Starting phenix.real_space_refine on Tue Sep 15 13:08:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nt5_12581/09_2026/7nt5_12581.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nt5_12581/09_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_12581/09_2026/7nt5_12581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nt5_12581/09_2026/7nt5_12581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nt5_12581/09_2026/7nt5_12581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nt5_12581/09_2026/7nt5_12581.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nt5_12581/09_2026/7nt5_12581.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nt5_12581/09_2026/7nt5_12581.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 78} Modifications used: {'rna2p_pyr': 14, 'rna3p_pyr': 63} Link IDs: {'rna2p': 14, 'rna3p': 63} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.23, per 1000 atoms: 0.20 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: 3.35 Conformation dependent library (CDL) restraints added in 1.7 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: 4.69 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: 7.81 Time building geometry restraints manager: 4.48 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=" O3' U N 35 " pdb=" P U N 36 " ideal model delta sigma weight residual 1.607 1.692 -0.085 1.20e-02 6.94e+03 5.07e+01 bond pdb=" O3' U N 41 " pdb=" P U N 42 " ideal model delta sigma weight residual 1.607 1.691 -0.084 1.20e-02 6.94e+03 4.95e+01 bond pdb=" O3' U N 25 " pdb=" P U N 26 " ideal model delta sigma weight residual 1.607 1.524 0.083 1.20e-02 6.94e+03 4.80e+01 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 ... (remaining 41011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 50973 3.72 - 7.44: 4428 7.44 - 11.15: 388 11.15 - 14.87: 63 14.87 - 18.59: 9 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=" NE ARG M 343 " pdb=" CZ ARG M 343 " pdb=" NH1 ARG M 343 " ideal model delta sigma weight residual 121.50 129.96 -8.46 1.00e+00 1.00e+00 7.15e+01 angle pdb=" C PRO C 309 " pdb=" CA PRO C 309 " pdb=" CB PRO C 309 " ideal model delta sigma weight residual 111.21 97.42 13.79 1.71e+00 3.42e-01 6.50e+01 ... (remaining 55856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 22036 17.99 - 35.98: 2140 35.98 - 53.97: 477 53.97 - 71.96: 107 71.96 - 89.96: 55 Dihedral angle restraints: 24815 sinusoidal: 10031 harmonic: 14784 Sorted by residual: dihedral pdb=" C4' U N 27 " pdb=" C3' U N 27 " pdb=" C2' U N 27 " pdb=" C1' U N 27 " ideal model delta sinusoidal sigma weight residual 36.35 -44.70 81.05 1 3.10e+00 1.04e-01 8.44e+02 dihedral pdb=" C4' U N 57 " pdb=" C3' U N 57 " pdb=" C2' U N 57 " pdb=" C1' U N 57 " ideal model delta sinusoidal sigma weight residual 36.35 -43.99 80.34 1 3.10e+00 1.04e-01 8.31e+02 dihedral pdb=" C4' U N 51 " pdb=" C3' U N 51 " pdb=" C2' U N 51 " pdb=" C1' U N 51 " ideal model delta sinusoidal sigma weight residual 36.34 -43.37 79.72 1 3.10e+00 1.04e-01 8.21e+02 ... (remaining 24812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 4939 0.180 - 0.360: 1371 0.360 - 0.541: 201 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 38.120 Find NCS groups from input model: 1.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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= 0.794 Angle : 2.209 18.592 55861 Z= 1.384 Chirality : 0.166 0.901 6549 Planarity : 0.014 0.102 6897 Dihedral : 15.815 89.956 15277 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/Z covalent geometry : bond 0.01300 / 0.79 (41016) covalent geometry : angle 2.20933 / 1.38 (55861) hydrogen bonds : bond 0.16282 / 10.99 ( 2201) hydrogen bonds : angle 6.77994 / 4.82 ( 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 : 1.664 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: 0.2715 time to fit residues: 576.4501 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 : 1.396 ------------------------------------------------------------------------------- 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... A 319 GLN B 15 GLN B 109 ASN B 292 ASN C 171 GLN C 292 ASN C 319 GLN D 93 ASN 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 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.157776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.132800 restraints weight = 71116.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.133089 restraints weight = 51335.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.134558 restraints weight = 44525.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.134436 restraints weight = 31043.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.134684 restraints weight = 31050.922| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 41016 Z= 0.172 Angle : 0.857 21.082 55861 Z= 0.406 Chirality : 0.066 1.239 6549 Planarity : 0.005 0.051 6897 Dihedral : 9.338 131.532 6536 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.52 % Allowed : 13.71 % Favored : 83.77 % 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: -0.56 (0.11), residues: 5088 helix: 0.05 (0.09), residues: 3073 sheet: -0.96 (0.32), residues: 186 loop : -0.83 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 60 TYR 0.034 0.002 TYR E 301 PHE 0.036 0.002 PHE M 207 TRP 0.020 0.002 TRP D 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (41016) covalent geometry : angle 0.85692 / 0.41 (55861) hydrogen bonds : bond 0.05349 / 3.60 ( 2201) hydrogen bonds : angle 4.83427 / 3.47 ( 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 : 1.367 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 190 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6311 (mt-10) REVERT: A 217 MET cc_start: 0.7584 (tpp) cc_final: 0.7199 (tpt) REVERT: A 231 MET cc_start: 0.6638 (mmp) cc_final: 0.5774 (mmm) REVERT: A 273 PHE cc_start: 0.5600 (m-80) cc_final: 0.5187 (m-80) REVERT: A 313 LEU cc_start: 0.7282 (tp) cc_final: 0.7013 (mt) REVERT: B 78 SER cc_start: 0.7973 (t) cc_final: 0.7476 (p) REVERT: B 80 TYR cc_start: 0.4816 (m-10) cc_final: 0.4479 (m-80) REVERT: B 125 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5975 (ptp) REVERT: B 273 PHE cc_start: 0.7021 (m-80) cc_final: 0.6715 (m-80) REVERT: B 331 TRP cc_start: 0.7205 (t60) cc_final: 0.6994 (t60) REVERT: B 364 GLN cc_start: 0.5739 (mt0) cc_final: 0.5513 (mt0) REVERT: C 140 LYS cc_start: 0.5527 (mtmm) cc_final: 0.5129 (ptpp) REVERT: C 335 MET cc_start: 0.7591 (mmp) cc_final: 0.7181 (mmm) REVERT: C 361 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6763 (tpt170) REVERT: D 67 SER cc_start: 0.8183 (p) cc_final: 0.7613 (t) REVERT: D 217 MET cc_start: 0.7528 (tpt) cc_final: 0.7006 (tpt) REVERT: D 254 ASP cc_start: 0.7343 (t0) cc_final: 0.6722 (t0) REVERT: D 278 ARG cc_start: 0.7320 (mtt180) cc_final: 0.6941 (ttp-170) REVERT: E 103 ASP cc_start: 0.6560 (p0) cc_final: 0.6321 (p0) REVERT: E 362 LEU cc_start: 0.7527 (tp) cc_final: 0.7089 (mp) REVERT: F 158 MET cc_start: 0.7396 (ttm) cc_final: 0.7149 (ttm) REVERT: F 217 MET cc_start: 0.7479 (tpt) cc_final: 0.7217 (tpt) REVERT: F 335 MET cc_start: 0.7590 (mmp) cc_final: 0.7223 (mmt) REVERT: G 43 ASN cc_start: 0.6740 (m-40) cc_final: 0.6352 (p0) REVERT: G 189 SER cc_start: 0.7929 (m) cc_final: 0.7703 (p) REVERT: H 67 SER cc_start: 0.7836 (p) cc_final: 0.7567 (t) REVERT: H 217 MET cc_start: 0.7638 (tpt) cc_final: 0.7278 (tpp) REVERT: H 270 THR cc_start: 0.8176 (p) cc_final: 0.7825 (p) REVERT: H 359 TYR cc_start: 0.5915 (m-80) cc_final: 0.5707 (m-80) REVERT: I 217 MET cc_start: 0.8054 (tpt) cc_final: 0.7770 (tpp) REVERT: I 279 TYR cc_start: 0.6261 (m-80) cc_final: 0.5735 (m-80) REVERT: J 4 ILE cc_start: 0.7387 (tt) cc_final: 0.6955 (tt) REVERT: J 114 MET cc_start: 0.4784 (ppp) cc_final: 0.3334 (ptm) REVERT: J 169 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7306 (mt-10) REVERT: J 217 MET cc_start: 0.8231 (tpt) cc_final: 0.7858 (tpt) REVERT: J 294 ILE cc_start: 0.8253 (mm) cc_final: 0.7969 (mm) REVERT: J 298 MET cc_start: 0.7374 (mtt) cc_final: 