Starting phenix.real_space_refine on Thu Mar 5 17:53:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzw_22582/03_2026/7jzw_22582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzw_22582/03_2026/7jzw_22582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jzw_22582/03_2026/7jzw_22582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzw_22582/03_2026/7jzw_22582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzw_22582/03_2026/7jzw_22582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzw_22582/03_2026/7jzw_22582.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 60 5.49 5 S 29 5.16 5 C 15040 2.51 5 N 4422 2.21 5 O 4715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24266 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 9, 'GLU:plan': 8, 'ARG:plan': 9, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 192 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 760 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.96, per 1000 atoms: 0.25 Number of scatterers: 24266 At special positions: 0 Unit cell: (130.2, 157.5, 148.05, 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 29 16.00 P 60 15.00 O 4715 8.00 N 4422 7.00 C 15040 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: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 56 sheets defined 32.4% alpha, 22.8% beta 6 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.417A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.663A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.600A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.500A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.785A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.658A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.819A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 removed outlier: 4.444A pdb=" N GLN A 273 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.515A pdb=" N SER A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 364 through 368 removed outlier: 4.044A pdb=" N ARG A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.590A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 381' Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.667A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.781A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 4.376A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.902A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.889A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'B' and resid 33 through 49 removed outlier: 3.904A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.648A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.581A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 322 through 331 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 322 through 332 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.633A pdb=" N SER F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.588A pdb=" N ALA F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 322 through 332 removed outlier: 3.504A pdb=" N LEU F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 209 through 223 removed outlier: 3.565A pdb=" N ALA G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 293 through 297 Processing helix chain 'G' and resid 322 through 331 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.739A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 5 through 14 removed outlier: 3.539A pdb=" N ILE J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR J 12 " --> pdb=" O ASP J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 78 Processing helix chain 'J' and resid 79 through 100 removed outlier: 3.690A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.211A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.211A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 254 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.534A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.534A pdb=" N HIS C 3 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.509A pdb=" N VAL C 184 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 60 removed outlier: 4.079A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.198A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 19 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AB5, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AB6, first strand: chain 'B' and resid 304 through 306 Processing sheet with id=AB7, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AB8, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.212A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.553A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 63 through 70 Processing sheet with id=AC2, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC3, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.519A