Starting phenix.real_space_refine on Sun Sep 13 15:43:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jzw_22582/09_2026/7jzw_22582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzw_22582/09_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_22582/09_2026/7jzw_22582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzw_22582/09_2026/7jzw_22582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jzw_22582/09_2026/7jzw_22582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzw_22582/09_2026/7jzw_22582.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7jzw_22582/09_2026/7jzw_22582.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jzw_22582/09_2026/7jzw_22582.cif" } 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-2.2.1-6174/lib/python3.11/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, 'RNAv2': 60} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.60, per 1000 atoms: 0.23 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: 1.86 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: 3.27 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: 5.14 Time building geometry restraints manager: 2.57 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 1.20e-02 6.94e+03 1.96e+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: 32214 2.02 - 4.05: 1550 4.05 - 6.07: 239 6.07 - 8.10: 56 8.10 - 10.12: 14 Bond angle restraints: 34073 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 34068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.79: 13029 18.79 - 37.59: 1306 37.59 - 56.38: 315 56.38 - 75.17: 128 75.17 - 93.97: 16 Dihedral angle restraints: 14794 sinusoidal: 6202 harmonic: 8592 Sorted by residual: dihedral pdb=" C4' C M 37 " pdb=" C3' C M 37 " pdb=" C2' C M 37 " pdb=" C1' C M 37 " ideal model delta sinusoidal sigma weight residual 36.34 -45.03 81.38 1 3.10e+00 1.04e-01 8.49e+02 dihedral pdb=" C4' G M 19 " pdb=" C3' G M 19 " pdb=" C2' G M 19 " pdb=" C1' G M 19 " ideal model delta sinusoidal sigma weight residual 36.35 -37.48 73.82 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' G M 40 " pdb=" C3' G M 40 " pdb=" C2' G M 40 " pdb=" C1' G M 40 " ideal model delta sinusoidal sigma weight residual 36.34 -37.16 73.50 1 3.10e+00 1.04e-01 7.15e+02 ... (remaining 14791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3449 0.099 - 0.199: 300 0.199 - 0.298: 80 0.298 - 0.398: 9 0.398 - 0.497: 1 Chirality restraints: 3839 Sorted by residual: chirality pdb=" C2' C M 37 " pdb=" C3' C M 37 " pdb=" O2' C M 37 " pdb=" C1' C M 37 " both_signs ideal model delta sigma weight residual False -2.79 -2.29 -0.50 2.00e-01 2.50e+01 6.18e+00 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=" C3' G M 40 " pdb=" C4' G M 40 " pdb=" O3' G M 40 " pdb=" C2' G M 40 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.46e+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: 1.470 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.240 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 1.018 10.119 34073 Z= 0.547 Chirality : 0.067 0.497 3839 Planarity : 0.007 0.079 4272 Dihedral : 17.071 93.967 9246 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/Z covalent geometry : bond 0.00961 / 0.41 (24880) covalent geometry : angle 1.01816 / 0.55 (34073) hydrogen bonds : bond 0.16316 / 10.98 ( 988) hydrogen bonds : angle 7.64732 / 5.67 ( 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 : 0.813 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: 0.2302 time to fit residues: 93.8272 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 : 0.795 ------------------------------------------------------------------------------- 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: 9.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN A 305 GLN B 69 GLN ** 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.094866 restraints weight = 49070.913| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.74 r_work: 0.2908 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24880 Z= 0.147 Angle : 0.875 19.639 34073 Z= 0.384 Chirality : 0.072 0.984 3839 Planarity : 0.005 0.057 4272 Dihedral : 12.384 145.674 3989 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 1.25 % Allowed : 11.84 % Favored : 86.91 % 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: -2.43 (0.13), residues: 2959 helix: -0.92 (0.15), residues: 950 sheet: -0.59 (0.23), residues: 457 loop : -2.45 (0.13), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 237 TYR 0.014 0.002 TYR C 176 PHE 0.012 0.001 PHE C 44 TRP 0.012 0.001 TRP F 49 HIS 0.008 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (24880) covalent geometry : angle 0.87527 / 0.38 (34073) hydrogen bonds : bond 0.03647 / 2.50 ( 