cc_final: 0.7017 (mmt) REVERT: F 364 GLN cc_start: 0.7253 (tm-30) cc_final: 0.6703 (tt0) REVERT: G 15 GLN cc_start: 0.7893 (mt0) cc_final: 0.7670 (mt0) REVERT: G 21 ASP cc_start: 0.8158 (m-30) cc_final: 0.7955 (p0) REVERT: G 34 LYS cc_start: 0.7187 (tttt) cc_final: 0.6446 (mttp) REVERT: G 43 ASN cc_start: 0.6713 (m-40) cc_final: 0.6478 (p0) REVERT: G 82 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8052 (pm20) REVERT: G 93 ASN cc_start: 0.6735 (t0) cc_final: 0.6397 (t0) REVERT: G 114 MET cc_start: 0.7364 (tpt) cc_final: 0.6808 (tpp) REVERT: G 189 SER cc_start: 0.8742 (m) cc_final: 0.8481 (p) REVERT: G 197 TYR cc_start: 0.8695 (m-80) cc_final: 0.7695 (m-80) REVERT: G 223 GLN cc_start: 0.8210 (tt0) cc_final: 0.7994 (tm-30) REVERT: G 257 ASN cc_start: 0.8799 (m110) cc_final: 0.8523 (m110) REVERT: G 272 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8256 (ttm-80) REVERT: G 345 MET cc_start: 0.8143 (mmt) cc_final: 0.7520 (mmt) REVERT: G 358 MET cc_start: 0.8098 (mpt) cc_final: 0.7759 (tmm) REVERT: G 361 ARG cc_start: 0.8345 (mtm110) cc_final: 0.8101 (mtt-85) REVERT: H 50 GLU cc_start: 0.8557 (tp30) cc_final: 0.8207 (tp30) REVERT: H 82 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7865 (tp30) REVERT: H 93 ASN cc_start: 0.7193 (t0) cc_final: 0.6980 (t0) REVERT: H 124 GLU cc_start: 0.8050 (tt0) cc_final: 0.7811 (pt0) REVERT: H 157 ASP cc_start: 0.6957 (m-30) cc_final: 0.6710 (p0) REVERT: H 166 ILE cc_start: 0.8393 (pt) cc_final: 0.8151 (mt) REVERT: H 180 VAL cc_start: 0.8706 (t) cc_final: 0.8239 (m) REVERT: H 217 MET cc_start: 0.7770 (tpt) cc_final: 0.7509 (tpp) REVERT: H 275 LEU cc_start: 0.8107 (tp) cc_final: 0.7729 (tt) REVERT: H 335 MET cc_start: 0.7893 (mmp) cc_final: 0.7295 (mmm) REVERT: H 345 MET cc_start: 0.7909 (mmt) cc_final: 0.7596 (mmp) REVERT: I 15 GLN cc_start: 0.8182 (mt0) cc_final: 0.7646 (mt0) REVERT: I 93 ASN cc_start: 0.7919 (m-40) cc_final: 0.7412 (p0) REVERT: I 142 LYS cc_start: 0.5949 (mttt) cc_final: 0.5721 (mptt) REVERT: I 147 ASP cc_start: 0.8319 (t0) cc_final: 0.7847 (t0) REVERT: I 160 THR cc_start: 0.8634 (p) cc_final: 0.8382 (t) REVERT: I 279 TYR cc_start: 0.6923 (m-80) cc_final: 0.6642 (m-80) REVERT: I 301 TYR cc_start: 0.8542 (t80) cc_final: 0.8274 (t80) REVERT: J 4 ILE cc_start: 0.8314 (tt) cc_final: 0.7943 (tp) REVERT: J 17 LYS cc_start: 0.8625 (mttt) cc_final: 0.8371 (pttt) REVERT: J 23 ARG cc_start: 0.7515 (mtt90) cc_final: 0.7301 (mtp-110) REVERT: J 78 SER cc_start: 0.8048 (t) cc_final: 0.7777 (p) REVERT: J 79 MET cc_start: 0.7403 (mmt) cc_final: 0.7148 (mmp) REVERT: J 114 MET cc_start: 0.5455 (OUTLIER) cc_final: 0.4704 (ptm) REVERT: J 129 MET cc_start: 0.8567 (tpt) cc_final: 0.8201 (mtp) REVERT: J 190 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7415 (tm-30) REVERT: J 233 GLU cc_start: 0.8029 (tp30) cc_final: 0.7797 (mt-10) REVERT: J 262 THR cc_start: 0.7716 (p) cc_final: 0.7441 (t) REVERT: J 272 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7572 (ttm110) REVERT: J 285 ASN cc_start: 0.7739 (m110) cc_final: 0.7071 (p0) REVERT: J 294 ILE cc_start: 0.8678 (mm) cc_final: 0.8420 (mm) REVERT: J 342 ASP cc_start: 0.6851 (t0) cc_final: 0.6566 (t0) REVERT: J 345 MET cc_start: 0.7094 (mmt) cc_final: 0.6488 (mmm) REVERT: J 361 ARG cc_start: 0.7446 (mtm110) cc_final: 0.7183 (ptt180) REVERT: J 365 LYS cc_start: 0.7581 (mttt) cc_final: 0.7231 (tttt) REVERT: K 12 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7522 (mmt180) REVERT: K 15 GLN cc_start: 0.7841 (mt0) cc_final: 0.7387 (mt0) REVERT: K 23 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7508 (ttm-80) REVERT: K 50 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7864 (tm-30) REVERT: K 54 PHE cc_start: 0.6676 (t80) cc_final: 0.6369 (t80) REVERT: K 103 ASP cc_start: 0.7546 (t0) cc_final: 0.7020 (p0) REVERT: K 147 ASP cc_start: 0.6773 (t0) cc_final: 0.6117 (m-30) REVERT: K 197 TYR cc_start: 0.8335 (m-80) cc_final: 0.8024 (m-80) REVERT: K 250 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7552 (mt-10) REVERT: K 275 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6754 (tp) REVERT: K 335 MET cc_start: 0.7120 (mmp) cc_final: 0.6686 (mmp) REVERT: L 5 PHE cc_start: 0.7294 (m-80) cc_final: 0.7029 (m-80) REVERT: L 39 VAL cc_start: 0.5535 (t) cc_final: 0.5284 (p) REVERT: L 107 MET cc_start: 0.5920 (tpt) cc_final: 0.5587 (tpp) REVERT: L 168 ILE cc_start: 0.7449 (pp) cc_final: 0.7141 (mt) REVERT: L 176 ILE cc_start: 0.8057 (tp) cc_final: 0.7837 (tt) REVERT: L 199 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7432 (tm-30) REVERT: L 223 GLN cc_start: 0.7232 (tt0) cc_final: 0.6630 (mp10) REVERT: L 260 GLU cc_start: 0.7043 (pt0) cc_final: 0.6806 (mt-10) REVERT: L 290 ASP cc_start: 0.8238 (m-30) cc_final: 0.8008 (m-30) REVERT: L 298 MET cc_start: 0.8525 (mtt) cc_final: 0.8101 (mtm) REVERT: L 299 LEU cc_start: 0.8371 (pp) cc_final: 0.8068 (tp) REVERT: L 310 TYR cc_start: 0.8147 (m-80) cc_final: 0.7792 (m-10) REVERT: L 322 PHE cc_start: 0.8523 (m-80) cc_final: 0.8301 (m-80) REVERT: L 331 TRP cc_start: 0.7256 (t60) cc_final: 0.6845 (t60) REVERT: L 335 MET cc_start: 0.6856 (mmp) cc_final: 0.6435 (mmm) REVERT: L 350 ILE cc_start: 0.7565 (pt) cc_final: 0.7128 (mm) REVERT: L 351 ASN cc_start: 0.7518 (m110) cc_final: 0.7315 (p0) REVERT: L 354 TYR cc_start: 0.7577 (p90) cc_final: 0.7123 (p90) REVERT: M 5 PHE cc_start: 0.6819 (m-80) cc_final: 0.6613 (m-80) REVERT: M 83 ARG cc_start: 0.6906 (mmm160) cc_final: 0.6534 (ptp-170) REVERT: M 123 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6303 (tp30) REVERT: M 158 MET cc_start: 0.6191 (mtm) cc_final: 0.5737 (tpt) REVERT: M 200 GLN cc_start: 0.8156 (tt0) cc_final: 0.7698 (mm110) REVERT: M 212 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6944 (tm-30) REVERT: M 237 GLU cc_start: 0.6179 (tm-30) cc_final: 0.5956 (tp30) REVERT: M 273 PHE cc_start: 0.7534 (m-80) cc_final: 0.7241 (m-80) REVERT: M 279 TYR cc_start: 0.5606 (m-10) cc_final: 0.5292 (m-10) REVERT: M 282 LEU cc_start: 0.5162 (mp) cc_final: 0.4924 (mp) REVERT: M 287 PHE cc_start: 0.7387 (m-80) cc_final: 0.6861 (m-80) REVERT: M 321 LYS cc_start: 0.7492 (mttt) cc_final: 0.7159 (mttm) REVERT: M 322 PHE cc_start: 0.8642 (m-80) cc_final: 0.8163 (m-80) REVERT: M 327 TYR cc_start: 0.7371 (p90) cc_final: 0.7155 (p90) REVERT: M 354 TYR cc_start: 0.7452 (p90) cc_final: 0.6769 (p90) REVERT: M 358 MET cc_start: 0.7596 (mmm) cc_final: 0.7073 (ttm) outliers start: 57 outliers final: 9 residues processed: 1357 average time/residue: 0.2936 time to fit residues: 618.8733 Evaluate side-chains 883 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 868 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 193 ARG Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 272 ARG Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain M residue 23 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 394 optimal weight: 0.9990 chunk 430 optimal weight: 0.0370 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 0.9980 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 30.0000 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN B 15 GLN B 109 ASN B 292 ASN C 171 GLN C 292 ASN ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN D 288 GLN D 364 GLN E 171 GLN E 223 GLN E 257 ASN F 223 GLN F 257 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 GLN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN I 109 ASN I 285 ASN K 257 ASN L 15 GLN L 43 ASN M 15 GLN M 93 ASN M 199 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.157014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.131817 restraints weight = 71113.