pdb=" N VAL E 307 " --> pdb=" O LYS E 312 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AC5, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.093A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D 176 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 188 " --> pdb=" O ARG D 185 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'D' and resid 63 through 66 removed outlier: 4.598A pdb=" N ALA D 101 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.603A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AD1, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AD2, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AD3, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.181A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 191 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD5, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.671A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD7, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.670A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.040A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 189 through 192 removed outlier: 3.670A pdb=" N ARG G 191 " --> pdb=" O HIS G 183 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 63 through 70 removed outlier: 3.611A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE4, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.569A pdb=" N GLY H 353 " --> pdb=" O PHE H 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.142A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 188 through 192 removed outlier: 6.731A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 63 through 66 removed outlier: 4.576A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 69 through 70 removed outlier: 3.697A pdb=" N GLY H 70 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 248 through 249 removed outlier: 4.702A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AF2, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.653A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AF4, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.528A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL I 177 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP I 196 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL I 179 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG I 194 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AF6, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.729A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.729A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS I 261 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR I 97 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS I 263 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF9, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.665A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 17 through 21 removed outlier: 12.893A pdb=" N TRP J 28 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N VAL J 47 " --> pdb=" O TRP J 28 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE J 30 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY J 55 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 17 through 21 1050 hydrogen bonds defined for protein. 2925 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 4.75 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5046 1.32 - 1.44: 5968 1.44 - 1.56: 13702 1.56 - 1.68: 120 1.68 - 1.80: 44 Bond restraints: 24880 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.382 -0.046 9.80e-03 1.04e+04 2.16e+01 bond pdb=" O3' A M 36 " pdb=" P C M 37 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.26e+01 bond pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.32e-02 5.74e+03 8.10e+00 bond pdb=" N GLN H 186 " pdb=" CA GLN H 186 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.19e+00 bond pdb=" CG LEU D 229 " pdb=" CD1 LEU D 229 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.90e+00 ... (remaining 24875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 32451 2.02 - 4.05: 1378 4.05 - 6.07: 181 6.07 - 8.10: 53 8.10 - 10.12: 13 Bond angle restraints: 34076 Sorted by residual: angle pdb=" O ARG H 185 " pdb=" C ARG H 185 " pdb=" N GLN H 186 " ideal model delta sigma weight residual 122.23 129.29 -7.06 1.33e+00 5.65e-01 2.82e+01 angle pdb=" C ARG F 185 " pdb=" N GLN F 186 " pdb=" CA GLN F 186 " ideal model delta sigma weight residual 120.82 128.71 -7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.79 127.65 -6.86 1.39e+00 5.18e-01 2.44e+01 angle pdb=" C ARG I 185 " pdb=" N GLN I 186 " pdb=" CA GLN I 186 " ideal model delta sigma weight residual 120.38 126.93 -6.55 1.37e+00 5.33e-01 2.28e+01 angle pdb=" C ARG H 185 " pdb=" N GLN H 186 " pdb=" CA GLN H 186 