0.7107 (mtt) REVERT: K 103 ASP cc_start: 0.5814 (t0) cc_final: 0.4807 (p0) REVERT: K 147 ASP cc_start: 0.5298 (t0) cc_final: 0.4786 (m-30) REVERT: K 358 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6371 (ptt) REVERT: K 361 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6968 (mtm110) REVERT: L 91 LEU cc_start: 0.7695 (mt) cc_final: 0.7300 (mp) REVERT: L 247 ARG cc_start: 0.5976 (OUTLIER) cc_final: 0.5422 (ttt90) REVERT: L 298 MET cc_start: 0.7902 (mtt) cc_final: 0.7544 (mtp) REVERT: L 310 TYR cc_start: 0.7859 (m-80) cc_final: 0.7588 (m-10) REVERT: L 331 TRP cc_start: 0.7341 (t60) cc_final: 0.7008 (t60) REVERT: M 83 ARG cc_start: 0.7063 (mmm160) cc_final: 0.6640 (ptp-170) REVERT: M 158 MET cc_start: 0.6613 (mtm) cc_final: 0.5737 (tpt) REVERT: M 178 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7077 (mmtt) REVERT: M 311 MET cc_start: 0.7898 (ptp) cc_final: 0.7638 (ptp) outliers start: 98 outliers final: 45 residues processed: 1029 average time/residue: 0.2527 time to fit residues: 418.5649 Evaluate side-chains 797 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 748 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 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 311 MET 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 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 282 LEU 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 108 VAL 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: 9.9990 chunk 485 optimal weight: 9.9990 chunk 465 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 408 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 340 optimal weight: 10.0000 chunk 498 optimal weight: 5.9990 chunk 496 optimal weight: 20.0000 chunk 504 optimal weight: 0.0470 chunk 90 optimal weight: 7.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 200 GLN C 319 GLN E 171 GLN E 292 ASN F 15 GLN F 212 GLN F 223 GLN F 285 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 351 ASN I 109 ASN I 211 GLN J 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.152344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.126068 restraints weight = 71194.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.126154 restraints weight = 50278.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.127364 restraints weight = 48849.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.127654 restraints weight = 33445.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.128030 restraints weight = 31981.825| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 41016 Z= 0.239 Angle : 0.803 12.096 55861 Z= 0.397 Chirality : 0.055 0.510 6549 Planarity : 0.005 0.055 6897 Dihedral : 9.398 146.186 6506 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.55 % Allowed : 16.29 % Favored : 80.16 % 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: -0.59 (0.11), residues: 5088 helix: 0.05 (0.09), residues: 3080 sheet: -0.78 (0.34), residues: 184 loop : -0.93 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 20 TYR 0.033 0.003 TYR H 80 PHE 0.030 0.002 PHE J 54 TRP 0.013 0.002 TRP D 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (41016) covalent geometry : angle 0.80254 / 0.40 (55861) hydrogen bonds : bond 0.05257 / 3.54 ( 2201) hydrogen bonds : angle 4.84717 / 3.47 ( 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 901 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 763 time to evaluate : 0.990 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: 0.4557 (OUTLIER) cc_final: 0.3986 (tt0) REVERT: A 273 PHE cc_start: 0.5602 (m-80) cc_final: 0.5163 (m-80) REVERT: A 313 LEU cc_start: 0.7552 (tp) cc_final: 0.7254 (mt) REVERT: B 42 THR cc_start: 0.3836 (OUTLIER) cc_final: 0.3523 (p) REVERT: B 78 SER cc_start: 0.8034 (t) cc_final: 0.7599 (p) REVERT: B 158 MET cc_start: 0.7347 (mtp) cc_final: 0.7108 (mmm) REVERT: B 292 ASN cc_start: 0.8356 (t160) cc_final: 0.7988 (t0) REVERT: B 364 GLN cc_start: 0.5642 (mt0) cc_final: 0.4887 (mt0) REVERT: C 43 ASN cc_start: 0.5672 (t0) cc_final: 0.5268 (t0) REVERT: C 286 GLU cc_start: 0.6272 (mp0) cc_final: 0.6006 (mp0) REVERT: C 361 ARG cc_start: 0.7202 (mtm-85) cc_final: 0.6688 (tpt170) REVERT: D 67 SER cc_start: 0.8288 (p) cc_final: 0.7737 (t) REVERT: D 114 MET cc_start: 0.6451 (tmm) cc_final: 0.6219 (tmm) REVERT: D 278 ARG cc_start: 0.7327 (mtt180) cc_final: 0.6975 (ttp-170) REVERT: E 96 ASP cc_start: 0.7133 (m-30) cc_final: 0.6433 (m-30) REVERT: E 147 ASP cc_start: 0.5969 (t0) cc_final: 0.5516 (m-30) REVERT: F 83 ARG cc_start: 0.6458 (mmm160) cc_final: 0.6244 (mmm-85) REVERT: F 158 MET cc_start: 0.7537 (ttm) cc_final: 0.7033 (ttm) REVERT: F 335 MET cc_start: 0.7716 (mmp) cc_final: 0.7510 (mmt) REVERT: G 43 ASN cc_start: 0.7109 (m-40) cc_final: 0.6341 (p0) REVERT: G 189 SER cc_start: 0.7979 (m) cc_final: 0.7765 (p) REVERT: G 290 ASP cc_start: 0.6504 (m-30) cc_final: 0.6182 (m-30) REVERT: H 67 SER cc_start: 0.7941 (p) cc_final: 0.7707 (t) REVERT: H 107 MET cc_start: 0.4174 (tmm) cc_final: 0.3784 (tmm) REVERT: H 217 MET cc_start: 0.7821 (tpt) cc_final: 0.7371 (tpp) REVERT: H 270 THR cc_start: 0.8190 (p) cc_final: 0.7826 (p) REVERT: I 114 MET cc_start: 0.5501 (tmm) cc_final: 0.5293 (tpt) REVERT: I 278 ARG cc_start: 0.6601 (ptt90) cc_final: 0.6378 (ptt-90) REVERT: I 279 TYR cc_start: 0.6365 (m-80) cc_final: 0.6019 (m-80) REVERT: I 335 MET cc_start: 0.7323 (mmp) cc_final: 0.6983 (mmp) REVERT: J 114 MET cc_start: 0.4723 (ppp) cc_final: 0.3799 (ttp) REVERT: J 131 ILE cc_start: 0.6913 (mm) cc_final: 0.6687 (mt) REVERT: J 169 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7560 (mt-10) REVERT: J 217 MET cc_start: 0.8437 (tpt) cc_final: 0.7889 (tpt) REVERT: J 361 ARG cc_start: 0.6687 (mtm110) cc_final: 0.6446 (ttm110) REVERT: K 80 TYR cc_start: 0.5923 (m-10) cc_final: 0.5637 (m-80) REVERT: K 103 ASP cc_start: 0.5866 (t0) cc_final: 0.4821 (p0) REVERT: K 169 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6906 (mt-10) REVERT: K 231 MET cc_start: 0.7137 (mtm) cc_final: 0.6789 (mtp) REVERT: K 358 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6499 (ptt) REVERT: L 5 PHE cc_start: 0.6698 (m-80) cc_final: 0.6444 (m-80) REVERT: L 50 GLU cc_start: 0.6637 (tt0) cc_final: 0.6282 (tt0) REVERT: L 129 MET cc_start: 0.6524 (mmt) cc_final: 0.6263 (mmt) REVERT: L 149 ARG cc_start: 0.6684 (mtm110) cc_final: 0.6373 (ptm160) REVERT: L 199 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7594 (tm-30) REVERT: L 247 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5969 (ttt90) REVERT: M 5 PHE cc_start: 0.6561 (m-80) cc_final: 0.6234 (m-80) REVERT: M 54 PHE cc_start: 0.6737 (t80) cc_final: 0.6258 (t80) REVERT: M 79 MET cc_start: 0.6669 (mmp) cc_final: 0.6444 (mmp) REVERT: M 80 TYR cc_start: 0.4833 (m-80) cc_final: 0.4395 (m-80) REVERT: M 83 ARG cc_start: 0.7152 (mmm160) cc_final: 0.6666 (ptp-170) REVERT: M 157 ASP cc_start: 0.5963 (t70) cc_final: 0.5468 (m-30) REVERT: M 158 MET cc_start: 0.6491 (mtm) cc_final: 0.5727 (tpt) REVERT: M 178 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6966 (mmtt) REVERT: M 181 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7323 (t) REVERT: M 196 LYS cc_start: 0.5285 (OUTLIER) cc_final: 0.5012 (tptm) outliers start: 138 outliers final: 84 residues processed: 847 average time/residue: 0.2407 time to fit residues: 331.7942 Evaluate side-chains 764 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 673 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 81 SER Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 212 GLN Chi-restraints excluded: chain D residue 282 LEU 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 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 137 ASP 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 301 TYR Chi-restraints excluded: chain F residue 311 MET 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 181 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 251 ILE 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 176 ILE 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 162 VAL Chi-restraints excluded: chain K residue 233 GLU 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 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 33 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 196 LYS 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: 9.9990 chunk 46 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 449 optimal weight: 3.9990 chunk 482 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 443 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 421 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN E 171 GLN F 15 GLN F 93 ASN G 93 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 ASN I 257 ASN K 93 ASN K 257 ASN L 257 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.157310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.132763 restraints weight = 71301.