988) hydrogen bonds : angle 5.14255 / 3.74 ( 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 263 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: A 290 ASP cc_start: 0.7927 (m-30) cc_final: 0.7707 (m-30) REVERT: C 84 GLN cc_start: 0.8452 (pt0) cc_final: 0.8109 (pt0) REVERT: B 76 LYS cc_start: 0.8880 (mttp) cc_final: 0.8532 (mttt) REVERT: B 200 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8011 (tp) REVERT: B 288 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8089 (tp30) REVERT: B 314 TYR cc_start: 0.8636 (m-80) cc_final: 0.8170 (m-80) REVERT: B 320 ARG cc_start: 0.7844 (ptp90) cc_final: 0.7002 (ptt180) REVERT: D 138 LEU cc_start: 0.8650 (mt) cc_final: 0.8329 (mt) REVERT: F 185 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7902 (mmp80) REVERT: G 290 TYR cc_start: 0.9181 (p90) cc_final: 0.8905 (p90) REVERT: H 80 ASP cc_start: 0.8046 (m-30) cc_final: 0.7310 (t0) REVERT: H 290 TYR cc_start: 0.8881 (p90) cc_final: 0.8626 (p90) REVERT: J 26 TRP cc_start: 0.8488 (m100) cc_final: 0.7846 (m100) REVERT: J 68 MET cc_start: 0.8671 (tpp) cc_final: 0.8381 (tpp) REVERT: J 79 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7734 (mtp180) outliers start: 29 outliers final: 15 residues processed: 254 average time/residue: 0.2213 time to fit residues: 80.7428 Evaluate side-chains 221 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 44 MET 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 203 ARG 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: 1.9990 chunk 67 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 283 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 248 optimal weight: 0.6980 chunk 117 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093018 restraints weight = 41443.235| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.22 r_work: 0.2927 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 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 = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24880 Z= 0.148 Angle : 0.705 15.244 34073 Z= 0.324 Chirality : 0.055 0.761 3839 Planarity : 0.004 0.051 4272 Dihedral : 12.618 164.188 3989 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.08 % Rotamer: Outliers : 1.90 % Allowed : 13.05 % Favored : 85.05 % 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: -1.66 (0.14), residues: 2959 helix: 0.11 (0.16), residues: 951 sheet: -0.37 (0.23), residues: 474 loop : -2.20 (0.14), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.023 0.002 TYR C 176 PHE 0.012 0.001 PHE C 155 TRP 0.012 0.001 TRP F 49 HIS 0.007 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (24880) covalent geometry : angle 0.70538 / 0.32 (34073) hydrogen bonds : bond 0.03271 / 2.24 ( 988) hydrogen bonds : angle 4.66227 / 3.39 ( 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 259 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8373 (mp10) REVERT: A 178 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8943 (mp) REVERT: A 276 ASN cc_start: 0.5639 (m-40) cc_final: 0.4915 (m110) REVERT: A 422 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8026 (mt) REVERT: C 84 GLN cc_start: 0.8520 (pt0) cc_final: 0.8191 (pt0) REVERT: B 76 LYS cc_start: 0.8961 (mttp) cc_final: 0.8631 (mttt) REVERT: B 143 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8877 (m) REVERT: B 152 PHE cc_start: 0.6880 (p90) cc_final: 0.6612 (p90) REVERT: B 200 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8096 (tp) REVERT: E 85 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8548 (tppt) REVERT: D 138 LEU cc_start: 0.8695 (mt) cc_final: 0.8339 (mt) REVERT: F 185 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8039 (mmp80) REVERT: G 290 TYR cc_start: 0.9207 (p90) cc_final: 0.9002 (p90) REVERT: H 290 TYR cc_start: 0.8977 (p90) cc_final: 0.8622 (p90) REVERT: H 307 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8531 (m) REVERT: I 208 ASP cc_start: 0.7725 (t0) cc_final: 0.7515 (t0) REVERT: J 26 TRP cc_start: 0.8497 (m100) cc_final: 0.7860 (m100) REVERT: J 68 MET cc_start: 0.8670 (tpp) cc_final: 0.8360 (tpp) outliers start: 44 outliers final: 23 residues processed: 249 average time/residue: 0.2162 time to fit residues: 78.2000 Evaluate side-chains 226 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 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 281 GLU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain D residue 333 ARG 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 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 307 VAL Chi-restraints excluded: chain H residue 319 GLN 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: 8.9990 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 