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 ... (remaining 34071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 14498 35.59 - 71.19: 468 71.19 - 106.78: 39 106.78 - 142.37: 1 142.37 - 177.96: 5 Dihedral angle restraints: 15011 sinusoidal: 6419 harmonic: 8592 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 53.90 146.10 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 65.69 134.31 1 1.50e+01 4.44e-03 7.25e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual -128.00 49.96 -177.96 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3034 0.063 - 0.127: 682 0.127 - 0.190: 113 0.190 - 0.254: 6 0.254 - 0.317: 4 Chirality restraints: 3839 Sorted by residual: chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE B 219 " pdb=" CA ILE B 219 " pdb=" CG1 ILE B 219 " pdb=" CG2 ILE B 219 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1' U M 33 " pdb=" O4' U M 33 " pdb=" C2' U M 33 " pdb=" N1 U M 33 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3836 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.95e+00 pdb=" N PRO A 72 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 73 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO C 74 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 103 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO D 104 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " 0.038 5.00e-02 4.00e+02 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4954 2.77 - 3.30: 21528 3.30 - 3.83: 42348 3.83 - 4.37: 51903 4.37 - 4.90: 87079 Nonbonded interactions: 207812 Sorted by model distance: nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR E 324 " pdb=" O SER F 73 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.256 3.040 nonbonded pdb=" O SER E 73 " pdb=" OH TYR D 324 " model vdw 2.266 3.040 ... (remaining 207807 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 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 24.850 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.010 0.080 24880 Z= 0.411 Angle : 0.973 10.119 34076 Z= 0.541 Chirality : 0.055 0.317 3839 Planarity : 0.007 0.079 4272 Dihedral : 17.319 177.963 9463 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.93 % Favored : 93.04 % Rotamer: Outliers : 0.13 % Allowed : 8.21 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -3.86 (0.12), residues: 2959 helix: -2.82 (0.11), residues: 933 sheet: -1.31 (0.22), residues: 482 loop : -2.85 (0.12), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 237 TYR 0.021 0.003 TYR F 290 PHE 0.027 0.003 PHE B 40 TRP 0.033 0.003 TRP I 49 HIS 0.010 0.002 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00959 (24880) covalent geometry : angle 0.97325 (34076) hydrogen bonds : bond 0.16316 ( 988) hydrogen bonds : angle 7.64732 ( 2953) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 285 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.7798 (m-30) cc_final: 0.7554 (m-30) REVERT: A 420 LYS cc_start: 0.7768 (ttpp) cc_final: 0.7522 (ttpp) REVERT: C 84 GLN cc_start: 0.8369 (pt0) cc_final: 0.8137 (pt0) REVERT: B 76 LYS cc_start: 0.8895 (mttp) cc_final: 0.8517 (mttt) REVERT: B 152 PHE cc_start: 0.6389 (p90) cc_final: 0.6107 (p90) REVERT: B 268 ARG cc_start: 0.6784 (tpt170) cc_final: 0.6581 (ttt90) REVERT: D 66 LYS cc_start: 0.7757 (ptmt) cc_final: 0.7439 (ptmt) REVERT: D 138 LEU cc_start: 0.8765 (mt) cc_final: 0.8448 (mp) REVERT: I 307 VAL cc_start: 0.8933 (t) cc_final: 0.8709 (t) REVERT: J 26 TRP cc_start: 0.8634 (m100) cc_final: 0.8087 (m100) outliers start: 3 outliers final: 2 residues processed: 288 average time/residue: 0.2378 time to fit residues: 96.1222 Evaluate side-chains 204 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain H residue 78 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 10.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 305 GLN C 29 HIS B 69 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS D 310 GLN F 242 GLN G 242 GLN H 129 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.122043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093752 restraints weight = 49292.180| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.73 r_work: 0.2880 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24880 Z= 0.122 Angle : 0.560 11.702 34076 Z= 0.297 Chirality : 0.040 0.212 3839 Planarity : 0.005 0.055 4272 Dihedral : 15.396 179.932 4206 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 1.30 % Allowed : 11.88 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -2.34 (0.13), residues: 2959 helix: -0.82 (0.15), residues: 950 sheet: -0.55 (0.23), residues: 460 loop : -2.42 (0.13), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 57 TYR 0.014 0.001 TYR G 290 PHE 0.013 0.001 PHE C 44 TRP 0.011 0.001 TRP F 49 HIS 0.005 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00256 (24880) covalent geometry : angle 0.55977 (34076) hydrogen bonds : bond 0.03502 ( 988) hydrogen bonds : angle 5.04409 ( 2953) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: A 276 ASN cc_start: 0.5783 (m-40) cc_final: 0.5510 (p0) REVERT: A 290 ASP cc_start: 0.7923 (m-30) cc_final: 0.7686 (m-30) REVERT: A 420 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7590 (ttpp) REVERT: C 84 GLN cc_start: 0.8477 (pt0) cc_final: 0.8135 (pt0) REVERT: B 57 ASP cc_start: 0.7716 (t0) cc_final: 0.7508 (t0) REVERT: B 76 LYS cc_start: 0.8896 (mttp) cc_final: 0.8560 (mttt) REVERT: B 170 ARG cc_start: 0.7582 (ttp80) cc_final: 0.7115 (mtp-110) REVERT: B 200 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7994 (tp) REVERT: B 288 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8117 (tp30) REVERT: D 138 LEU cc_start: 0.8643 (mt) cc_final: 0.8319 (mt) REVERT: F 185 ARG cc_start: 0.8360 (tpp80) cc_final: 0.7915 (mmp80) REVERT: G 95 LEU cc_start: 0.8996 (mm) cc_final: 0.8783 (mt) REVERT: G 290 TYR cc_start: 0.9198 (p90) cc_final: 0.8967 (p90) REVERT: H 80 ASP cc_start: 0.8054 (m-30) cc_final: 0.7326 (t0) REVERT: H 290 TYR cc_start: 0.8880 (p90) cc_final: 0.8625 (p90) REVERT: J 26 TRP cc_start: 0.8474 (m100) cc_final: 0.7830 (m100) REVERT: J 79 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7719 (mtp180) outliers start: 30 outliers final: 13 residues processed: 263 average time/residue: 0.2273 time to fit residues: 85.1878 Evaluate side-chains 225 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 319 GLN Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 79 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 227 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 184 optimal weight: 0.3980 chunk 283 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN B 69 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 348 ASN D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.091396 restraints weight = 41635.395| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.33 r_work: 0.2891 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24880 Z= 0.141 Angle : 0.542 11.097 34076 Z= 0.282 Chirality : 0.040 0.204 3839 Planarity : 0.004 0.052 4272 Dihedral : 15.223 179.809 4206 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.02 % Rotamer: Outliers : 1.77 % Allowed : 12.87 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 2959 helix: 0.09 (0.16), residues: 950 sheet: -0.36 (0.23), residues: 466 loop : -2.20 (0.14), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 8 TYR 0.019 0.002 TYR C 176 PHE 0.010 0.001 PHE A 425 TRP 0.011 0.001 TRP F 49 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00316 (24880) covalent geometry : angle 0.54176 (34076) hydrogen bonds : bond 0.03264 ( 988) hydrogen bonds : angle 4.67328 ( 2953) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: A 276 ASN cc_start: 0.5805 (m-40) cc_final: 0.5570 (p0) REVERT: A 420 LYS cc_start: 0.7936 (ttpp) cc_final: 0.7687 (ttpp) REVERT: A 422 LEU cc_start: 0.8413 (mm) cc_final: 0.8049 (mt) REVERT: C 84 GLN cc_start: 0.8542 (pt0) cc_final: 0.8231 (pt0) REVERT: B 76 LYS cc_start: 0.8953 (mttp) cc_final: 0.8612 (mttt) REVERT: B 143 SER cc_start: 0.9097 (OUTLIER) cc_final: 0.8872 (m) REVERT: B 152 PHE cc_start: 0.6924 (p90) cc_final: 0.6644 (p90) REVERT: B 200 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8084 (tp) REVERT: D 138 LEU cc_start: 0.8705 (mt) cc_final: 0.8347 (mt) REVERT: F 185 ARG cc_start: 0.8508 (tpp80) cc_final: 0.8063 (mmp80) REVERT: G 53 ASP cc_start: 0.8993 (m-30) cc_final: 0.8766 (m-30) REVERT: H 290 TYR cc_start: 0.8991 (p90) cc_final: 0.8630 (p90) REVERT: J 26 TRP cc_start: 0.8522 (m100) cc_final: 0.7870 (m100) outliers start: 41 outliers final: 26 residues processed: 250 average time/residue: 0.2116 time to fit residues: 76.8623 Evaluate side-chains 233 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 319 GLN Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 222 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN G 342 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN J 80 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.090262 restraints weight = 54690.254| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.09 r_work: 0.2820 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24880 Z= 0.176 Angle : 0.555 12.703 34076 Z= 0.288 Chirality : 0.041 0.201 3839 Planarity : 0.004 0.053 4272 Dihedral : 15.166 179.230 4206 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 2.12 % Allowed : 14.08 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.15), residues: 2959 helix: 0.52 (0.16), residues: 952 sheet: -0.39 (0.22), residues: 491 loop : -2.10 (0.14), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.014 0.002 TYR C 176 PHE 0.012 0.001 PHE H 114 TRP 