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.133310 restraints weight = 52976.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.134670 restraints weight = 45845.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.134550 restraints weight = 32109.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.134808 restraints weight = 31897.063| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4136 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= 0.156 Angle : 0.694 12.310 55861 Z= 0.339 Chirality : 0.051 0.486 6549 Planarity : 0.004 0.055 6897 Dihedral : 9.109 141.247 6502 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.34 % Allowed : 17.70 % Favored : 78.96 % 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: 0.34 (0.09), residues: 3076 sheet: -0.69 (0.34), residues: 184 loop : -0.73 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 361 TYR 0.036 0.002 TYR E 80 PHE 0.033 0.002 PHE J 54 TRP 0.011 0.001 TRP B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (41016) covalent geometry : angle 0.69446 / 0.34 (55861) hydrogen bonds : bond 0.04454 / 3.00 ( 2201) hydrogen bonds : angle 4.54050 / 3.25 ( 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 898 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 768 time to evaluate : 1.579 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 4 ILE cc_start: 0.3837 (OUTLIER) cc_final: 0.3505 (tp) REVERT: A 6 GLU cc_start: 0.4531 (OUTLIER) cc_final: 0.4085 (tt0) REVERT: A 231 MET cc_start: 0.6514 (mmp) cc_final: 0.5864 (mmm) REVERT: A 273 PHE cc_start: 0.5299 (m-80) cc_final: 0.4916 (m-80) REVERT: B 42 THR cc_start: 0.3719 (OUTLIER) cc_final: 0.3491 (p) REVERT: B 78 SER cc_start: 0.7877 (t) cc_final: 0.7556 (p) REVERT: B 80 TYR cc_start: 0.5269 (m-10) cc_final: 0.4968 (m-80) REVERT: B 245 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7399 (mtpt) REVERT: B 292 ASN cc_start: 0.8231 (t160) cc_final: 0.7869 (t0) REVERT: B 354 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: B 364 GLN cc_start: 0.5646 (mt0) cc_final: 0.4908 (mt0) REVERT: C 286 GLU cc_start: 0.5951 (mp0) cc_final: 0.5490 (mp0) REVERT: D 7 GLU cc_start: 0.6069 (mp0) cc_final: 0.5839 (pm20) REVERT: D 67 SER cc_start: 0.8283 (p) cc_final: 0.7693 (t) REVERT: D 114 MET cc_start: 0.6468 (tmm) cc_final: 0.6083 (tmm) REVERT: D 115 GLU cc_start: 0.4818 (OUTLIER) cc_final: 0.4376 (mp0) REVERT: D 278 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6905 (ttp-170) REVERT: E 96 ASP cc_start: 0.6778 (m-30) cc_final: 0.6026 (m-30) REVERT: E 362 LEU cc_start: 0.7557 (tp) cc_final: 0.7137 (mp) REVERT: F 158 MET cc_start: 0.7540 (ttm) cc_final: 0.7136 (ttm) REVERT: F 290 ASP cc_start: 0.6435 (m-30) cc_final: 0.6119 (m-30) REVERT: F 335 MET cc_start: 0.7394 (mmp) cc_final: 0.6937 (mmt) REVERT: G 43 ASN cc_start: 0.6653 (m-40) cc_final: 0.6167 (p0) REVERT: H 67 SER cc_start: 0.7844 (p) cc_final: 0.7566 (t) REVERT: H 154 ARG cc_start: 0.6136 (mmt-90) cc_final: 0.5402 (tpp-160) REVERT: H 217 MET cc_start: 0.7689 (tpt) cc_final: 0.7227 (tpp) REVERT: H 270 THR cc_start: 0.8092 (p) cc_final: 0.7685 (p) REVERT: I 114 MET cc_start: 0.5460 (tmm) cc_final: 0.5221 (tpt) REVERT: I 153 LEU cc_start: 0.6236 (mt) cc_final: 0.5924 (tp) REVERT: I 279 TYR cc_start: 0.6154 (m-80) cc_final: 0.5895 (m-10) REVERT: J 114 MET cc_start: 0.4785 (ppp) cc_final: 0.3847 (ttp) REVERT: J 131 ILE cc_start: 0.6576 (mm) cc_final: 0.6347 (mt) REVERT: J 169 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7132 (mt-10) REVERT: J 217 MET cc_start: 0.8395 (tpt) cc_final: 0.7963 (tpt) REVERT: J 355 LEU cc_start: 0.8167 (pt) cc_final: 0.7606 (tt) REVERT: J 361 ARG cc_start: 0.6609 (mtm110) cc_final: 0.6332 (ttm110) REVERT: K 80 TYR cc_start: 0.6021 (m-10) cc_final: 0.5695 (m-80) REVERT: K 103 ASP cc_start: 0.5685 (t0) cc_final: 0.4713 (p0) REVERT: K 147 ASP cc_start: 0.5683 (t0) cc_final: 0.5103 (m-30) REVERT: K 156 THR cc_start: 0.4156 (OUTLIER) cc_final: 0.3865 (p) REVERT: K 169 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7045 (mt-10) REVERT: L 5 PHE cc_start: 0.6635 (m-80) cc_final: 0.6325 (m-80) REVERT: L 149 ARG cc_start: 0.6468 (mtm110) cc_final: 0.6183 (ptm160) REVERT: L 197 TYR cc_start: 0.6459 (m-80) cc_final: 0.6026 (m-80) REVERT: L 282 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6820 (pp) REVERT: L 310 TYR cc_start: 0.7775 (m-80) cc_final: 0.7404 (m-10) REVERT: M 80 TYR cc_start: 0.4923 (m-10) cc_final: 0.4507 (m-80) REVERT: M 83 ARG cc_start: 0.7093 (mmm160) cc_final: 0.6820 (ptt-90) REVERT: M 157 ASP cc_start: 0.5881 (t70) cc_final: 0.5458 (m-30) REVERT: M 158 MET cc_start: 0.6454 (mtm) cc_final: 0.5650 (tpt) REVERT: M 178 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7004 (mmtt) REVERT: M 181 THR cc_start: 0.7630 (p) cc_final: 0.7424 (t) REVERT: M 196 LYS cc_start: 0.5385 (OUTLIER) cc_final: 0.5148 (tptm) outliers start: 130 outliers final: 65 residues processed: 851 average time/residue: 0.2462 time to fit residues: 342.2942 Evaluate side-chains 760 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 686 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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 161 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 184 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 212 GLN 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 156 THR 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 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 181 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 301 TYR 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 167 THR 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 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 176 ILE Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain J residue 39 VAL 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 156 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 91 LEU 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 178 LYS Chi-restraints excluded: chain M residue 196 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 428 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 472 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 464 optimal weight: 6.9990 chunk 494 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 380 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 364 GLN B 15 GLN C 15 GLN C 285 ASN E 171 GLN E 292 ASN F 93 ASN G 93 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN J 15 GLN K 93 ASN K 257 ASN L 257 ASN L 288 GLN M 93 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.153238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.128990 restraints weight = 71256.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129370 restraints weight = 57979.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.130542 restraints weight = 52853.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.130354 restraints weight = 35413.