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.131967 restraints weight = 51899.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.133155 restraints weight = 47476.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.133251 restraints weight = 33457.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.133505 restraints weight = 32431.336| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 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 : 0.004 0.049 41016 Z= 0.170 Angle : 0.720 9.060 55861 Z= 0.387 Chirality : 0.045 0.299 6549 Planarity : 0.005 0.056 6897 Dihedral : 11.062 92.500 6846 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.52 % Allowed : 13.69 % Favored : 83.79 % 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: -0.67 (0.11), residues: 5088 helix: -0.01 (0.09), residues: 3109 sheet: -1.00 (0.32), residues: 186 loop : -0.96 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 60 TYR 0.033 0.002 TYR E 301 PHE 0.032 0.002 PHE M 207 TRP 0.022 0.002 TRP D 213 Details of bonding type rmsd covalent geometry : bond 0.00360 (41016) covalent geometry : angle 0.71968 (55861) hydrogen bonds : bond 0.05575 ( 2201) hydrogen bonds : angle 4.85606 ( 6300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 970 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.7636 (tpp) cc_final: 0.7223 (tpt) REVERT: A 231 MET cc_start: 0.6660 (mmp) cc_final: 0.5816 (mmm) REVERT: A 273 PHE cc_start: 0.5561 (m-80) cc_final: 0.5157 (m-80) REVERT: A 313 LEU cc_start: 0.7489 (tp) cc_final: 0.7012 (mt) REVERT: B 78 SER cc_start: 0.7990 (t) cc_final: 0.7490 (p) REVERT: B 80 TYR cc_start: 0.4791 (m-10) cc_final: 0.4503 (m-80) REVERT: B 125 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5980 (ptp) REVERT: B 273 PHE cc_start: 0.7008 (m-80) cc_final: 0.6135 (m-80) REVERT: B 331 TRP cc_start: 0.7205 (t60) cc_final: 0.6982 (t60) REVERT: B 364 GLN cc_start: 0.5768 (mt0) cc_final: 0.5526 (mt0) REVERT: C 140 LYS cc_start: 0.5530 (mtmm) cc_final: 0.5133 (ptpp) REVERT: C 335 MET cc_start: 0.7610 (mmp) cc_final: 0.7207 (mmm) REVERT: C 358 MET cc_start: 0.5128 (mmm) cc_final: 0.4924 (tpp) REVERT: C 361 ARG cc_start: 0.7234 (mtm-85) cc_final: 0.6759 (tpt170) REVERT: D 67 SER cc_start: 0.8197 (p) cc_final: 0.7614 (t) REVERT: D 217 MET cc_start: 0.7557 (tpt) cc_final: 0.7043 (tpt) REVERT: D 254 ASP cc_start: 0.7358 (t0) cc_final: 0.6739 (t0) REVERT: D 278 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6988 (ttp-170) REVERT: E 103 ASP cc_start: 0.6643 (p0) cc_final: 0.6415 (p0) REVERT: E 362 LEU cc_start: 0.7550 (tp) cc_final: 0.7109 (mp) REVERT: F 158 MET cc_start: 0.7417 (ttm) cc_final: 0.7210 (ttm) REVERT: F 217 MET cc_start: 0.7493 (tpt) cc_final: 0.7235 (tpt) REVERT: F 285 ASN cc_start: 0.6416 (m110) cc_final: 0.6034 (m-40) REVERT: F 335 MET cc_start: 0.7576 (mmp) cc_final: 0.7174 (mmt) REVERT: G 43 ASN cc_start: 0.6782 (m-40) cc_final: 0.6362 (p0) REVERT: G 189 SER cc_start: 0.7933 (m) cc_final: 0.7717 (p) REVERT: H 67 SER cc_start: 0.7781 (p) cc_final: 0.7541 (t) REVERT: H 217 MET cc_start: 0.7648 (tpt) cc_final: 0.7295 (tpp) REVERT: H 270 THR cc_start: 0.8229 (p) cc_final: 0.7890 (p) REVERT: H 359 TYR cc_start: 0.5909 (m-80) cc_final: 0.5694 (m-80) REVERT: I 217 MET cc_start: 0.8051 (tpt) cc_final: 0.7778 (tpp) REVERT: I 279 TYR cc_start: 0.6288 (m-80) cc_final: 0.5819 (m-80) REVERT: J 4 ILE cc_start: 0.7387 (tt) cc_final: 0.6878 (tt) REVERT: J 114 MET cc_start: 0.4793 (ppp) cc_final: 0.3331 (ptm) REVERT: J 169 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7308 (mt-10) REVERT: J 217 MET cc_start: 0.8240 (tpt) cc_final: 0.7879 (tpt) REVERT: J 294 ILE cc_start: 0.8253 (mm) cc_final: 0.7956 (mm) REVERT: J 298 MET cc_start: 0.7354 (mtt) cc_final: 0.7033 (mtt) REVERT: K 103 ASP cc_start: 0.5772 (t0) cc_final: 0.4818 (p0) REVERT: K 147 ASP cc_start: 0.5325 (t0) cc_final: 0.4816 (m-30) REVERT: K 358 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6315 (ptt) REVERT: L 91 LEU cc_start: 0.7700 (mt) cc_final: 0.7354 (mp) REVERT: L 114 MET cc_start: 0.4364 (ttp) cc_final: 0.3967 (ttp) REVERT: L 247 ARG cc_start: 0.5976 (OUTLIER) cc_final: 0.5400 (ttt90) REVERT: L 298 MET cc_start: 0.7914 (mtt) cc_final: 0.7542 (mtp) REVERT: L 310 TYR cc_start: 0.7864 (m-80) cc_final: 0.7624 (m-80) REVERT: M 83 ARG cc_start: 0.7072 (mmm160) cc_final: 0.6652 (ptp-170) REVERT: M 158 MET cc_start: 0.6619 (mtm) cc_final: 0.5956 (tpt) REVERT: M 178 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7054 (mmtt) REVERT: M 311 MET cc_start: 0.7853 (ptp) cc_final: 0.7564 (ptp) outliers start: 98 outliers final: 44 residues processed: 1028 average time/residue: 0.2613 time to fit residues: 430.5339 Evaluate side-chains 792 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 744 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain K residue 358 MET Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 247 ARG Chi-restraints excluded: chain L residue 285 ASN Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 254 ASP Chi-restraints excluded: chain M residue 299 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 385 optimal weight: 7.9990 chunk 485 optimal weight: 9.9990 chunk 465 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 408 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 340 optimal weight: 20.0000 chunk 498 optimal weight: 8.9990 chunk 496 optimal weight: 7.9990 chunk 504 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN E 171 GLN E 292 ASN F 15 GLN F 212 GLN F 223 GLN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 351 ASN I 109 ASN I 211 GLN K 109 ASN L 43 ASN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 GLN L 257 ASN M 93 ASN M 200 GLN M 288 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.152979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126628 restraints weight = 70984.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.126894 restraints weight = 51197.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.128186 restraints weight = 47915.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128271 restraints weight = 32173.