0.012 0.001 TRP F 49 HIS 0.004 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00406 (24880) covalent geometry : angle 0.55534 (34076) hydrogen bonds : bond 0.03251 ( 988) hydrogen bonds : angle 4.52924 ( 2953) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8089 (pt0) REVERT: A 290 ASP cc_start: 0.8035 (m-30) cc_final: 0.7716 (m-30) REVERT: A 420 LYS cc_start: 0.7931 (ttpp) cc_final: 0.7696 (ttpp) REVERT: A 422 LEU cc_start: 0.8427 (mm) cc_final: 0.8114 (mt) REVERT: C 84 GLN cc_start: 0.8432 (pt0) cc_final: 0.8160 (pt0) REVERT: B 76 LYS cc_start: 0.8891 (mttp) cc_final: 0.8515 (mttt) REVERT: B 143 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8778 (m) REVERT: B 152 PHE cc_start: 0.6767 (p90) cc_final: 0.6503 (p90) REVERT: B 200 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7952 (tp) REVERT: B 268 ARG cc_start: 0.6851 (tpt170) cc_final: 0.6553 (ttt90) REVERT: E 43 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8777 (mp) REVERT: E 85 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8539 (tppt) REVERT: D 138 LEU cc_start: 0.8597 (mt) cc_final: 0.8142 (mp) REVERT: F 146 ASN cc_start: 0.8860 (t0) cc_final: 0.8650 (t0) REVERT: F 185 ARG cc_start: 0.8417 (tpp80) cc_final: 0.8031 (mmp80) REVERT: G 290 TYR cc_start: 0.9257 (p90) cc_final: 0.8951 (p90) REVERT: H 290 TYR cc_start: 0.8919 (p90) cc_final: 0.8598 (p90) REVERT: H 307 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8372 (m) REVERT: J 26 TRP cc_start: 0.8478 (m100) cc_final: 0.7845 (m100) outliers start: 49 outliers final: 33 residues processed: 259 average time/residue: 0.2139 time to fit residues: 80.3167 Evaluate side-chains 242 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 319 GLN Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 214 optimal weight: 4.9990 chunk 157 optimal weight: 0.0470 chunk 184 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 262 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 143 optimal weight: 5.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN G 348 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088656 restraints weight = 39084.830| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.20 r_work: 0.2843 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24880 Z= 0.199 Angle : 0.565 12.773 34076 Z= 0.293 Chirality : 0.041 0.203 3839 Planarity : 0.004 0.054 4272 Dihedral : 15.178 179.070 4206 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.61 % Rotamer: Outliers : 2.42 % Allowed : 15.51 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.15), residues: 2959 helix: 0.68 (0.16), residues: 956 sheet: -0.34 (0.23), residues: 491 loop : -2.04 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 237 TYR 0.014 0.002 TYR C 176 PHE 0.014 0.002 PHE C 44 TRP 0.015 0.001 TRP G 49 HIS 0.005 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00464 (24880) covalent geometry : angle 0.56514 (34076) hydrogen bonds : bond 0.03280 ( 988) hydrogen bonds : angle 4.48408 ( 2953) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 211 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8114 (pt0) REVERT: A 290 ASP cc_start: 0.8052 (m-30) cc_final: 0.7762 (m-30) REVERT: A 422 LEU cc_start: 0.8466 (mm) cc_final: 0.8156 (mt) REVERT: C 84 GLN cc_start: 0.8529 (pt0) cc_final: 0.8211 (pt0) REVERT: B 76 LYS cc_start: 0.8987 (mttp) cc_final: 0.8608 (mttt) REVERT: B 152 PHE cc_start: 0.6919 (p90) cc_final: 0.6646 (p90) REVERT: B 200 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8000 (tp) REVERT: B 268 ARG cc_start: 0.6960 (tpt170) cc_final: 0.6663 (ttt90) REVERT: B 288 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: E 43 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8846 (mp) REVERT: E 85 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8557 (tppt) REVERT: E 314 TYR cc_start: 0.8385 (m-80) cc_final: 0.7962 (m-80) REVERT: D 138 LEU cc_start: 0.8668 (mt) cc_final: 0.8205 (mp) REVERT: D 212 ASP cc_start: 0.8189 (m-30) cc_final: 0.7639 (t0) REVERT: F 185 ARG cc_start: 0.8603 (tpp80) cc_final: 0.8207 (mmp80) REVERT: G 290 TYR cc_start: 0.9286 (p90) cc_final: 0.8994 (p90) REVERT: H 290 TYR cc_start: 0.8994 (p90) cc_final: 0.8651 (p90) REVERT: H 307 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8469 (m) REVERT: J 26 TRP cc_start: 0.8526 (m100) cc_final: 0.7858 (m100) outliers start: 56 outliers final: 39 residues processed: 252 average time/residue: 0.2110 time to fit residues: 76.8897 Evaluate side-chains 241 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 319 GLN Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 chunk 143 optimal weight: 0.3980 chunk 156 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.090401 restraints weight = 39692.629| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.20 r_work: 0.2877 