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.130581 restraints weight = 34574.491| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 41016 Z= 0.239 Angle : 0.769 11.681 55861 Z= 0.377 Chirality : 0.053 0.410 6549 Planarity : 0.005 0.060 6897 Dihedral : 9.199 142.726 6502 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.06 % Allowed : 18.27 % Favored : 77.67 % 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: -0.44 (0.11), residues: 5088 helix: 0.20 (0.09), residues: 3067 sheet: -0.63 (0.35), residues: 184 loop : -0.93 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 20 TYR 0.052 0.003 TYR E 80 PHE 0.036 0.002 PHE J 54 TRP 0.015 0.002 TRP B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (41016) covalent geometry : angle 0.76912 / 0.38 (55861) hydrogen bonds : bond 0.04874 / 3.27 ( 2201) hydrogen bonds : angle 4.74472 / 3.40 ( 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 869 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 711 time to evaluate : 1.344 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 217 MET cc_start: 0.7461 (tpt) cc_final: 0.7117 (tpp) REVERT: A 273 PHE cc_start: 0.5327 (m-80) cc_final: 0.4967 (m-80) REVERT: B 42 THR cc_start: 0.4094 (OUTLIER) cc_final: 0.3819 (p) REVERT: B 78 SER cc_start: 0.7896 (t) cc_final: 0.7644 (p) REVERT: B 217 MET cc_start: 0.6864 (tpp) cc_final: 0.6594 (tpt) REVERT: B 245 LYS cc_start: 0.8043 (mmmm) cc_final: 0.7525 (mtpt) REVERT: B 264 MET cc_start: 0.7557 (mtp) cc_final: 0.6956 (mtp) REVERT: B 292 ASN cc_start: 0.8244 (t160) cc_final: 0.7875 (t0) REVERT: B 335 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6746 (mmm) REVERT: B 354 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: B 364 GLN cc_start: 0.5754 (mt0) cc_final: 0.5422 (mt0) REVERT: D 67 SER cc_start: 0.8207 (p) cc_final: 0.7594 (t) REVERT: D 114 MET cc_start: 0.6464 (tmm) cc_final: 0.6159 (tmm) REVERT: D 115 GLU cc_start: 0.4850 (OUTLIER) cc_final: 0.4423 (mp0) REVERT: D 278 ARG cc_start: 0.7212 (mtt180) cc_final: 0.6905 (ttp-170) REVERT: E 59 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7475 (mp) REVERT: E 96 ASP cc_start: 0.6861 (m-30) cc_final: 0.6450 (m-30) REVERT: E 147 ASP cc_start: 0.5875 (t0) cc_final: 0.5484 (m-30) REVERT: E 270 THR cc_start: 0.7744 (p) cc_final: 0.7397 (t) REVERT: F 158 MET cc_start: 0.7554 (ttm) cc_final: 0.7111 (ttm) REVERT: G 43 ASN cc_start: 0.6738 (m-40) cc_final: 0.6103 (p0) REVERT: G 158 MET cc_start: 0.6845 (mtm) cc_final: 0.6641 (mtm) REVERT: H 154 ARG cc_start: 0.6083 (mmt-90) cc_final: 0.5431 (tpp-160) REVERT: H 217 MET cc_start: 0.7813 (tpt) cc_final: 0.7252 (tpp) REVERT: H 270 THR cc_start: 0.8045 (p) cc_final: 0.7577 (p) REVERT: I 153 LEU cc_start: 0.6174 (mt) cc_final: 0.5876 (tp) REVERT: I 335 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6558 (mmt) REVERT: J 114 MET cc_start: 0.4871 (ppp) cc_final: 0.4098 (ttp) REVERT: J 131 ILE cc_start: 0.6423 (mm) cc_final: 0.6125 (mt) REVERT: J 217 MET cc_start: 0.8595 (tpt) cc_final: 0.8360 (tpt) REVERT: J 276 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6963 (mt-10) REVERT: J 361 ARG cc_start: 0.6765 (mtm110) cc_final: 0.6439 (ttm110) REVERT: K 68 MET cc_start: 0.7295 (ttt) cc_final: 0.7001 (ttt) REVERT: K 93 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6811 (t0) REVERT: K 103 ASP cc_start: 0.5616 (t0) cc_final: 0.4538 (p0) REVERT: K 147 ASP cc_start: 0.5961 (t0) cc_final: 0.5371 (m-30) REVERT: L 5 PHE cc_start: 0.6682 (m-80) cc_final: 0.6386 (m-80) REVERT: L 197 TYR cc_start: 0.6426 (m-80) cc_final: 0.6115 (m-80) REVERT: L 282 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6823 (pp) REVERT: M 80 TYR cc_start: 0.4925 (m-10) cc_final: 0.4557 (m-80) REVERT: M 158 MET cc_start: 0.6522 (mtm) cc_final: 0.5587 (tpt) REVERT: M 178 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7016 (mmtt) REVERT: M 181 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7501 (t) REVERT: M 196 LYS cc_start: 0.5549 (OUTLIER) cc_final: 0.5273 (tptt) REVERT: M 235 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7583 (tp) outliers start: 158 outliers final: 93 residues processed: 815 average time/residue: 0.2393 time to fit residues: 321.4901 Evaluate side-chains 761 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 655 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 212 GLN 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 32 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 299 LEU 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 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 196 LYS 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 100 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 181 THR 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 I residue 33 THR Chi-restraints excluded: chain I residue 53 LEU 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 176 ILE Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain I residue 335 MET Chi-restraints excluded: chain I residue 341 ILE 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 104 VAL Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 189 SER 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 K residue 93 ASN Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 351 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 149 ARG 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 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 235 LEU Chi-restraints excluded: chain M residue 255 ILE Chi-restraints excluded: chain M residue 292 ASN 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: 5.9990 chunk 14 optimal weight: 0.0970 chunk 305 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 271 optimal weight: 50.0000 chunk 212 optimal weight: 1.9990 chunk 367 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 446 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 GLN C 285 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 257 ASN L 257 ASN M 93 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.157765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.133248 restraints weight = 70893.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.134255 restraints weight = 52040.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.135461 restraints weight = 46002.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.135342 restraints weight = 31626.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.135499 restraints weight = 30193.852| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41016 Z= 0.134 Angle : 0.681 12.067 55861 Z= 0.330 Chirality : 0.049 0.398 6549 Planarity : 0.004 0.063 6897 Dihedral : 8.986 135.928 6502 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.96 % Allowed : 19.30 % Favored : 77.75 % 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: 0.05 (0.12), residues: 5088 helix: 0.57 (0.09), residues: 3032 sheet: -0.52 (0.36), residues: 184 loop : -0.67 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 343 TYR 0.041 0.002 TYR J 80 PHE 0.035 0.001 PHE J 54 TRP 0.017 0.001 TRP B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (41016) covalent geometry : angle 0.68121 / 0.33 (55861) hydrogen bonds : bond 0.04173 / 2.80 ( 2201) hydrogen bonds : angle 4.46014 / 3.20 ( 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 868 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 753 time to evaluate : 1.595 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: 0.4796 (OUTLIER) cc_final: 0.4190 (tt0) REVERT: A 109 ASN cc_start: 0.6085 (p0) cc_final: 0.5747 (p0) REVERT: A 231 MET cc_start: 0.6544 (mmp) cc_final: 0.5912 (mmm) REVERT: A 273 PHE cc_start: 0.5260 (m-80) cc_final: 0.4939 (m-80) REVERT: B 42 THR cc_start: 0.3821 (OUTLIER) cc_final: 0.3519 (p) REVERT: B 78 SER cc_start: 0.7728 (t) cc_final: 0.7507 (p) REVERT: B 245 LYS cc_start: 0.8011 (mmmm) cc_final: 0.7560 (mtpt) REVERT: B 290 ASP cc_start: 0.6960 (m-30) cc_final: 0.6720 (m-30) REVERT: B 292 ASN cc_start: 0.8243 (t160) cc_final: 0.7922 (t0) REVERT: B 335 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6390 (mmm) REVERT: B 354 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.6603 (m-80) REVERT: B 364 