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.128539 restraints weight = 31344.380| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 41016 Z= 0.216 Angle : 0.710 9.905 55861 Z= 0.376 Chirality : 0.045 0.285 6549 Planarity : 0.005 0.052 6897 Dihedral : 10.818 89.839 6816 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.27 % Allowed : 16.18 % Favored : 80.55 % 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: -0.48 (0.11), residues: 5088 helix: 0.13 (0.09), residues: 3073 sheet: -0.81 (0.34), residues: 184 loop : -0.84 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 361 TYR 0.033 0.003 TYR H 80 PHE 0.029 0.002 PHE J 54 TRP 0.013 0.002 TRP D 213 Details of bonding type rmsd covalent geometry : bond 0.00491 (41016) covalent geometry : angle 0.71007 (55861) hydrogen bonds : bond 0.05107 ( 2201) hydrogen bonds : angle 4.78162 ( 6300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 771 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.4503 (OUTLIER) cc_final: 0.3982 (tt0) REVERT: A 273 PHE cc_start: 0.5583 (m-80) cc_final: 0.5134 (m-80) REVERT: A 313 LEU cc_start: 0.7685 (tp) cc_final: 0.7371 (mt) REVERT: A 335 MET cc_start: 0.5460 (mmp) cc_final: 0.5240 (mmp) REVERT: B 42 THR cc_start: 0.3770 (OUTLIER) cc_final: 0.3458 (p) REVERT: B 78 SER cc_start: 0.7965 (t) cc_final: 0.7554 (p) REVERT: B 292 ASN cc_start: 0.8270 (t160) cc_final: 0.7926 (t0) REVERT: B 331 TRP cc_start: 0.7160 (t60) cc_final: 0.6911 (t60) REVERT: B 364 GLN cc_start: 0.5728 (mt0) cc_final: 0.5351 (mt0) REVERT: C 43 ASN cc_start: 0.5614 (t0) cc_final: 0.5309 (t0) REVERT: C 286 GLU cc_start: 0.6205 (mp0) cc_final: 0.5936 (mp0) REVERT: C 358 MET cc_start: 0.5213 (mmm) cc_final: 0.4966 (tpp) REVERT: C 361 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6616 (tpt170) REVERT: D 67 SER cc_start: 0.8277 (p) cc_final: 0.7710 (t) REVERT: D 114 MET cc_start: 0.6441 (tmm) cc_final: 0.6201 (tmm) REVERT: D 217 MET cc_start: 0.7583 (tpt) cc_final: 0.7210 (tpt) REVERT: D 250 GLU cc_start: 0.7822 (tp30) cc_final: 0.7263 (tp30) REVERT: E 5 PHE cc_start: 0.7346 (m-80) cc_final: 0.6922 (m-10) REVERT: E 96 ASP cc_start: 0.7085 (m-30) cc_final: 0.6380 (m-30) REVERT: E 147 ASP cc_start: 0.5862 (t0) cc_final: 0.5407 (m-30) REVERT: F 158 MET cc_start: 0.7556 (ttm) cc_final: 0.7051 (ttm) REVERT: F 335 MET cc_start: 0.7652 (mmp) cc_final: 0.7368 (mmt) REVERT: G 32 THR cc_start: 0.7499 (p) cc_final: 0.7275 (p) REVERT: G 43 ASN cc_start: 0.7081 (m-40) cc_final: 0.6350 (p0) REVERT: G 290 ASP cc_start: 0.6503 (m-30) cc_final: 0.6183 (m-30) REVERT: H 67 SER cc_start: 0.7917 (p) cc_final: 0.7666 (t) REVERT: H 217 MET cc_start: 0.7771 (tpt) cc_final: 0.7337 (tpp) REVERT: H 270 THR cc_start: 0.8215 (p) cc_final: 0.7858 (p) REVERT: I 279 TYR cc_start: 0.6289 (m-80) cc_final: 0.6046 (m-10) REVERT: J 114 MET cc_start: 0.5099 (ppp) cc_final: 0.3842 (ttp) REVERT: J 131 ILE cc_start: 0.6922 (mm) cc_final: 0.6702 (mt) REVERT: J 169 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7552 (mt-10) REVERT: J 365 LYS cc_start: 0.7322 (mttt) cc_final: 0.6969 (tttt) REVERT: K 103 ASP cc_start: 0.5800 (t0) cc_final: 0.4672 (p0) REVERT: K 147 ASP cc_start: 0.5360 (t0) cc_final: 0.4863 (m-30) REVERT: L 5 PHE cc_start: 0.6740 (m-80) cc_final: 0.6450 (m-80) REVERT: L 50 GLU cc_start: 0.6641 (tt0) cc_final: 0.6242 (tt0) REVERT: L 129 MET cc_start: 0.6526 (mmt) cc_final: 0.6267 (mmt) REVERT: L 149 ARG cc_start: 0.6724 (mtm110) cc_final: 0.6435 (ptm160) REVERT: L 199 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7578 (tm-30) REVERT: L 247 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5842 (ttt90) REVERT: M 5 PHE cc_start: 0.6501 (m-80) cc_final: 0.6172 (m-80) REVERT: M 54 PHE cc_start: 0.6750 (t80) cc_final: 0.6293 (t80) REVERT: M 80 TYR cc_start: 0.4685 (m-80) cc_final: 0.4232 (m-80) REVERT: M 158 MET cc_start: 0.6602 (mtm) cc_final: 0.5834 (tpt) REVERT: M 178 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.6949 (mmtt) REVERT: M 181 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7367 (t) outliers start: 127 outliers final: 71 residues processed: 844 average time/residue: 0.2571 time to fit residues: 350.8214 Evaluate side-chains 748 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 672 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 301 TYR Chi-restraints excluded: chain F residue 311 MET Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 253 SER Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 247 ARG Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 356 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 7 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 449 optimal weight: 5.9990 chunk 482 optimal weight: 9.9990 chunk 287 optimal weight: 0.7980 chunk 443 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 421 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN E 171 GLN G 93 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 ASN I 257 ASN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 257 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 ASN M 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.154681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.130176 restraints weight = 71509.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.129607 restraints weight = 59705.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.130843 restraints weight = 54250.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131208 restraints weight = 39315.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.131373 restraints weight = 37935.584| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 41016 Z= 0.194 Angle : 0.672 10.199 55861 Z= 0.354 Chirality : 0.044 0.298 6549 Planarity : 0.005 0.054 6897 Dihedral : 10.679 89.322 6812 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.63 % Allowed : 17.44 % Favored : 78.93 % 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: -0.38 (0.11), residues: 5088 helix: 0.21 (0.09), residues: 3072 sheet: -0.68 (0.34), residues: 184 loop : -0.83 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 149 TYR 0.042 0.003 TYR E 80 PHE 0.033 0.002 PHE J 54 TRP 0.010 0.001 TRP I 331 Details of bonding type rmsd covalent geometry : bond 0.00446 (41016) covalent geometry : angle 0.67174 (55861) hydrogen bonds : bond 0.04756 ( 2201) hydrogen bonds : angle 4.68991 ( 6300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 734 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.3476 (OUTLIER) cc_final: 0.3250 (tp) REVERT: A 273 PHE cc_start: 0.5341 (m-80) cc_final: 0.4976 (m-80) REVERT: B 42 THR cc_start: 0.3893 (OUTLIER) cc_final: 0.3627 (p) REVERT: B 78 SER cc_start: 0.7932 (t) cc_final: 0.7577 (p) REVERT: B 292 ASN cc_start: 0.8254 (t160) cc_final: 0.7917 (t0) REVERT: B 361 ARG cc_start: 0.6913 (ptp-170) cc_final: 0.6615 (ptp-170) REVERT: B 364 GLN cc_start: 0.5863 (mt0) cc_final: 0.5486 (mt0) REVERT: D 67 SER cc_start: 0.8271 (p) cc_final: 0.7685 (t) REVERT: D 114 MET cc_start: 0.6465 (tmm) cc_final: 0.6063 (tmm) REVERT: D 115 GLU cc_start: 0.4814 (OUTLIER) cc_final: 0.4316 (mp0) REVERT: D 217 MET cc_start: 0.7536 (tpt) cc_final: 0.7297 (tpt) REVERT: E 96 ASP cc_start: 0.6825 (m-30) cc_final: 0.6082 (m-30) REVERT: E 270 THR cc_start: 0.7778 (p) cc_final: 0.7420 (t) REVERT: F 158 MET cc_start: 0.7564 (ttm) cc_final: 0.7162 (ttm) REVERT: F 217 MET cc_start: 0.7750 (tpt) cc_final: 0.7473 (tpt) REVERT: F 290 ASP cc_start: 0.6417 (m-30) cc_final: 0.6192 (m-30) REVERT: F 335 MET cc_start: 0.7365 (mmp) cc_final: 0.7159 (mmt) REVERT: G 43 ASN cc_start: 0.6803 (m-40) cc_final: 0.6180 (p0) REVERT: G 169 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7316 (mt-10) REVERT: H 67 SER cc_start: 0.7835 (p) cc_final: 0.7594 (t) REVERT: H 217 MET cc_start: 0.7771 (tpt) cc_final: 0.7304 (tpp) REVERT: H 270 THR cc_start: 0.8052 (p) cc_final: 0.7685 (p) REVERT: I 