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24880 Z= 0.141 Angle : 0.527 12.487 34076 Z= 0.274 Chirality : 0.040 0.201 3839 Planarity : 0.004 0.053 4272 Dihedral : 15.115 179.829 4206 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.02 % Rotamer: Outliers : 2.33 % Allowed : 16.33 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 2959 helix: 0.94 (0.17), residues: 956 sheet: -0.39 (0.22), residues: 502 loop : -1.92 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 237 TYR 0.011 0.001 TYR C 176 PHE 0.011 0.001 PHE C 155 TRP 0.012 0.001 TRP F 49 HIS 0.003 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00322 (24880) covalent geometry : angle 0.52742 (34076) hydrogen bonds : bond 0.03040 ( 988) hydrogen bonds : angle 4.32173 ( 2953) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8130 (pt0) REVERT: A 290 ASP cc_start: 0.8048 (m-30) cc_final: 0.7748 (m-30) REVERT: A 422 LEU cc_start: 0.8430 (mm) cc_final: 0.8158 (mt) REVERT: C 84 GLN cc_start: 0.8490 (pt0) cc_final: 0.8232 (pt0) REVERT: B 76 LYS cc_start: 0.8937 (mttp) cc_final: 0.8559 (mttt) REVERT: B 143 SER cc_start: 0.9134 (OUTLIER) cc_final: 0.8924 (m) REVERT: B 152 PHE cc_start: 0.6853 (p90) cc_final: 0.6619 (p90) REVERT: B 170 ARG cc_start: 0.7411 (mtp-110) cc_final: 0.6692 (tmm-80) REVERT: B 200 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7951 (tp) REVERT: B 268 ARG cc_start: 0.6960 (tpt170) cc_final: 0.6655 (ttt90) REVERT: E 43 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8786 (mp) REVERT: E 85 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8558 (tppt) REVERT: E 314 TYR cc_start: 0.8353 (m-80) cc_final: 0.8022 (m-80) REVERT: D 212 ASP cc_start: 0.8089 (m-30) cc_final: 0.7613 (t0) REVERT: F 185 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8113 (mmp80) REVERT: G 290 TYR cc_start: 0.9233 (p90) cc_final: 0.8986 (p90) REVERT: H 251 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7320 (mp) REVERT: H 290 TYR cc_start: 0.9000 (p90) cc_final: 0.8651 (p90) REVERT: H 307 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8430 (m) REVERT: I 307 VAL cc_start: 0.8855 (t) cc_final: 0.8529 (t) REVERT: J 26 TRP cc_start: 0.8473 (m100) cc_final: 0.7850 (m100) outliers start: 54 outliers final: 42 residues processed: 252 average time/residue: 0.2149 time to fit residues: 78.4864 Evaluate side-chains 247 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 316 GLN Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 242 optimal weight: 0.7980 chunk 241 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 274 optimal weight: 0.0050 chunk 276 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 247 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092644 restraints weight = 41463.440| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.14 r_work: 0.2935 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24880 Z= 0.110 Angle : 0.503 12.152 34076 Z= 0.262 Chirality : 0.039 0.197 3839 Planarity : 0.003 0.052 4272 Dihedral : 15.026 179.187 4203 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 2.20 % Allowed : 16.85 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.81 (0.15), residues: 2959 helix: 1.19 (0.17), residues: 957 sheet: -0.32 (0.22), residues: 502 loop : -1.83 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 237 TYR 0.012 0.001 TYR A 235 PHE 0.010 0.001 PHE C 44 TRP 0.010 0.001 TRP F 49 HIS 0.004 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00243 (24880) covalent geometry : angle 0.50328 (34076) hydrogen bonds : bond 0.02872 ( 988) hydrogen bonds : angle 4.15907 ( 2953) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8195 (pt0) REVERT: A 290 ASP cc_start: 0.8018 (m-30) cc_final: 0.7716 (m-30) REVERT: A 422 LEU cc_start: 0.8431 (mm) cc_final: 0.8160 (mt) REVERT: C 84 GLN cc_start: 0.8450 (pt0) cc_final: 0.8225 (pt0) REVERT: B 76 LYS cc_start: 0.8915 (mttp) cc_final: 0.8550 (mttt) REVERT: B 152 PHE cc_start: 0.6733 (p90) cc_final: 0.6527 (p90) REVERT: B 268 ARG cc_start: 0.6956 (tpt170) cc_final: 0.6670 (ttt90) REVERT: E 85 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8550 (tppt) REVERT: E 308 THR cc_start: 0.8619 (t) cc_final: 0.8400 (p) REVERT: E 314 TYR cc_start: 0.8327 (m-80) cc_final: 0.7948 (m-80) REVERT: E 316 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8127 (mm-40) REVERT: D 102 ASN cc_start: 0.8646 (m110) cc_final: 0.8386 (m110) REVERT: D 139 GLN cc_start: 0.8102 (tt0) cc_final: 0.7871 (tt0) REVERT: D 212 ASP cc_start: 0.8048 (m-30) cc_final: 0.7591 (t0) REVERT: F 185 ARG cc_start: 0.8458 (tpp80) cc_final: 0.8132 (mmp80) REVERT: G 290 TYR cc_start: 0.9184 (p90) cc_final: 0.8955 (p90) REVERT: H 251 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7328 (mp) REVERT: H 290 TYR cc_start: 0.8938 (p90) cc_final: 0.8646 (p90) REVERT: H 307 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8429 (m) REVERT: I 94 ASN cc_start: 0.8661 (p0) cc_final: 0.7989 (t0) REVERT: I 307 VAL cc_start: 0.8831 (t) cc_final: 0.8510 (t) REVERT: I 333 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8474 (ptp90) REVERT: J 26 TRP cc_start: 0.8432 (m100) cc_final: 0.7854 (m100) outliers start: 51 outliers final: 34 residues processed: 247 average time/residue: 0.2148 time to fit residues: 76.9646 Evaluate side-chains 239 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 316 GLN Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 221 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 193 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.122679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093666 restraints weight = 46544.768| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.46 r_work: 0.2914 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24880 Z= 0.113 Angle : 0.500 12.319 34076 Z= 0.259 Chirality : 0.039 0.195 3839 Planarity : 0.003 0.052 4272 Dihedral : 14.960 179.259 4203 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.12 % Allowed : 17.24 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 2959 helix: 1.32 (0.17), residues: 958 sheet: -0.27 (0.22), residues: 508 loop : -1.76 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 134 TYR 0.013 0.001 TYR I 304 PHE 0.010 0.001 PHE B 40 TRP 0.008 0.001 TRP F 49 HIS 0.006 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00252 (24880) covalent geometry : angle 0.49956 (34076) hydrogen bonds : bond 0.02813 ( 988) hydrogen bonds : angle 4.09277 ( 2953) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: A 289 HIS cc_start: 0.7203 (m-70) cc_final: 0.6706 (m-70) REVERT: A 422 LEU cc_start: 0.8438 (mm) cc_final: 0.8194 (mt) REVERT: C 84 GLN cc_start: 0.8381 (pt0) cc_final: 0.8168 (pt0) REVERT: B 76 LYS cc_start: 0.8877 (mttp) cc_final: 0.8524 (mttt) REVERT: B 268 ARG cc_start: 0.6827 (tpt170) cc_final: 0.6532 (ttt90) REVERT: B 288 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: E 82 ASP cc_start: 0.8122 (m-30) cc_final: 0.7859 (t0) REVERT: E 308 THR cc_start: 0.8555 (t) cc_final: 0.8333 (p) REVERT: D 139 GLN cc_start: 0.7964 (tt0) cc_final: 0.7747 (tt0) REVERT: D 212 ASP cc_start: 0.7869 (m-30) cc_final: 0.7479 (t0) REVERT: F 185 ARG cc_start: 0.8302 (tpp80) cc_final: 0.7958 (mmp80) REVERT: G 290 TYR cc_start: 0.9141 (p90) cc_final: 0.8917 (p90) REVERT: H 251 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7299 (mp) REVERT: H 290 TYR cc_start: 0.8829 (p90) cc_final: 0.8625 (p90) REVERT: H 307 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8347 (m) REVERT: I 94 ASN cc_start: 0.8566 (p0) cc_final: 0.7918 (t0) REVERT: I 307 VAL cc_start: 0.8788 (t) cc_final: 0.8469 (t) REVERT: J 26 TRP cc_start: 0.8408 (m100) cc_final: 0.7870 (m100) outliers start: 49 outliers final: 34 residues processed: 247 average time/residue: 0.2077 time to fit residues: 74.2346 Evaluate side-chains 239 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 122 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 28 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 148 optimal weight: 0.0270 chunk 35 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093600 restraints weight = 46669.913| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.46 r_work: 0.2917 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24880 Z= 0.109 Angle : 0.496 12.281 34076 Z= 0.257 Chirality : 0.039 0.194 3839 Planarity : 0.003 0.052 4272 Dihedral : 14.937 178.550 4203 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.86 % Allowed : 17.67 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.57 (0.15), residues: 2959 helix: 1.43 (0.17), residues: 957 sheet: -0.21 (0.22), residues: 508 loop : -1.73 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 170 TYR 0.017 0.001 TYR C 176 PHE 0.011 0.001 PHE B 40 TRP 0.008 0.001 TRP G 49 HIS 0.013 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00243 (24880) covalent geometry : angle 0.49601 (34076) hydrogen bonds : bond 0.02771 ( 988) hydrogen bonds : angle 4.04203 ( 2953) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8173 (pt0) REVERT: A 289 HIS cc_start: 0.7163 (m-70) cc_final: 0.6808 (m90) REVERT: A 417 GLU cc_start: 0.7198 (pp20) cc_final: 0.6824 (mm-30) REVERT: A 422 LEU cc_start: 0.8392 (mm) cc_final: 0.8152 (mt) REVERT: C 84 GLN cc_start: 0.8362 (pt0) cc_final: 0.8152 (pt0) REVERT: B 76 LYS cc_start: 0.8831 (mttp) cc_final: 0.8479 (mttt) REVERT: B 170 ARG cc_start: 0.7283 (mtp-110) cc_final: 0.6718 (tmm-80) REVERT: B 268 ARG cc_start: 0.6812 (tpt170) cc_final: 0.6530 (ttt90) REVERT: B 288 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: E 82 ASP cc_start: 0.8130 (m-30) cc_final: 0.7873 (t0) REVERT: D 