GLN cc_start: 0.5575 (mt0) cc_final: 0.4825 (mt0) REVERT: C 217 MET cc_start: 0.7648 (tpp) cc_final: 0.7143 (tpt) REVERT: D 67 SER cc_start: 0.8322 (p) cc_final: 0.7704 (t) REVERT: D 114 MET cc_start: 0.6148 (tmm) cc_final: 0.5886 (tmm) REVERT: D 115 GLU cc_start: 0.4676 (OUTLIER) cc_final: 0.4344 (mp0) REVERT: D 278 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6888 (ttp-170) REVERT: E 59 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7537 (mp) REVERT: E 80 TYR cc_start: 0.5769 (m-10) cc_final: 0.5520 (m-80) REVERT: E 96 ASP cc_start: 0.6674 (m-30) cc_final: 0.6116 (m-30) REVERT: E 270 THR cc_start: 0.7739 (p) cc_final: 0.7381 (t) REVERT: E 362 LEU cc_start: 0.7581 (tp) cc_final: 0.7127 (mp) REVERT: F 158 MET cc_start: 0.7608 (ttm) cc_final: 0.7385 (ttm) REVERT: F 273 PHE cc_start: 0.6975 (m-80) cc_final: 0.6510 (m-80) REVERT: G 43 ASN cc_start: 0.6631 (m-40) cc_final: 0.6154 (p0) REVERT: G 189 SER cc_start: 0.7993 (m) cc_final: 0.7668 (t) REVERT: G 345 MET cc_start: 0.8180 (mmt) cc_final: 0.7954 (mmt) REVERT: H 101 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7609 (mt) REVERT: H 154 ARG cc_start: 0.6143 (mmt-90) cc_final: 0.5614 (tpp-160) REVERT: H 217 MET cc_start: 0.7659 (tpt) cc_final: 0.7200 (tpp) REVERT: H 270 THR cc_start: 0.8020 (p) cc_final: 0.7805 (p) REVERT: I 114 MET cc_start: 0.5343 (tmm) cc_final: 0.5021 (tpt) REVERT: I 153 LEU cc_start: 0.6405 (mt) cc_final: 0.6201 (tp) REVERT: I 279 TYR cc_start: 0.6233 (m-80) cc_final: 0.5775 (m-80) REVERT: J 114 MET cc_start: 0.4641 (ppp) cc_final: 0.3909 (ttp) REVERT: J 131 ILE cc_start: 0.6483 (mm) cc_final: 0.6221 (mt) REVERT: J 217 MET cc_start: 0.8440 (tpt) cc_final: 0.7995 (tpt) REVERT: J 276 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: J 335 MET cc_start: 0.7774 (mmp) cc_final: 0.7351 (mmp) REVERT: J 361 ARG cc_start: 0.6758 (mtm110) cc_final: 0.6459 (ttm110) REVERT: J 362 LEU cc_start: 0.6276 (mm) cc_final: 0.6065 (mm) REVERT: K 68 MET cc_start: 0.7403 (ttt) cc_final: 0.7200 (ttt) REVERT: K 80 TYR cc_start: 0.5697 (m-10) cc_final: 0.5474 (m-80) REVERT: K 103 ASP cc_start: 0.5691 (t0) cc_final: 0.4458 (p0) REVERT: K 147 ASP cc_start: 0.5718 (t0) cc_final: 0.5106 (m-30) REVERT: K 156 THR cc_start: 0.4111 (OUTLIER) cc_final: 0.3793 (p) REVERT: K 169 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6980 (mt-10) REVERT: L 5 PHE cc_start: 0.6515 (m-80) cc_final: 0.6152 (m-80) REVERT: L 50 GLU cc_start: 0.6612 (tt0) cc_final: 0.5819 (tt0) REVERT: L 107 MET cc_start: 0.2682 (tpp) cc_final: 0.2021 (mtt) REVERT: L 197 TYR cc_start: 0.6553 (m-80) cc_final: 0.6255 (m-80) REVERT: L 282 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6864 (pp) REVERT: L 310 TYR cc_start: 0.7762 (m-80) cc_final: 0.7410 (m-10) REVERT: M 80 TYR cc_start: 0.5223 (m-10) cc_final: 0.4755 (m-80) REVERT: M 133 LYS cc_start: 0.7490 (mttm) cc_final: 0.7117 (mtmt) REVERT: M 158 MET cc_start: 0.6574 (mtm) cc_final: 0.5484 (tpt) REVERT: M 178 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6961 (mmtt) REVERT: M 196 LYS cc_start: 0.5362 (OUTLIER) cc_final: 0.5047 (tptm) outliers start: 115 outliers final: 61 residues processed: 831 average time/residue: 0.2348 time to fit residues: 321.5180 Evaluate side-chains 757 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 684 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 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 42 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 47 LEU 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 D residue 21 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 212 GLN Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 39 VAL 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 255 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 355 LEU 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 301 TYR Chi-restraints excluded: chain F residue 335 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 153 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 101 ILE 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 176 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 276 GLU Chi-restraints excluded: chain J residue 313 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 77 ILE Chi-restraints excluded: chain L residue 102 ILE 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 168 ILE Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 196 LYS Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 297 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 494 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 287 optimal weight: 0.0670 chunk 61 optimal weight: 5.9990 chunk 318 optimal weight: 0.9980 chunk 276 optimal weight: 6.9990 chunk 477 optimal weight: 30.0000 chunk 290 optimal weight: 0.7980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 285 ASN D 351 ASN E 171 GLN E 292 ASN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 GLN ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 288 GLN K 93 ASN K 212 GLN L 257 ASN M 93 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.159124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.134864 restraints weight = 70812.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.135358 restraints weight = 51349.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.136735 restraints weight = 45024.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.136686 restraints weight = 31156.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.136956 restraints weight = 31121.986| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41016 Z= 0.129 Angle : 0.675 11.594 55861 Z= 0.327 Chirality : 0.048 0.392 6549 Planarity : 0.004 0.074 6897 Dihedral : 8.835 134.819 6502 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.65 % Allowed : 20.92 % Favored : 76.43 % 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: 0.68 (0.09), residues: 3039 sheet: -0.61 (0.37), residues: 182 loop : -0.58 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 272 TYR 0.027 0.002 TYR E 80 PHE 0.039 0.001 PHE J 54 TRP 0.023 0.001 TRP B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (41016) covalent geometry : angle 0.67522 / 0.33 (55861) hydrogen bonds : bond 0.04022 / 2.69 ( 2201) hydrogen bonds : angle 4.42376 / 3.17 ( 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 861 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 758 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: A 6 GLU cc_start: 0.4775 (OUTLIER) cc_final: 0.4237 (tt0) REVERT: A 83 ARG cc_start: 0.7093 (mpt180) cc_final: 0.6632 (mmp-170) REVERT: A 273 PHE cc_start: 0.5188 (m-80) cc_final: 0.4884 (m-80) REVERT: B 42 THR cc_start: 0.3680 (OUTLIER) cc_final: 0.3439 (p) REVERT: B 78 SER cc_start: 0.7659 (t) cc_final: 0.7397 (p) REVERT: B 245 LYS cc_start: 0.8045 (mmmm) cc_final: 0.7593 (mtpt) REVERT: B 272 ARG cc_start: 0.5651 (mtm110) cc_final: 0.5409 (ttp-170) REVERT: B 290 ASP cc_start: 0.6843 (m-30) cc_final: 0.6572 (m-30) REVERT: B 292 ASN cc_start: 0.8232 (t160) cc_final: 0.7894 (t0) REVERT: B 354 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: B 364 GLN cc_start: 0.5548 (mt0) cc_final: 0.4804 (mt0) REVERT: C 107 MET cc_start: 0.3742 (tpt) cc_final: 0.3223 (tpt) REVERT: C 217 MET cc_start: 0.7833 (tpp) cc_final: 0.7303 (tpt) REVERT: D 67 SER cc_start: 0.8272 (p) cc_final: 0.7661 (t) REVERT: D 115 GLU cc_start: 0.4728 (OUTLIER) cc_final: 0.4337 (mp0) REVERT: D 155 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7251 (mt) REVERT: E 5 PHE cc_start: 0.6958 (m-80) cc_final: 0.6610 (m-10) REVERT: E 59 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7515 (mp) REVERT: E 96 ASP cc_start: 0.6692 (m-30) cc_final: 0.6263 (m-30) REVERT: E 223 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: E 270 THR cc_start: 0.7905 (p) cc_final: 0.7509 (t) REVERT: E 299 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8201 (mp) REVERT: E 362 LEU cc_start: 0.7522 (tp) cc_final: 0.7073 (mp) REVERT: F 158 MET cc_start: 