279 TYR cc_start: 0.6267 (m-80) cc_final: 0.5933 (m-80) REVERT: J 114 MET cc_start: 0.4911 (ppp) cc_final: 0.3950 (ttp) REVERT: J 131 ILE cc_start: 0.6597 (mm) cc_final: 0.6346 (mt) REVERT: J 169 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7172 (mt-10) REVERT: J 217 MET cc_start: 0.8568 (tpt) cc_final: 0.8318 (tpt) REVERT: J 276 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6881 (mt-10) REVERT: K 80 TYR cc_start: 0.5985 (m-10) cc_final: 0.5771 (m-80) REVERT: K 97 ILE cc_start: 0.7473 (pt) cc_final: 0.7228 (mm) REVERT: K 103 ASP cc_start: 0.5703 (t0) cc_final: 0.4717 (p0) REVERT: K 147 ASP cc_start: 0.5799 (t0) cc_final: 0.5198 (m-30) REVERT: L 5 PHE cc_start: 0.6688 (m-80) cc_final: 0.6423 (m-80) REVERT: L 50 GLU cc_start: 0.6660 (tt0) cc_final: 0.6423 (tt0) REVERT: L 149 ARG cc_start: 0.6490 (mtm110) cc_final: 0.6172 (ptm160) REVERT: L 199 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7539 (tm-30) REVERT: L 282 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6859 (pp) REVERT: L 310 TYR cc_start: 0.7819 (m-80) cc_final: 0.7378 (m-10) REVERT: M 80 TYR cc_start: 0.4966 (m-10) cc_final: 0.4552 (m-80) REVERT: M 158 MET cc_start: 0.6439 (mtm) cc_final: 0.5703 (tpt) REVERT: M 178 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6996 (mmtt) REVERT: M 181 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7489 (t) REVERT: M 196 LYS cc_start: 0.5429 (OUTLIER) cc_final: 0.5073 (tptm) outliers start: 141 outliers final: 91 residues processed: 824 average time/residue: 0.2492 time to fit residues: 336.0434 Evaluate side-chains 773 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 674 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 311 MET Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 301 TYR Chi-restraints excluded: chain F residue 311 MET Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 285 ASN Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 276 GLU Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 196 LYS Chi-restraints excluded: chain M residue 356 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 428 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 472 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 464 optimal weight: 9.9990 chunk 494 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 380 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 43 ASN C 285 ASN E 171 GLN F 15 GLN F 93 ASN G 93 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 351 ASN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN K 257 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 ASN M 93 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.155898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.131623 restraints weight = 70748.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.131007 restraints weight = 60013.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.132234 restraints weight = 54024.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.132547 restraints weight = 39677.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.132774 restraints weight = 38346.717| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 41016 Z= 0.162 Angle : 0.643 10.687 55861 Z= 0.336 Chirality : 0.042 0.289 6549 Planarity : 0.005 0.059 6897 Dihedral : 10.572 89.126 6812 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.42 % Allowed : 18.96 % Favored : 77.62 % 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: -0.20 (0.11), residues: 5088 helix: 0.38 (0.09), residues: 3058 sheet: -0.59 (0.35), residues: 184 loop : -0.78 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 20 TYR 0.042 0.002 TYR E 80 PHE 0.034 0.002 PHE J 54 TRP 0.011 0.001 TRP B 331 Details of bonding type rmsd covalent geometry : bond 0.00370 (41016) covalent geometry : angle 0.64325 (55861) hydrogen bonds : bond 0.04473 ( 2201) hydrogen bonds : angle 4.58564 ( 6300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 748 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.3857 (OUTLIER) cc_final: 0.3572 (tp) REVERT: A 6 GLU cc_start: 0.4644 (OUTLIER) cc_final: 0.4133 (tt0) REVERT: A 91 LEU cc_start: 0.6734 (mt) cc_final: 0.6171 (mp) REVERT: A 273 PHE cc_start: 0.5294 (m-80) cc_final: 0.4898 (m-80) REVERT: B 42 THR cc_start: 0.3740 (OUTLIER) cc_final: 0.3489 (p) REVERT: B 78 SER cc_start: 0.7816 (t) cc_final: 0.7528 (p) REVERT: B 272 ARG cc_start: 0.5733 (mtm110) cc_final: 0.5488 (ttp-170) REVERT: B 292 ASN cc_start: 0.8278 (t160) cc_final: 0.7901 (t0) REVERT: B 354 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6605 (m-80) REVERT: B 361 ARG cc_start: 0.6878 (ptp-170) cc_final: 0.6505 (ptp-170) REVERT: B 364 GLN cc_start: 0.5805 (mt0) cc_final: 0.5095 (mt0) REVERT: C 217 MET cc_start: 0.7895 (tpp) cc_final: 0.7476 (tpp) REVERT: D 67 SER cc_start: 0.8350 (p) cc_final: 0.7730 (t) REVERT: D 114 MET cc_start: 0.6427 (tmm) cc_final: 0.6073 (tmm) REVERT: D 115 GLU cc_start: 0.4792 (OUTLIER) cc_final: 0.4340 (mp0) REVERT: E 59 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7445 (mp) REVERT: E 96 ASP cc_start: 0.6796 (m-30) cc_final: 0.6097 (m-30) REVERT: E 147 ASP cc_start: 0.5895 (t0) cc_final: 0.5451 (m-30) REVERT: E 223 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: E 270 THR cc_start: 0.7797 (p) cc_final: 0.7436 (t) REVERT: F 217 MET cc_start: 0.7703 (tpt) cc_final: 0.7456 (tpt) REVERT: F 335 MET cc_start: 0.7254 (mmp) cc_final: 0.6988 (mmt) REVERT: G 43 ASN cc_start: 0.6844 (m-40) cc_final: 0.6183 (p0) REVERT: G 158 MET cc_start: 0.6774 (mtm) cc_final: 0.6539 (mtm) REVERT: G 169 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7275 (mt-10) REVERT: H 67 SER cc_start: 0.7877 (p) cc_final: 0.7610 (t) REVERT: H 154 ARG cc_start: 0.6113 (mmt-90) cc_final: 0.5484 (tpp-160) REVERT: H 217 MET cc_start: 0.7718 (tpt) cc_final: 0.7256 (tpp) REVERT: H 270 THR cc_start: 0.8034 (p) cc_final: 0.7584 (p) REVERT: I 153 LEU cc_start: 0.6318 (mt) cc_final: 0.5988 (tp) REVERT: I 279 TYR cc_start: 0.6384 (m-80) cc_final: 0.5986 (m-80) REVERT: I 335 MET cc_start: 0.7129 (mmp) cc_final: 0.6876 (mmp) REVERT: J 114 MET cc_start: 0.4858 (ppp) cc_final: 0.4026 (ttp) REVERT: J 131 ILE cc_start: 0.6520 (mm) cc_final: 0.6245 (mt) REVERT: J 217 MET cc_start: 0.8475 (tpt) cc_final: 0.8149 (tpt) REVERT: J 221 LEU cc_start: 0.7704 (mt) cc_final: 0.7494 (mt) REVERT: J 276 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: J 329 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7540 (mp) REVERT: J 355 LEU cc_start: 0.8270 (pt) cc_final: 0.7717 (tt) REVERT: K 103 ASP cc_start: 0.5364 (t0) cc_final: 0.4386 (p0) REVERT: K 147 ASP cc_start: 0.5909 (t0) cc_final: 0.5272 (m-30) REVERT: K 156 THR cc_start: 0.4223 (OUTLIER) cc_final: 0.3909 (p) REVERT: L 5 PHE cc_start: 0.6675 (m-80) cc_final: 0.6348 (m-80) REVERT: L 197 TYR cc_start: 0.6551 (m-80) cc_final: 0.6273 (m-80) REVERT: L 282 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6769 (pp) REVERT: L 310 TYR cc_start: 0.7788 (m-80) cc_final: 0.7366 (m-10) REVERT: M 80 TYR cc_start: 0.5146 (m-10) cc_final: 0.4653 (m-80) REVERT: M 158 MET cc_start: 0.6473 (mtm) cc_final: 0.5554 (tpt) REVERT: M 178 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7040 (mmtt) REVERT: M 181 THR cc_start: 0.7701 (OUTLIER) cc_final: 0.7454 (t) REVERT: M 196 LYS cc_start: 0.5467 (OUTLIER) cc_final: 0.5187 (tptm) outliers start: 133 outliers final: 81 residues processed: 835 average time/residue: 0.2406 time to fit residues: 328.6016 Evaluate side-chains 781 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 686 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 311 MET Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 301 TYR Chi-restraints excluded: chain F residue 311 MET Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 276 GLU Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 251 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 196 LYS Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 394 optimal weight: 9.9990 chunk 14 optimal weight: 0.1980 chunk 305 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 chunk 271 optimal weight: 0.0770 chunk 212 optimal weight: 0.9990 chunk 367 optimal weight: 0.9980 chunk 215 optimal weight: 0.2980 chunk 220 optimal weight: 0.9980 chunk 446 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN C 285 ASN C 292 ASN E 171 GLN E 285 ASN E 292 ASN F 93 ASN G 93 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN H 211 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN K 171 GLN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 ASN M 93 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.159272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.134522 restraints weight = 70959.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.134700 restraints weight = 57094.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.135555 restraints weight = 45555.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.136025 restraints weight = 34962.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136149 restraints weight = 31841.106| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 41016 Z= 0.126 Angle : 0.609 10.655 55861 Z= 0.317 Chirality : 0.041 0.264 6549 Planarity : 0.004 0.066 6897 Dihedral : 10.394 88.524 6812 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.88 % Allowed : 19.73 % Favored : 77.39 % 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: 0.19 (0.12), residues: 5088 helix: 0.65 (0.09), residues: 3041 sheet: -0.60 (0.36), residues: 182 loop : -0.54 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 20 TYR 0.043 0.002 TYR J 80 PHE 0.033 0.001 PHE J 54 TRP 0.017 0.001 TRP B 331 Details of bonding type rmsd covalent geometry : bond 0.00267 (41016) covalent geometry : angle 0.60895 (55861) hydrogen bonds : bond 0.04005 ( 2201) hydrogen bonds : angle 4.37698 ( 6300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 785 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.4635 (OUTLIER) cc_final: 0.4161 (tt0) REVERT: A 109 ASN cc_start: 0.6136 (p0) cc_final: 0.5776 (p0) REVERT: A 231 MET cc_start: 0.6534 (mmp) cc_final: 0.5941 (mmm) REVERT: A 273 PHE cc_start: 0.5254 (m-80) cc_final: 0.4890 (m-80) REVERT: B 42 THR cc_start: 0.3624 (OUTLIER) cc_final: 0.3384 (p) REVERT: B 78 SER cc_start: 0.7585 (t) cc_final: 0.7307 (p) REVERT: B 292 ASN cc_start: 0.8218 (t160) cc_final: 0.7861 (t0) REVERT: B 354 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.6525 (m-80) REVERT: B 364 GLN cc_start: 0.5510 (mt0) cc_final: 0.5243 (mt0) REVERT: C 217 MET cc_start: 0.7807 (tpp) cc_final: 0.7203 (tpt) REVERT: D 67 SER cc_start: 0.8254 (p) cc_final: 0.7647 (t) REVERT: D 114 MET cc_start: 0.6066 (tmm) cc_final: 0.5858 (tmm) REVERT: D 115 GLU cc_start: 0.4716 (OUTLIER) cc_final: 0.4481 (mp0) REVERT: D 155 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7175 (mt) REVERT: D 217 MET cc_start: 0.7239 (tpt) cc_final: 0.7002 (tpt) REVERT: E 59 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7488 (mp) REVERT: E 96 ASP cc_start: 0.6641 (m-30) cc_final: 0.6061 (m-30) REVERT: E 223 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: E 270 THR cc_start: 0.7890 (p) cc_final: 0.7491 (t) REVERT: E 362 LEU cc_start: 0.7584 (tp) cc_final: 0.7171 (mp) REVERT: F 261 GLU cc_start: 0.6856 (pp20) cc_final: 0.6654 (pp20) REVERT: G 43 ASN cc_start: 0.6814 (m-40) cc_final: 0.6223 (p0) REVERT: G 169 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7125 (mt-10) REVERT: G 188 GLU cc_start: 0.6362 (tt0) cc_final: 0.6119 (tt0) REVERT: H 154 ARG cc_start: 0.6202 (mmt-90) cc_final: 0.5671 (tpp-160) REVERT: H 217 MET cc_start: 0.7773 (tpt) cc_final: 0.7320 (tpp) REVERT: H 270 THR cc_start: 0.8013 (p) cc_final: 0.7803 (p) REVERT: I 153 LEU cc_start: 0.6612 (mt) cc_final: 0.6398 (tp) REVERT: I 279 TYR cc_start: 0.6187 (m-80) cc_final: 0.5973 (m-10) REVERT: J 114 MET cc_start: 0.4688 (ppp) cc_final: 0.3951 (ttp) REVERT: J 131 ILE cc_start: 0.6546 (mm) cc_final: 0.6315 (mt) REVERT: J 217 MET cc_start: 0.8456 (tpt) cc_final: 0.8065 (tpt) REVERT: J 276 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6467 (mt-10) REVERT: J 329 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7594 (mp) REVERT: J 335 MET cc_start: 0.7686 (mmp) cc_final: 0.7395 (mmp) REVERT: J 355 LEU cc_start: 0.8273 (pt) cc_final: 0.7848 (tt) REVERT: K 103 ASP cc_start: 0.5590 (t0) cc_final: 0.4328 (p0) REVERT: K 147 ASP cc_start: 0.5820 (t0) cc_final: 0.5155 (m-30) REVERT: K 156 THR cc_start: 0.4244 (OUTLIER) cc_final: 0.3966 (p) REVERT: L 5 PHE cc_start: 0.6459 (m-80) cc_final: 0.6159 (m-80) REVERT: L 50 GLU cc_start: 0.6545 (tt0) cc_final: 0.5744 (tt0) REVERT: L 284 LEU cc_start: 0.4770 (mm) cc_final: 0.4540 (mp) REVERT: L 310 TYR cc_start: 0.7671 (m-80) cc_final: 0.7244 (m-10) REVERT: M 157 ASP cc_start: 0.6052 (t0) cc_final: 0.5709 (m-30) REVERT: M 158 MET cc_start: 0.6296 (mtm) cc_final: 0.5370 (tpt) REVERT: M 178 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6941 (mmtt) REVERT: M 181 THR cc_start: 0.7709 (p) cc_final: 0.7483 (t) REVERT: M 342 ASP cc_start: 0.7173 (t0) cc_final: 0.6793 (t0) outliers start: 112 outliers final: 54 residues processed: 854 average time/residue: 0.2509 time to fit residues: 349.7561 Evaluate side-chains 768 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 703 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 301 TYR Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 276 GLU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 204 ASN Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 254 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 297 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 494 optimal weight: 0.3980 chunk 189 optimal weight: 0.7980 chunk 287 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 318 optimal weight: 0.7980 chunk 276 optimal weight: 0.9990 chunk 477 optimal weight: 6.9990 chunk 290 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN E 171 GLN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN H 211 GLN I 288 GLN J 15 GLN K 15 GLN K 93 ASN K 212 GLN K 257 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 ASN M 93 ASN M 288 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.159795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.135469 restraints weight = 71101.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.135135 restraints weight = 51444.