139 GLN cc_start: 0.8000 (tt0) cc_final: 0.7779 (tt0) REVERT: D 212 ASP cc_start: 0.7855 (m-30) cc_final: 0.7461 (t0) REVERT: F 185 ARG cc_start: 0.8283 (tpp80) cc_final: 0.7916 (mmp80) REVERT: G 290 TYR cc_start: 0.9126 (p90) cc_final: 0.8918 (p90) REVERT: H 251 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7291 (mp) REVERT: H 290 TYR cc_start: 0.8820 (p90) cc_final: 0.8613 (p90) REVERT: H 307 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8305 (m) REVERT: I 94 ASN cc_start: 0.8566 (p0) cc_final: 0.7936 (t0) REVERT: I 307 VAL cc_start: 0.8704 (t) cc_final: 0.8385 (t) REVERT: J 26 TRP cc_start: 0.8393 (m100) cc_final: 0.7846 (m100) outliers start: 43 outliers final: 34 residues processed: 233 average time/residue: 0.2104 time to fit residues: 71.5634 Evaluate side-chains 233 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 90 optimal weight: 0.0030 chunk 70 optimal weight: 0.6980 chunk 225 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093600 restraints weight = 39176.888| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.20 r_work: 0.2950 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24880 Z= 0.107 Angle : 0.500 12.380 34076 Z= 0.258 Chirality : 0.039 0.193 3839 Planarity : 0.003 0.051 4272 Dihedral : 14.917 178.362 4203 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.64 % Allowed : 18.01 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.53 (0.15), residues: 2959 helix: 1.49 (0.17), residues: 958 sheet: -0.18 (0.23), residues: 504 loop : -1.72 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 170 TYR 0.021 0.001 TYR C 176 PHE 0.011 0.001 PHE B 40 TRP 0.007 0.001 TRP B 29 HIS 0.014 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00241 (24880) covalent geometry : angle 0.49968 (34076) hydrogen bonds : bond 0.02760 ( 988) hydrogen bonds : angle 4.02035 ( 2953) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5918 Ramachandran restraints generated. 2959 Oldfield, 0 Emsley, 2959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: A 289 HIS cc_start: 0.7315 (m-70) cc_final: 0.6974 (m90) REVERT: A 417 GLU cc_start: 0.7223 (pp20) cc_final: 0.6839 (mm-30) REVERT: A 422 LEU cc_start: 0.8474 (mm) cc_final: 0.8137 (mt) REVERT: C 84 GLN cc_start: 0.8432 (pt0) cc_final: 0.8211 (pt0) REVERT: B 76 LYS cc_start: 0.8882 (mttp) cc_final: 0.8536 (mttt) REVERT: B 268 ARG cc_start: 0.6937 (tpt170) cc_final: 0.6653 (ttt90) REVERT: B 288 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: E 82 ASP cc_start: 0.8146 (m-30) cc_final: 0.7862 (t0) REVERT: E 314 TYR cc_start: 0.8360 (m-80) cc_final: 0.8033 (m-80) REVERT: D 139 GLN cc_start: 0.8090 (tt0) cc_final: 0.7856 (tt0) REVERT: D 212 ASP cc_start: 0.8027 (m-30) cc_final: 0.7572 (t0) REVERT: F 185 ARG cc_start: 0.8402 (tpp80) cc_final: 0.7998 (mmp80) REVERT: H 251 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7308 (mp) REVERT: H 304 TYR cc_start: 0.7869 (m-80) cc_final: 0.7661 (m-80) REVERT: H 307 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8383 (m) REVERT: I 94 ASN cc_start: 0.8670 (p0) cc_final: 0.8035 (t0) REVERT: I 307 VAL cc_start: 0.8759 (t) cc_final: 0.8461 (t) REVERT: J 26 TRP cc_start: 0.8413 (m100) cc_final: 0.7823 (m100) outliers start: 38 outliers final: 33 residues processed: 223 average time/residue: 0.2165 time to fit residues: 69.8724 Evaluate side-chains 232 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 248 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 230 optimal weight: 0.8980 chunk 273 optimal weight: 0.0570 chunk 221 optimal weight: 0.0270 chunk 32 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 241 optimal weight: 0.0470 chunk 39 optimal weight: 5.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN I 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095250 restraints weight = 39830.012| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.23 r_work: 0.2981 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24880 Z= 0.088 Angle : 0.487 12.273 34076 Z= 0.252 Chirality : 0.038 0.191 3839 Planarity : 0.003 0.050 4272 Dihedral : 14.866 178.885 4203 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.43 % Allowed : 18.44 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.40 (0.15), residues: 2959 helix: 1.61 (0.17), residues: 957 sheet: 0.05 (0.23), residues: 491 loop : -1.71 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 170 TYR 0.018 0.001 TYR A 235 PHE 0.011 0.001 PHE A 118 TRP 0.010 0.001 TRP F 193 HIS 0.012 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00190 (24880) covalent geometry : angle 0.48739 (34076) hydrogen bonds : bond 0.02646 ( 988) hydrogen bonds : angle 3.92309 ( 2953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6210.30 seconds wall clock time: 106 minutes 50.55 seconds (6410.55 seconds total)