0.7684 (ttm) cc_final: 0.7432 (ttm) REVERT: G 43 ASN cc_start: 0.6555 (m-40) cc_final: 0.6123 (p0) REVERT: G 189 SER cc_start: 0.8089 (m) cc_final: 0.7711 (t) REVERT: G 313 LEU cc_start: 0.8495 (mt) cc_final: 0.8274 (mp) REVERT: G 345 MET cc_start: 0.8148 (mmt) cc_final: 0.7889 (mmt) REVERT: G 350 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7723 (pt) REVERT: H 154 ARG cc_start: 0.6074 (mmt-90) cc_final: 0.5593 (tpp-160) REVERT: H 217 MET cc_start: 0.7673 (tpt) cc_final: 0.7179 (tpp) REVERT: H 335 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7013 (mmm) REVERT: J 17 LYS cc_start: 0.7939 (pttm) cc_final: 0.7508 (ptpp) REVERT: J 114 MET cc_start: 0.4560 (ppp) cc_final: 0.3847 (ttp) REVERT: J 217 MET cc_start: 0.8500 (tpt) cc_final: 0.8130 (tpt) REVERT: J 335 MET cc_start: 0.7845 (mmp) cc_final: 0.7426 (mmp) REVERT: J 361 ARG cc_start: 0.6733 (mtm110) cc_final: 0.6429 (ttm110) REVERT: J 362 LEU cc_start: 0.6314 (mm) cc_final: 0.6108 (mm) REVERT: K 80 TYR cc_start: 0.5373 (m-10) cc_final: 0.5168 (m-80) REVERT: K 147 ASP cc_start: 0.5822 (t0) cc_final: 0.5224 (m-30) REVERT: K 156 THR cc_start: 0.4123 (OUTLIER) cc_final: 0.3841 (p) REVERT: K 169 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6943 (mt-10) REVERT: L 5 PHE cc_start: 0.6438 (m-80) cc_final: 0.6082 (m-80) REVERT: L 107 MET cc_start: 0.2451 (tpp) cc_final: 0.2086 (mtt) REVERT: L 197 TYR cc_start: 0.6692 (m-80) cc_final: 0.6457 (m-80) REVERT: L 264 MET cc_start: 0.7796 (mtt) cc_final: 0.7520 (mtp) REVERT: L 282 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6780 (pp) REVERT: L 298 MET cc_start: 0.7974 (mtm) cc_final: 0.7696 (mtp) REVERT: L 310 TYR cc_start: 0.7559 (m-80) cc_final: 0.7226 (m-10) REVERT: M 80 TYR cc_start: 0.5503 (m-10) cc_final: 0.5291 (m-80) REVERT: M 133 LYS cc_start: 0.7489 (mttm) cc_final: 0.7081 (mtmt) REVERT: M 157 ASP cc_start: 0.5956 (t0) cc_final: 0.5659 (m-30) REVERT: M 158 MET cc_start: 0.6257 (mtm) cc_final: 0.5361 (tpt) REVERT: M 178 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7205 (mmtt) REVERT: M 342 ASP cc_start: 0.7182 (t0) cc_final: 0.6974 (t0) outliers start: 103 outliers final: 64 residues processed: 820 average time/residue: 0.2367 time to fit residues: 317.5251 Evaluate side-chains 761 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 684 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 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 47 LEU 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 180 VAL Chi-restraints excluded: chain C residue 184 ASP 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 155 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 39 VAL 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 299 LEU Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 335 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 153 LEU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 33 THR 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 111 ILE Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 313 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 77 ILE Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 102 ILE 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 L residue 282 LEU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 178 LYS Chi-restraints excluded: chain M residue 254 ASP Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 103 optimal weight: 0.0470 chunk 52 optimal weight: 6.9990 chunk 349 optimal weight: 30.0000 chunk 400 optimal weight: 0.0170 chunk 1 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 352 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 403 optimal weight: 20.0000 chunk 481 optimal weight: 6.9990 chunk 485 optimal weight: 9.9990 overall best weight: 4.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN B 288 GLN C 285 ASN D 351 ASN E 171 GLN E 288 GLN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN H 211 GLN I 109 ASN ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN J 200 GLN K 257 ASN L 257 ASN M 93 ASN M 288 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.154439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.130654 restraints weight = 71431.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.130022 restraints weight = 60214.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.131526 restraints weight = 58127.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.131623 restraints weight = 40012.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.131920 restraints weight = 38705.810| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 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 : 0.005 0.063 41016 Z= 0.228 Angle : 0.761 14.376 55861 Z= 0.373 Chirality : 0.052 0.411 6549 Planarity : 0.005 0.065 6897 Dihedral : 9.025 141.146 6502 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.27 % Allowed : 20.71 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.11), residues: 5088 helix: 0.43 (0.09), residues: 3053 sheet: -0.54 (0.38), residues: 182 loop : -0.84 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 272 TYR 0.054 0.003 TYR J 80 PHE 0.040 0.002 PHE J 54 TRP 0.025 0.002 TRP B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (41016) covalent geometry : angle 0.76119 / 0.37 (55861) hydrogen bonds : bond 0.04570 / 3.06 ( 2201) hydrogen bonds : angle 4.67994 / 3.35 ( 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 822 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 695 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7262 (mpt180) cc_final: 0.6658 (mmp-170) REVERT: A 264 MET cc_start: 0.7690 (mmt) cc_final: 0.7073 (mmt) REVERT: A 273 PHE cc_start: 0.5209 (m-80) cc_final: 0.4850 (m-80) REVERT: B 217 MET cc_start: 0.6912 (tpp) cc_final: 0.6550 (tpt) REVERT: B 245 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7620 (mtpt) REVERT: B 292 ASN cc_start: 0.8246 (t160) cc_final: 0.7967 (t0) REVERT: B 364 GLN cc_start: 0.5765 (mt0) cc_final: 0.5449 (mt0) REVERT: D 67 SER cc_start: 0.8190 (p) cc_final: 0.7549 (t) REVERT: D 125 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.6187 (tpt) REVERT: D 155 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7347 (mt) REVERT: E 59 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7468 (mp) REVERT: E 96 ASP cc_start: 0.6825 (m-30) cc_final: 0.6565 (m-30) REVERT: E 114 MET cc_start: 0.6033 (tmm) cc_final: 0.5757 (tmm) REVERT: E 270 THR cc_start: 0.7796 (p) cc_final: 0.7431 (t) REVERT: E 299 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8214 (mp) REVERT: F 77 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7693 (mm) REVERT: F 158 MET cc_start: 0.7716 (ttm) cc_final: 0.7273 (ttm) REVERT: F 250 GLU cc_start: 0.6894 (tp30) cc_final: 0.6585 (mm-30) REVERT: G 43 ASN cc_start: 0.6688 (m-40) cc_final: 0.6129 (p0) REVERT: G 158 MET cc_start: 0.6832 (mtm) cc_final: 0.6589 (mtm) REVERT: G 189 SER cc_start: 0.8195 (m) cc_final: 0.7887 (t) REVERT: H 154 ARG cc_start: 0.6025 (mmt-90) cc_final: 0.5526 (tpp-160) REVERT: H 217 MET cc_start: 0.7758 (tpt) cc_final: 0.7178 (tpp) REVERT: J 114 MET cc_start: 0.4454 (ppp) cc_final: 0.3893 (ttp) REVERT: J 217 MET cc_start: 0.8505 (tpt) cc_final: 0.8116 (tpt) REVERT: J 361 ARG cc_start: 0.6693 (mtm110) cc_final: 0.6428 (ttm110) REVERT: K 103 ASP cc_start: 0.5577 (t0) cc_final: 0.4213 (p0) REVERT: K 147 ASP cc_start: 0.6346 (t0) cc_final: 0.5574 (m-30) REVERT: K 156 THR cc_start: 0.4227 (OUTLIER) cc_final: 0.3909 (p) REVERT: L 5 PHE cc_start: 0.6615 (m-80) cc_final: 0.6265 (m-80) REVERT: L 50 GLU cc_start: 0.6589 (tt0) cc_final: 0.5984 (tt0) REVERT: L 107 MET cc_start: 0.2644 (tpp) cc_final: 0.2054 (mtt) REVERT: L 197 TYR cc_start: 0.6468 (m-80) cc_final: 0.6229 (m-80) REVERT: L 282 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6880 (pp) REVERT: L 310 TYR cc_start: 0.7690 (m-80) cc_final: 0.7449 (m-10) REVERT: L 345 MET cc_start: 0.6350 (mmt) cc_final: 0.5461 (mmt) REVERT: M 80 TYR cc_start: 0.5267 (m-10) cc_final: 0.5006 (m-80) REVERT: M 133 LYS cc_start: 0.7460 (mttm) cc_final: 0.7034 (mtmt) REVERT: M 157 ASP cc_start: 0.5774 (t0) cc_final: 0.5488 (m-30) REVERT: M 158 MET cc_start: 0.6336 (mtm) cc_final: 0.5545 (tpt) REVERT: M 178 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7247 (mmtt) outliers start: 127 outliers final: 77 residues processed: 773 average time/residue: 0.2396 time to fit residues: 305.3300 Evaluate side-chains 740 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 655 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 A residue 317 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 47 LEU 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 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 103 ASP Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 197 TYR Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 299 LEU 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 E residue 355 LEU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 301 TYR Chi-restraints excluded: chain F residue 311 MET Chi-restraints excluded: chain F residue 335 MET 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 167 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 43 ASN 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 111 ILE Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain J residue 32 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 132 LEU Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain K residue 156 THR Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 98 GLU Chi-restraints excluded: chain L residue 102 ILE 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 L residue 282 LEU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 178 LYS 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: 3.9990 chunk 99 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 375 optimal weight: 8.9990 chunk 259 optimal weight: 0.7980 chunk 307 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 285 ASN D 351 ASN E 223 GLN E 292 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN I 288 GLN J 15 GLN K 93 ASN K 257 ASN 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 = 0.4231 r_free = 0.4231 target = 0.157424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133205 restraints weight = 71073.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.133338 restraints weight = 54249.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.134808 restraints weight = 47649.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.134669 restraints weight = 32575.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.134962 restraints weight = 32087.240| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41016 Z= 0.146 Angle : 0.708 15.272 55861 Z= 0.345 Chirality : 0.049 0.396 6549 Planarity : 0.004 0.075 6897 Dihedral : 8.945 138.779 6502 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.52 % Allowed : 21.71 % Favored : 75.77 % 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: 0.04 (0.12), residues: 5088 helix: 0.59 (0.09), residues: 3045 sheet: -0.58 (0.38), residues: 182 loop : -0.72 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 272 TYR 0.079 0.002 TYR J 80 PHE 0.039 0.001 PHE J 54 TRP 0.028 0.001 TRP B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (41016) covalent geometry : angle 0.70829 / 0.34 (55861) hydrogen bonds : bond 0.04191 / 2.80 ( 2201) hydrogen bonds : angle 4.52786 / 3.25 ( 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 811 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 713 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7216 (mpt180) cc_final: 0.6611 (mmp-170) REVERT: A 264 MET cc_start: 0.7666 (mmt) cc_final: 0.7056 (mmt) REVERT: A 273 PHE cc_start: 0.5146 (m-80) cc_final: 0.4796 (m-80) REVERT: B 245 LYS cc_start: 0.8098 (mmmm) cc_final: 0.7622 (mtpt) REVERT: B 272 ARG cc_start: 0.5732 (mtm110) cc_final: 0.5347 (ttp-170) REVERT: B 290 ASP cc_start: 0.6848 (m-30) cc_final: 0.6558 (m-30) REVERT: B 292 ASN cc_start: 0.8230 (t160) cc_final: 0.7958 (t0) REVERT: B 335 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6407 (mmm) REVERT: B 364 GLN cc_start: 0.5691 (mt0) cc_final: 0.4949 (mt0) REVERT: D 67 SER cc_start: 0.8287 (p) cc_final: 0.7649 (t) REVERT: D 125 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6190 (tpt) REVERT: D 155 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7340 (mt) REVERT: E 59 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7484 (mp) REVERT: E 96 ASP cc_start: 0.6862 (m-30) cc_final: 0.6637 (m-30) REVERT: E 114 MET cc_start: 0.6041 (tmm) cc_final: 0.5789 (tmm) REVERT: E 270 THR cc_start: 0.7755 (p) cc_final: 0.7404 (t) REVERT: E 362 LEU cc_start: 0.7544 (tp) cc_final: 0.7020 (mp) REVERT: F 77 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7704 (mm) REVERT: F 158 MET cc_start: 0.7717 (ttm) cc_final: 0.7478 (ttm) REVERT: G 43 ASN cc_start: 0.6561 (m-40) cc_final: 0.6181 (p0) REVERT: G 158 MET cc_start: 0.6760 (mtm) cc_final: 0.6499 (mtm) REVERT: G 189 SER cc_start: 0.8066 (m) cc_final: 0.7753 (t) REVERT: G 345 MET cc_start: 0.8259 (mmt) cc_final: 0.8003 (mmt) REVERT: H 154 ARG cc_start: 0.5995 (mmt-90) cc_final: 0.5557 (tpp-160) REVERT: H 217 MET cc_start: 0.7814 (tpt) cc_final: 0.7278 (tpp) REVERT: I 169 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7283 (mt-10) REVERT: I 233 GLU cc_start: 0.7014 (tp30) cc_final: 0.6557 (tp30) REVERT: I 279 TYR cc_start: 0.6305 (m-80) cc_final: 0.5978 (m-80) REVERT: J 114 MET cc_start: 0.4423 (ppp) cc_final: 0.3882 (ttp) REVERT: J 361 ARG cc_start: 0.6746 (mtm110) cc_final: 0.6480 (ttm110) REVERT: J 362 LEU cc_start: 0.6240 (mm) cc_final: 0.5998 (mm) REVERT: K 147 ASP cc_start: 0.6107 (t0) cc_final: 0.5501 (m-30) REVERT: K 156 THR cc_start: 0.4098 (OUTLIER) cc_final: 0.3758 (p) REVERT: L 5 PHE cc_start: 0.6575 (m-80) cc_final: 0.6247 (m-80) REVERT: L 50 GLU cc_start: 0.6730 (tt0) cc_final: 0.5947 (tt0) REVERT: L 107 MET cc_start: 0.2518 (tpp) cc_final: 0.1770 (mtt) REVERT: L 197 TYR cc_start: 0.6418 (m-80) cc_final: 0.6196 (m-80) REVERT: L 282 LEU cc_start: 0.7134 (mt) cc_final: 0.6801 (pp) REVERT: L 310 TYR cc_start: 0.7633 (m-80) cc_final: 0.7398 (m-10) REVERT: M 133 LYS cc_start: 0.7443 (mttm) cc_final: 0.7059 (mtmt) REVERT: M 157 ASP cc_start: 0.5980 (t0) cc_final: 0.5659 (m-30) REVERT: M 158 MET cc_start: 0.6260 (mtm) cc_final: 0.5651 (tpt) REVERT: M 178 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7200 (mmtt) REVERT: M 235 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7387 (tp) outliers start: 98 outliers final: 68 residues processed: 773 average time/residue: 0.2407 time to fit residues: 307.4772 Evaluate side-chains 759 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 683 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 A residue 317 SER Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 47 LEU 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 180 VAL Chi-restraints excluded: chain C residue 184 ASP 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 103 ASP Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 351 ASN Chi-restraints excluded: chain E residue 39 VAL 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 255 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 355 LEU 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 335 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 167 THR Chi-restraints excluded: chain H residue 33 THR 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 111 ILE Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain K residue 43 ASN 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 77 ILE Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 102 ILE 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 39 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 168 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 393 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 328 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 269 optimal weight: 9.9990 chunk 391 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 317 optimal weight: 0.9980 chunk 408 optimal weight: 0.7980 chunk 390 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 285 ASN D 351 ASN E 171 GLN F 15 GLN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 GLN ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN K 257 ASN L 257 ASN M 93 ASN M 285 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.156110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.130723 restraints weight = 70930.