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.136425 restraints weight = 46640.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.136752 restraints weight = 33862.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.136886 restraints weight = 33338.314| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41016 Z= 0.125 Angle : 0.613 11.730 55861 Z= 0.319 Chirality : 0.041 0.270 6549 Planarity : 0.004 0.074 6897 Dihedral : 10.274 89.140 6812 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.52 % Allowed : 20.58 % Favored : 76.90 % 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: 0.28 (0.12), residues: 5088 helix: 0.72 (0.09), residues: 3055 sheet: -0.53 (0.37), residues: 182 loop : -0.48 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 20 TYR 0.053 0.002 TYR K 80 PHE 0.045 0.001 PHE J 273 TRP 0.023 0.001 TRP B 331 Details of bonding type rmsd covalent geometry : bond 0.00271 (41016) covalent geometry : angle 0.61257 (55861) hydrogen bonds : bond 0.03985 ( 2201) hydrogen bonds : angle 4.39757 ( 6300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 772 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ILE cc_start: 0.3896 (OUTLIER) cc_final: 0.3587 (tp) REVERT: A 6 GLU cc_start: 0.4686 (OUTLIER) cc_final: 0.4275 (tt0) REVERT: A 190 GLU cc_start: 0.6494 (mt-10) cc_final: 0.5770 (mp0) REVERT: A 273 PHE cc_start: 0.5290 (m-80) cc_final: 0.4880 (m-80) REVERT: B 42 THR cc_start: 0.3659 (OUTLIER) cc_final: 0.3393 (p) REVERT: B 78 SER cc_start: 0.7367 (t) cc_final: 0.7144 (p) REVERT: B 292 ASN cc_start: 0.8184 (t160) cc_final: 0.7816 (t0) REVERT: B 354 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.6558 (m-80) REVERT: B 364 GLN cc_start: 0.5554 (mt0) cc_final: 0.5213 (mt0) REVERT: C 217 MET cc_start: 0.7917 (tpp) cc_final: 0.7125 (tpt) REVERT: C 221 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6819 (mt) REVERT: D 5 PHE cc_start: 0.5471 (m-80) cc_final: 0.5014 (m-80) REVERT: D 155 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7220 (mt) REVERT: E 59 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7398 (mp) REVERT: E 96 ASP cc_start: 0.6691 (m-30) cc_final: 0.6336 (m-30) REVERT: E 223 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: E 250 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7137 (mm-30) REVERT: E 270 THR cc_start: 0.8008 (p) cc_final: 0.7608 (t) REVERT: E 362 LEU cc_start: 0.7488 (tp) cc_final: 0.7032 (mp) REVERT: F 78 SER cc_start: 0.7383 (t) cc_final: 0.6938 (p) REVERT: G 43 ASN cc_start: 0.6566 (m-40) cc_final: 0.6167 (p0) REVERT: G 157 ASP cc_start: 0.6062 (p0) cc_final: 0.4854 (m-30) REVERT: G 169 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7106 (mt-10) REVERT: H 154 ARG cc_start: 0.6115 (mmt-90) cc_final: 0.5620 (tpp-160) REVERT: H 217 MET cc_start: 0.7780 (tpt) cc_final: 0.7292 (tpp) REVERT: H 335 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7055 (mmm) REVERT: I 137 ASP cc_start: 0.7470 (m-30) cc_final: 0.7207 (p0) REVERT: I 279 TYR cc_start: 0.6143 (m-80) cc_final: 0.5876 (m-10) REVERT: I 358 MET cc_start: 0.6142 (mpp) cc_final: 0.5854 (mpp) REVERT: J 114 MET cc_start: 0.4595 (ppp) cc_final: 0.3914 (ttp) REVERT: J 217 MET cc_start: 0.8578 (tpt) cc_final: 0.8205 (tpt) REVERT: J 276 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6781 (mt-10) REVERT: J 335 MET cc_start: 0.7887 (mmp) cc_final: 0.7514 (mmp) REVERT: J 355 LEU cc_start: 0.8255 (pt) cc_final: 0.7828 (tt) REVERT: K 93 ASN cc_start: 0.7096 (OUTLIER) cc_final: 0.6844 (t0) REVERT: K 147 ASP cc_start: 0.5804 (t0) cc_final: 0.5156 (m-30) REVERT: K 156 THR cc_start: 0.4228 (OUTLIER) cc_final: 0.3966 (p) REVERT: L 5 PHE cc_start: 0.6370 (m-80) cc_final: 0.6084 (m-80) REVERT: L 310 TYR cc_start: 0.7537 (m-80) cc_final: 0.7227 (m-10) REVERT: M 157 ASP cc_start: 0.5873 (t0) cc_final: 0.5563 (m-30) REVERT: M 158 MET cc_start: 0.6185 (mtm) cc_final: 0.5652 (tpt) REVERT: M 178 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7056 (mmtt) REVERT: M 181 THR cc_start: 0.7753 (p) cc_final: 0.7488 (t) outliers start: 98 outliers final: 48 residues processed: 837 average time/residue: 0.2555 time to fit residues: 348.4850 Evaluate side-chains 763 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 702 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 335 MET Chi-restraints excluded: chain H residue 345 MET Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 276 GLU Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 103 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 349 optimal weight: 50.0000 chunk 400 optimal weight: 0.6980 chunk 1 optimal weight: 0.0970 chunk 168 optimal weight: 1.9990 chunk 352 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 403 optimal weight: 3.9990 chunk 481 optimal weight: 5.9990 chunk 485 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN C 285 ASN E 171 GLN E 292 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN I 109 ASN J 15 GLN K 15 GLN K 93 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 257 ASN M 93 ASN ** M 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.158351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.133783 restraints weight = 71146.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.133903 restraints weight = 53998.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.135223 restraints weight = 48487.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.135244 restraints weight = 34707.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.135473 restraints weight = 33630.204| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 41016 Z= 0.149 Angle : 0.637 13.208 55861 Z= 0.329 Chirality : 0.042 0.296 6549 Planarity : 0.004 0.061 6897 Dihedral : 10.278 89.660 6812 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.32 % Allowed : 21.51 % Favored : 76.18 % 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: 0.28 (0.12), residues: 5088 helix: 0.72 (0.09), residues: 3064 sheet: -0.49 (0.38), residues: 182 loop : -0.52 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 272 TYR 0.046 0.002 TYR E 80 PHE 0.035 0.002 PHE J 54 TRP 0.024 0.001 TRP B 331 Details of bonding type rmsd covalent geometry : bond 0.00342 (41016) covalent geometry : angle 0.63692 (55861) hydrogen bonds : bond 0.04089 ( 2201) hydrogen bonds : angle 4.45883 ( 6300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 719 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 PHE cc_start: 0.5216 (m-80) cc_final: 0.4825 (m-80) REVERT: B 42 THR cc_start: 0.3641 (OUTLIER) cc_final: 0.3376 (p) REVERT: B 292 ASN cc_start: 0.8220 (t160) cc_final: 0.7850 (t0) REVERT: B 364 GLN cc_start: 0.5587 (mt0) cc_final: 0.5312 (mt0) REVERT: D 67 SER cc_start: 0.8248 (p) cc_final: 0.7631 (t) REVERT: D 103 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6192 (p0) REVERT: D 155 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7198 (mt) REVERT: E 59 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7546 (mp) REVERT: E 114 MET cc_start: 0.6076 (tmm) cc_final: 0.5759 (tmm) REVERT: E 223 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: E 250 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7136 (mm-30) REVERT: E 270 THR cc_start: 0.7848 (p) cc_final: 0.7458 (t) REVERT: E 362 LEU cc_start: 0.7517 (tp) cc_final: 0.7098 (mp) REVERT: G 43 ASN cc_start: 0.6597 (m-40) cc_final: 0.6157 (p0) REVERT: G 157 ASP cc_start: 0.6197 (p0) cc_final: 0.4928 (m-30) REVERT: G 169 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7129 (mt-10) REVERT: H 154 ARG cc_start: 0.6012 (mmt-90) cc_final: 0.5499 (tpp-160) REVERT: H 217 MET cc_start: 0.7701 (tpt) cc_final: 0.7198 (tpp) REVERT: H 335 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7140 (mmm) REVERT: I 233 GLU cc_start: 0.7045 (tp30) cc_final: 0.6606 (tp30) REVERT: I 279 TYR cc_start: 0.6253 (m-80) cc_final: 0.5798 (m-80) REVERT: J 114 MET cc_start: 0.4487 (ppp) cc_final: 0.3971 (ttp) REVERT: J 169 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7064 (mt-10) REVERT: J 217 MET cc_start: 0.8549 (tpt) cc_final: 0.8175 (tpt) REVERT: J 276 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6490 (mt-10) REVERT: J 355 LEU cc_start: 0.8336 (pt) cc_final: 0.7888 (tt) REVERT: K 93 ASN cc_start: 0.7127 (OUTLIER) cc_final: 0.6745 (t0) REVERT: K 147 ASP cc_start: 0.5773 (t0) cc_final: 0.5096 (m-30) REVERT: K 156 THR cc_start: 0.4283 (OUTLIER) cc_final: 0.3977 (p) REVERT: L 5 PHE cc_start: 0.6596 (m-80) cc_final: 0.6237 (m-80) REVERT: L 288 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7669 (tp40) REVERT: L 310 TYR cc_start: 0.7565 (m-80) cc_final: 0.7246 (m-10) REVERT: L 335 MET cc_start: 0.7554 (mmp) cc_final: 0.7294 (mmt) REVERT: M 5 PHE cc_start: 0.6126 (m-80) cc_final: 0.5802 (m-10) REVERT: M 129 MET cc_start: 0.6453 (mmm) cc_final: 0.6099 (tpp) REVERT: M 133 LYS cc_start: 0.7521 (mmtm) cc_final: 0.7090 (mmtt) REVERT: M 158 MET cc_start: 0.6221 (mtm) cc_final: 0.5652 (tpt) REVERT: M 178 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7222 (mmtt) REVERT: M 235 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7283 (tp) outliers start: 90 outliers final: 56 residues processed: 778 average time/residue: 0.2409 time to fit residues: 305.6195 Evaluate side-chains 747 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 680 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 335 MET Chi-restraints excluded: chain H residue 345 MET Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 276 GLU Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 201 optimal weight: 0.0870 chunk 99 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 375 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 307 optimal weight: 0.0570 chunk 176 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN E 171 GLN E 292 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.161071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.136905 restraints weight = 71212.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.137780 restraints weight = 55016.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.138860 restraints weight = 47937.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.138910 restraints weight = 33141.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.139048 restraints weight = 31157.404| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41016 Z= 0.124 Angle : 0.625 15.610 55861 Z= 0.322 Chirality : 0.041 0.264 6549 Planarity : 0.004 0.073 6897 Dihedral : 10.208 87.546 6812 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.80 % Allowed : 22.25 % Favored : 75.95 % 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: 0.37 (0.12), residues: 5088 helix: 0.78 (0.09), residues: 3078 sheet: -0.51 (0.39), residues: 182 loop : -0.44 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 154 TYR 0.039 0.002 TYR E 80 PHE 0.043 0.001 PHE J 54 TRP 0.028 0.001 TRP B 331 Details of bonding type rmsd covalent geometry : bond 0.00267 (41016) covalent geometry : angle 0.62547 (55861) hydrogen bonds : bond 0.03872 ( 2201) hydrogen bonds : angle 4.36518 ( 6300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 746 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.4604 (OUTLIER) cc_final: 0.4197 (tt0) REVERT: A 223 GLN cc_start: 0.6917 (pt0) cc_final: 0.6317 (pt0) REVERT: A 273 PHE cc_start: 0.5181 (m-80) cc_final: 0.4737 (m-80) REVERT: B 42 THR cc_start: 0.3596 (OUTLIER) cc_final: 0.3371 (p) REVERT: B 292 ASN cc_start: 0.8105 (t160) cc_final: 0.7729 (t0) REVERT: B 364 GLN cc_start: 0.5580 (mt0) cc_final: 0.5375 (mt0) REVERT: C 217 MET cc_start: 0.7671 (tpp) cc_final: 0.6943 (tpt) REVERT: D 103 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.5998 (p0) REVERT: D 155 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7219 (mt) REVERT: D 284 LEU cc_start: 0.5658 (mt) cc_final: 0.4873 (mp) REVERT: E 59 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7476 (mp) REVERT: E 114 MET cc_start: 0.6001 (tmm) cc_final: 0.5775 (tmm) REVERT: E 223 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7272 (tm130) REVERT: E 250 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6900 (mm-30) REVERT: E 270 THR cc_start: 0.7820 (p) cc_final: 0.7439 (t) REVERT: F 78 SER cc_start: 0.7367 (t) cc_final: 0.6827 (p) REVERT: F 93 ASN cc_start: 0.6238 (t0) cc_final: 0.5739 (t0) REVERT: F 273 PHE cc_start: 0.6752 (m-80) cc_final: 0.6328 (m-10) REVERT: G 43 ASN cc_start: 0.6519 (m-40) cc_final: 0.6145 (p0) REVERT: G 157 ASP cc_start: 0.6125 (p0) cc_final: 0.4647 (m-30) REVERT: G 169 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7025 (mt-10) REVERT: H 154 ARG cc_start: 0.5993 (mmt-90) cc_final: 0.5518 (tpp-160) REVERT: H 217 MET cc_start: 0.7880 (tpt) cc_final: 0.7361 (tpp) REVERT: I 279 TYR cc_start: 0.6110 (m-80) cc_final: 0.5830 (m-10) REVERT: J 17 LYS cc_start: 0.7782 (pttm) cc_final: 0.7397 (ptpp) REVERT: J 114 MET cc_start: 0.4465 (ppp) cc_final: 0.4021 (ttp) REVERT: J 217 MET cc_start: 0.8425 (tpt) cc_final: 0.8214 (tpt) REVERT: J 276 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6473 (mt-10) REVERT: J 355 LEU cc_start: 0.8262 (pt) cc_final: 0.7858 (tt) REVERT: K 147 ASP cc_start: 0.5836 (t0) cc_final: 0.5257 (m-30) REVERT: K 156 THR cc_start: 0.4252 (OUTLIER) cc_final: 0.3957 (p) REVERT: L 5 PHE cc_start: 0.6549 (m-80) cc_final: 0.6109 (m-80) REVERT: L 288 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7606 (tp40) REVERT: L 310 TYR cc_start: 0.7452 (m-80) cc_final: 0.7063 (m-80) REVERT: L 335 MET cc_start: 0.7507 (mmp) cc_final: 0.7245 (mmt) REVERT: M 83 ARG cc_start: 0.7283 (mmm160) cc_final: 0.6931 (ptt-90) REVERT: M 129 MET cc_start: 0.6482 (mmm) cc_final: 0.5894 (mmm) REVERT: M 137 ASP cc_start: 0.6964 (t70) cc_final: 0.6738 (p0) REVERT: M 157 ASP cc_start: 0.5981 (t0) cc_final: 0.5608 (m-30) REVERT: M 158 MET cc_start: 0.6159 (mtm) cc_final: 0.5698 (tpt) REVERT: M 178 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7059 (mmtt) REVERT: M 181 THR cc_start: 0.7760 (p) cc_final: 0.7509 (t) outliers start: 70 outliers final: 47 residues processed: 791 average time/residue: 0.2379 time to fit residues: 307.2394 Evaluate side-chains 747 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 691 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 345 MET Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 276 GLU Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 393 optimal weight: 0.0970 chunk 175 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 328 optimal weight: 7.9990 chunk 294 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 391 optimal weight: 0.5980 chunk 266 optimal weight: 0.6980 chunk 317 optimal weight: 30.0000 chunk 408 optimal weight: 6.9990 chunk 390 optimal weight: 0.9980 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 285 ASN E 171 GLN F 15 GLN F 223 GLN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN I 212 GLN ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN ** L 200 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 = 0.4270 r_free = 0.4270 target = 0.160377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.136353 restraints weight = 70955.