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.130856 restraints weight = 47869.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.132111 restraints weight = 45086.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.132418 restraints weight = 30980.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.132790 restraints weight = 29362.848| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 41016 Z= 0.143 Angle : 0.721 21.178 55861 Z= 0.350 Chirality : 0.049 0.398 6549 Planarity : 0.005 0.073 6897 Dihedral : 8.873 137.552 6502 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.24 % Allowed : 22.13 % Favored : 75.64 % 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: 0.04 (0.12), residues: 5088 helix: 0.56 (0.09), residues: 3087 sheet: -0.59 (0.38), residues: 182 loop : -0.68 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 352 TYR 0.085 0.002 TYR J 80 PHE 0.041 0.001 PHE J 54 TRP 0.034 0.001 TRP B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (41016) covalent geometry : angle 0.72103 / 0.35 (55861) hydrogen bonds : bond 0.04147 / 2.77 ( 2201) hydrogen bonds : angle 4.50864 / 3.23 ( 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 803 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 716 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.7183 (mpt180) cc_final: 0.6535 (mmp-170) REVERT: A 273 PHE cc_start: 0.5321 (m-80) cc_final: 0.4846 (m-80) REVERT: B 245 LYS cc_start: 0.8152 (mmmm) cc_final: 0.7619 (mtpt) REVERT: B 290 ASP cc_start: 0.7104 (m-30) cc_final: 0.6871 (m-30) REVERT: B 292 ASN cc_start: 0.8312 (t160) cc_final: 0.7959 (t0) REVERT: B 335 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6211 (mmm) REVERT: B 364 GLN cc_start: 0.5524 (mt0) cc_final: 0.4774 (mt0) REVERT: C 217 MET cc_start: 0.7728 (tpp) cc_final: 0.7108 (tpt) REVERT: D 67 SER cc_start: 0.8357 (p) cc_final: 0.7720 (t) REVERT: D 155 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7330 (mt) REVERT: D 251 ILE cc_start: 0.8191 (tp) cc_final: 0.7976 (tt) REVERT: D 311 MET cc_start: 0.6404 (ptt) cc_final: 0.6096 (ptt) REVERT: E 59 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7519 (mp) REVERT: E 96 ASP cc_start: 0.6831 (m-30) cc_final: 0.6608 (m-30) REVERT: E 114 MET cc_start: 0.6070 (tmm) cc_final: 0.5793 (tmm) REVERT: E 250 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7175 (mm-30) REVERT: E 270 THR cc_start: 0.7955 (p) cc_final: 0.7558 (t) REVERT: E 362 LEU cc_start: 0.7738 (tp) cc_final: 0.7169 (mp) REVERT: F 158 MET cc_start: 0.7770 (ttm) cc_final: 0.7542 (ttm) REVERT: G 43 ASN cc_start: 0.6591 (m-40) cc_final: 0.6209 (p0) REVERT: G 158 MET cc_start: 0.6758 (mtm) cc_final: 0.6509 (mtm) REVERT: G 189 SER cc_start: 0.8153 (m) cc_final: 0.7845 (t) REVERT: G 345 MET cc_start: 0.8271 (mmt) cc_final: 0.8043 (mmt) REVERT: H 154 ARG cc_start: 0.6027 (mmt-90) cc_final: 0.5614 (tpp-160) REVERT: H 217 MET cc_start: 0.7860 (tpt) cc_final: 0.7317 (tpp) REVERT: I 169 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7352 (mt-10) REVERT: I 233 GLU cc_start: 0.7151 (tp30) cc_final: 0.6629 (tp30) REVERT: I 279 TYR cc_start: 0.6260 (m-80) cc_final: 0.5992 (m-80) REVERT: J 17 LYS cc_start: 0.8081 (pttm) cc_final: 0.7620 (ptpp) REVERT: J 114 MET cc_start: 0.4472 (ppp) cc_final: 0.3898 (ttp) REVERT: J 361 ARG cc_start: 0.6693 (mtm110) cc_final: 0.6416 (ttm110) REVERT: J 362 LEU cc_start: 0.6379 (mm) cc_final: 0.6138 (mm) REVERT: K 156 THR cc_start: 0.4145 (OUTLIER) cc_final: 0.3798 (p) REVERT: K 314 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6507 (pp) REVERT: L 5 PHE cc_start: 0.6456 (m-80) cc_final: 0.6059 (m-80) REVERT: L 50 GLU cc_start: 0.6899 (tt0) cc_final: 0.6064 (tt0) REVERT: L 107 MET cc_start: 0.2377 (tpp) cc_final: 0.1646 (mtt) REVERT: L 310 TYR cc_start: 0.7611 (m-80) cc_final: 0.7277 (m-10) REVERT: M 157 ASP cc_start: 0.6232 (t0) cc_final: 0.5854 (m-30) REVERT: M 158 MET cc_start: 0.6301 (mtm) cc_final: 0.5647 (tpt) REVERT: M 178 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7123 (mmtt) REVERT: M 235 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7248 (tp) outliers start: 87 outliers final: 68 residues processed: 775 average time/residue: 0.2372 time to fit residues: 304.1771 Evaluate side-chains 755 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 680 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 A residue 317 SER Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 335 MET 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 180 VAL 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 103 ASP Chi-restraints excluded: chain D residue 155 ILE 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 294 ILE Chi-restraints excluded: chain E residue 39 VAL 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 255 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 318 ILE Chi-restraints excluded: chain F residue 335 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 167 THR Chi-restraints excluded: chain H residue 33 THR 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 111 ILE Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 212 GLN Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 189 SER Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 293 THR 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 314 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 44 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 102 ILE 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 39 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 168 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 506 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 314 optimal weight: 0.0040 chunk 326 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 471 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 294 optimal weight: 6.9990 overall best weight: 2.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 285 ASN E 171 GLN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN K 257 ASN L 257 ASN M 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.155747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.130232 restraints weight = 71647.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.130897 restraints weight = 48562.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.131985 restraints weight = 45255.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.132212 restraints weight = 30335.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.132547 restraints weight = 29050.725| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 41016 Z= 0.196 Angle : 0.894 59.200 55861 Z= 0.488 Chirality : 0.051 0.868 6549 Planarity : 0.005 0.082 6897 Dihedral : 8.873 137.416 6502 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.29 % Allowed : 22.64 % Favored : 75.07 % Cbeta Deviations : 0.06 % 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: 0.04 (0.12), residues: 5088 helix: 0.56 (0.09), residues: 3087 sheet: -0.59 (0.38), residues: 182 loop : -0.68 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 352 TYR 0.071 0.003 TYR J 80 PHE 0.038 0.001 PHE J 54 TRP 0.030 0.001 TRP B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (41016) covalent geometry : angle 0.89351 / 0.49 (55861) hydrogen bonds : bond 0.04174 / 2.78 ( 2201) hydrogen bonds : angle 4.51169 / 3.23 ( 6300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7883.61 seconds wall clock time: 136 minutes 32.43 seconds (8192.43 seconds total)