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.136722 restraints weight = 53874.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.138004 restraints weight = 48279.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.138066 restraints weight = 33271.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.138312 restraints weight = 32311.570| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41016 Z= 0.130 Angle : 0.632 19.237 55861 Z= 0.326 Chirality : 0.041 0.268 6549 Planarity : 0.004 0.067 6897 Dihedral : 10.178 88.500 6812 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.80 % Allowed : 22.46 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.12), residues: 5088 helix: 0.81 (0.09), residues: 3066 sheet: -0.49 (0.39), residues: 178 loop : -0.47 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 149 TYR 0.049 0.002 TYR J 80 PHE 0.042 0.001 PHE J 54 TRP 0.034 0.001 TRP B 331 Details of bonding type rmsd covalent geometry : bond 0.00290 (41016) covalent geometry : angle 0.63230 (55861) hydrogen bonds : bond 0.03914 ( 2201) hydrogen bonds : angle 4.38351 ( 6300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 713 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.4486 (OUTLIER) cc_final: 0.4068 (tt0) REVERT: A 223 GLN cc_start: 0.6921 (pt0) cc_final: 0.6316 (pt0) REVERT: A 273 PHE cc_start: 0.5075 (m-80) cc_final: 0.4613 (m-80) REVERT: B 42 THR cc_start: 0.3580 (OUTLIER) cc_final: 0.3358 (p) REVERT: B 292 ASN cc_start: 0.8103 (t160) cc_final: 0.7744 (t0) REVERT: B 364 GLN cc_start: 0.5619 (mt0) cc_final: 0.5399 (mt0) REVERT: C 217 MET cc_start: 0.7715 (tpp) cc_final: 0.6990 (tpt) REVERT: D 103 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.5920 (p0) REVERT: D 155 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7410 (mt) REVERT: E 59 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7451 (mp) REVERT: E 66 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7236 (mm-30) REVERT: E 96 ASP cc_start: 0.6613 (m-30) cc_final: 0.6405 (m-30) REVERT: E 114 MET cc_start: 0.6074 (tmm) cc_final: 0.5865 (tmm) REVERT: E 223 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7340 (tm130) REVERT: E 362 LEU cc_start: 0.7729 (tp) cc_final: 0.7170 (mp) REVERT: F 78 SER cc_start: 0.7344 (t) cc_final: 0.6801 (p) REVERT: F 93 ASN cc_start: 0.6420 (t0) cc_final: 0.6149 (t0) REVERT: F 273 PHE cc_start: 0.6683 (m-80) cc_final: 0.6321 (m-10) REVERT: G 43 ASN cc_start: 0.6384 (m-40) cc_final: 0.6147 (p0) REVERT: G 157 ASP cc_start: 0.6176 (p0) cc_final: 0.4684 (m-30) REVERT: G 169 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7060 (mt-10) REVERT: H 67 SER cc_start: 0.7897 (p) cc_final: 0.7618 (t) REVERT: H 154 ARG cc_start: 0.5913 (mmt-90) cc_final: 0.5442 (tpp-160) REVERT: H 217 MET cc_start: 0.7873 (tpt) cc_final: 0.7383 (tpp) REVERT: I 279 TYR cc_start: 0.6116 (m-80) cc_final: 0.5831 (m-10) REVERT: J 17 LYS cc_start: 0.7740 (pttm) cc_final: 0.7320 (ptpp) REVERT: J 114 MET cc_start: 0.4481 (ppp) cc_final: 0.4147 (ttp) REVERT: J 131 ILE cc_start: 0.6461 (mm) cc_final: 0.6091 (mt) REVERT: J 217 MET cc_start: 0.8526 (tpt) cc_final: 0.8175 (tpt) REVERT: J 355 LEU cc_start: 0.8253 (pt) cc_final: 0.7790 (tt) REVERT: K 147 ASP cc_start: 0.5962 (t0) cc_final: 0.5376 (m-30) REVERT: K 156 THR cc_start: 0.4248 (OUTLIER) cc_final: 0.3977 (p) REVERT: K 361 ARG cc_start: 0.7144 (mtm110) cc_final: 0.6943 (ptt-90) REVERT: L 158 MET cc_start: 0.6007 (mtt) cc_final: 0.5261 (ttm) REVERT: L 288 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7568 (tp40) REVERT: L 310 TYR cc_start: 0.7486 (m-80) cc_final: 0.7102 (m-80) REVERT: L 335 MET cc_start: 0.7544 (mmp) cc_final: 0.7271 (mmt) REVERT: M 83 ARG cc_start: 0.7316 (mmm160) cc_final: 0.6946 (ptt-90) REVERT: M 157 ASP cc_start: 0.5962 (t0) cc_final: 0.5584 (m-30) REVERT: M 158 MET cc_start: 0.6197 (mtm) cc_final: 0.5792 (tpt) REVERT: M 178 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7029 (mmtt) REVERT: M 181 THR cc_start: 0.7774 (p) cc_final: 0.7536 (t) outliers start: 70 outliers final: 49 residues processed: 757 average time/residue: 0.2482 time to fit residues: 306.4179 Evaluate side-chains 742 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 685 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 355 LEU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 345 MET Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 212 GLN Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 294 ILE Chi-restraints excluded: chain J residue 335 MET Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 252 ILE Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 506 optimal weight: 20.0000 chunk 14 optimal weight: 0.0870 chunk 28 optimal weight: 0.0980 chunk 125 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 314 optimal weight: 8.9990 chunk 326 optimal weight: 1.9990 chunk 259 optimal weight: 0.3980 chunk 471 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 294 optimal weight: 6.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 364 GLN E 171 GLN F 15 GLN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN M 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.158574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.133315 restraints weight = 71716.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.133912 restraints weight = 48558.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.135222 restraints weight = 41676.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.135243 restraints weight = 29614.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.135432 restraints weight = 28827.685| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41016 Z= 0.126 Angle : 0.640 17.825 55861 Z= 0.328 Chirality : 0.041 0.263 6549 Planarity : 0.004 0.064 6897 Dihedral : 10.144 88.630 6812 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.60 % Allowed : 23.08 % Favored : 75.33 % 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: 0.42 (0.12), residues: 5088 helix: 0.83 (0.09), residues: 3067 sheet: -0.51 (0.39), residues: 178 loop : -0.43 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 149 TYR 0.054 0.002 TYR K 80 PHE 0.059 0.001 PHE D 54 TRP 0.035 0.001 TRP B 331 Details of bonding type rmsd covalent geometry : bond 0.00276 (41016) covalent geometry : angle 0.63986 (55861) hydrogen bonds : bond 0.03827 ( 2201) hydrogen bonds : angle 4.36625 ( 6300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8059.88 seconds wall clock time: 139 minutes 34.13 seconds (8374.13 seconds total)