252 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 165 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** 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 D 348 ASN G 342 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094133 restraints weight = 54511.767| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.88 r_work: 0.2906 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24880 Z= 0.131 Angle : 0.656 14.394 34073 Z= 0.303 Chirality : 0.051 0.375 3839 Planarity : 0.003 0.052 4272 Dihedral : 12.507 173.085 3989 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.62 % Rotamer: Outliers : 1.86 % Allowed : 14.13 % Favored : 84.02 % 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: -1.21 (0.15), residues: 2959 helix: 0.70 (0.16), residues: 954 sheet: -0.33 (0.22), residues: 494 loop : -2.03 (0.14), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 8 TYR 0.012 0.001 TYR C 176 PHE 0.010 0.001 PHE C 155 TRP 0.010 0.001 TRP F 49 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (24880) covalent geometry : angle 0.65589 / 0.30 (34073) hydrogen bonds : bond 0.02983 / 2.05 ( 988) hydrogen bonds : angle 4.37779 / 3.18 ( 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 254 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: A 290 ASP cc_start: 0.8022 (m-30) cc_final: 0.7689 (m-30) REVERT: A 422 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8031 (mt) REVERT: C 84 GLN cc_start: 0.8348 (pt0) cc_final: 0.8084 (pt0) REVERT: C 154 HIS cc_start: 0.6926 (m90) cc_final: 0.6474 (m170) REVERT: C 176 TYR cc_start: 0.7156 (m-10) cc_final: 0.6899 (m-10) REVERT: B 76 LYS cc_start: 0.8885 (mttp) cc_final: 0.8538 (mttt) REVERT: B 139 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8471 (tp) REVERT: B 143 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8724 (m) REVERT: B 152 PHE cc_start: 0.6741 (p90) cc_final: 0.6507 (p90) REVERT: E 85 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8527 (tppt) REVERT: E 308 THR cc_start: 0.8684 (t) cc_final: 0.8352 (p) REVERT: D 138 LEU cc_start: 0.8593 (mt) cc_final: 0.8128 (mp) REVERT: D 139 GLN cc_start: 0.7940 (tt0) cc_final: 0.7717 (tt0) REVERT: F 185 ARG cc_start: 0.8290 (tpp80) cc_final: 0.7907 (mmp80) REVERT: H 290 TYR cc_start: 0.8894 (p90) cc_final: 0.8608 (p90) REVERT: J 26 TRP cc_start: 0.8437 (m100) cc_final: 0.7857 (m100) REVERT: J 68 MET cc_start: 0.8484 (tpp) cc_final: 0.8159 (tpp) outliers start: 43 outliers final: 22 residues processed: 243 average time/residue: 0.2047 time to fit residues: 72.9070 Evaluate side-chains 216 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU 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 281 GLU Chi-restraints excluded: chain E residue 94 ASN 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 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG 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 203 ARG Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 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: 0.9990 chunk 184 optimal weight: 3.9990 chunk 211 optimal weight: 0.0470 chunk 45 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 143 optimal weight: 5.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** 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 281 ASN F 148 GLN G 163 ASN G 348 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.088274 restraints weight = 39022.009| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.22 r_work: 0.2853 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 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 = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 24880 Z= 0.266 Angle : 0.750 15.223 34073 Z= 0.349 Chirality : 0.057 0.483 3839 Planarity : 0.004 0.054 4272 Dihedral : 12.650 171.561 3988 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.20 % Rotamer: Outliers : 2.16 % Allowed : 15.42 % Favored : 82.42 % 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: -1.24 (0.15), residues: 2959 helix: 0.67 (0.16), residues: 956 sheet: -0.47 (0.22), residues: 523 loop : -2.03 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 170 TYR 0.015 0.002 TYR E 290 PHE 0.016 0.002 PHE C 44 TRP 0.016 0.002 TRP I 49 HIS 0.008 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 (24880) covalent geometry : angle 0.74958 / 0.35 (34073) hydrogen bonds : bond 0.03443 / 2.35 ( 988) hydrogen bonds : angle 4.59069 / 3.34 ( 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 255 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 0.877 Fit side-chains REVERT: A 177 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: A 178 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8960 (mp) REVERT: A 422 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8048 (mt) REVERT: C 84 GLN cc_start: 0.8480 (pt0) cc_final: 0.8170 (pt0) REVERT: B 76 LYS cc_start: 0.8997 (mttp) cc_final: 0.8618 (mttt) REVERT: B 152 PHE cc_start: 0.6857 (p90) cc_final: 0.6578 (p90) REVERT: B 170 ARG cc_start: 0.7328 (mtp-110) cc_final: 0.6761 (tmm-80) REVERT: B 288 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: E 85 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8563 (tppt) REVERT: E 314 TYR cc_start: 0.8395 (m-80) cc_final: 0.8029 (m-80) REVERT: D 138 LEU cc_start: 0.8700 (mt) cc_final: 0.8257 (mp) REVERT: F 185 ARG cc_start: 0.8589 (tpp80) cc_final: 0.8206 (mmp80) REVERT: G 290 TYR cc_start: 0.9302 (p90) cc_final: 0.8891 (p90) REVERT: H 251 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7347 (mp) REVERT: H 307 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8494 (m) REVERT: J 26 TRP cc_start: 0.8530 (m100) cc_final: 0.7854 (m100) REVERT: J 68 MET cc_start: 0.8633 (tpp) cc_final: 0.8315 (tpp) outliers start: 50 outliers final: 34 residues processed: 240 average time/residue: 0.2134 time to fit residues: 74.4093 Evaluate side-chains 228 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU 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 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 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 307 VAL Chi-restraints excluded: chain F residue 339 VAL 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 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 Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 268 optimal weight: 0.5980 chunk 242 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** 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 = 0.3624 r_free = 0.3624 target = 0.123076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.092077 restraints weight = 39573.829| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.24 r_work: 0.2927 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24880 Z= 0.130 Angle : 0.652 13.786 34073 Z= 0.303 Chirality : 0.050 0.357 3839 Planarity : 0.003 0.054 4272 Dihedral : 12.453 172.967 3988 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.62 % Rotamer: Outliers : 2.16 % Allowed : 16.07 % Favored : 81.77 % 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: -0.92 (0.15), residues: 2959 helix: 1.02 (0.17), residues: 954 sheet: -0.25 (0.22), residues: 498 loop : -1.90 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 68 TYR 0.013 0.001 TYR C 176 PHE 0.011 0.001 PHE C 155 TRP 0.012 0.001 TRP G 49 HIS 0.006 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (24880) covalent geometry : angle 0.65185 / 0.30 (34073) hydrogen bonds : bond 0.02957 / 2.02 ( 988) hydrogen bonds : angle 4.28271 / 3.11 ( 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 249 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8099 (pt0) REVERT: A 178 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8842 (mp) REVERT: A 290 ASP cc_start: 0.8061 (m-30) cc_final: 0.7745 (m-30) REVERT: A 422 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8090 (mt) REVERT: C 84 GLN cc_start: 0.8459 (pt0) cc_final: 0.8196 (pt0) REVERT: B 76 LYS cc_start: 0.8938 (mttp) cc_final: 0.8566 (mttt) REVERT: B 139 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8449 (tp) REVERT: B 143 SER cc_start: 0.9103 (OUTLIER) cc_final: 0.8894 (m) REVERT: B 152 PHE cc_start: 0.6799 (p90) cc_final: 0.6576 (p90) REVERT: B 170 ARG cc_start: 0.7282 (mtp-110) cc_final: 0.6716 (tmm-80) REVERT: E 82 ASP cc_start: 0.8245 (m-30) cc_final: 0.7961 (t0) REVERT: E 85 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8553 (tppt) REVERT: E 308 THR cc_start: 0.8725 (t) cc_final: 0.8413 (p) REVERT: E 314 TYR cc_start: 0.8315 (m-80) cc_final: 0.7895 (m-80) REVERT: D 139 GLN cc_start: 0.8107 (tt0) cc_final: 0.7877 (tt0) REVERT: D 212 ASP cc_start: 0.8071 (m-30) cc_final: 0.7628 (t0) REVERT: F 185 ARG cc_start: 0.8506 (tpp80) cc_final: 0.8069 (mmp80) REVERT: G 53 ASP cc_start: 0.8957 (m-30) cc_final: 0.8743 (m-30) REVERT: G 250 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8138 (pt) REVERT: G 290 TYR cc_start: 0.9227 (p90) cc_final: 0.8941 (p90) REVERT: H 290 TYR cc_start: 0.9017 (p90) cc_final: 0.8707 (p90) REVERT: H 307 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8455 (m) REVERT: J 26 TRP cc_start: 0.8459 (m100) cc_final: 0.7869 (m100) REVERT: J 68 MET cc_start: 0.8547 (tpp) cc_final: 0.8320 (tpp) outliers start: 50 outliers final: 36 residues processed: 234 average time/residue: 0.2110 time to fit residues: 71.9510 Evaluate side-chains 234 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU 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 139 LEU Chi-restraints excluded: chain B residue 143 SER 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 E residue 250 LEU Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain D residue 304 TYR 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 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 H residue 43 LEU 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 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 Chi-restraints excluded: chain J residue 46 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 242 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 199 optimal weight: 0.5980 chunk 216 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 274 optimal weight: 0.0010 chunk 276 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 247 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3637 r_free = 0.3637 target = 0.123971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093144 restraints weight = 41296.280| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.28 r_work: 0.2940 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24880 Z= 0.117 Angle : 0.635 13.310 34073 Z= 0.295 Chirality : 0.049 0.353 3839 Planarity : 0.003 0.053 4272 Dihedral : 12.334 174.943 3988 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 2.12 % Allowed : 16.72 % Favored : 81.17 % 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: -0.77 (0.15), residues: 2959 helix: 1.20 (0.17), residues: 958 sheet: -0.22 (0.22), residues: 504 loop : -1.83 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 68 TYR 0.024 0.001 TYR A 179 PHE 0.010 0.001 PHE C 155 TRP 0.010 0.001 TRP F 49 HIS 0.007 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (24880) covalent geometry : angle 0.63484 / 0.29 (34073) hydrogen bonds : bond 0.02857 / 1.95 ( 988) hydrogen bonds : angle 4.17208 / 3.03 ( 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 251 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: A 178 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8767 (mp) REVERT: A 422 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8062 (mt) REVERT: C 84 GLN cc_start: 0.8368 (pt0) cc_final: 0.8133 (pt0) REVERT: B 76 LYS cc_start: 0.8883 (mttp) cc_final: 0.8519 (mttt) REVERT: B 143 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8706 (m) REVERT: B 170 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.6686 (tmm-80) REVERT: E 308 THR cc_start: 0.8637 (t) cc_final: 0.8390 (p) REVERT: E 314 TYR cc_start: 0.8267 (m-80) cc_final: 0.7952 (m-80) REVERT: D 139 GLN cc_start: 0.8012 (tt0) cc_final: 0.7804 (tt0) REVERT: D 212 ASP cc_start: 0.7838 (m-30) cc_final: 0.7463 (t0) REVERT: F 185 ARG cc_start: 0.8325 (tpp80) cc_final: 0.7974 (mmp80) REVERT: G 290 TYR cc_start: 0.9173 (p90) cc_final: 0.8916 (p90) REVERT: H 290 TYR cc_start: 0.8905 (p90) cc_final: 0.8651 (p90) REVERT: H 307 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8323 (m) REVERT: I 333 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8434 (ptp90) REVERT: J 26 TRP cc_start: 0.8413 (m100) cc_final: 0.7876 (m100) REVERT: J 68 MET cc_start: 0.8474 (tpp) cc_final: 0.8224 (tpp) outliers start: 49 outliers final: 36 residues processed: 237 average time/residue: 0.2049 time to fit residues: 71.0920 Evaluate side-chains 234 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 100 VAL 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 143 SER 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 304 TYR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 TYR 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 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 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 247 SER Chi-restraints excluded: chain H residue 250 LEU 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 I residue 333 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 46 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 221 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 177 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 342 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 = 0.3628 r_free = 0.3628 target = 0.123341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.092368 restraints weight = 46432.565| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.49 r_work: 0.2915 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24880 Z= 0.137 Angle : 0.640 13.325 34073 Z= 0.297 Chirality : 0.050 0.367 3839 Planarity : 0.003 0.054 4272 Dihedral : 12.304 176.562 3986 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.16 % Allowed : 16.93 % Favored : 80.91 % 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: -0.71 (0.15), residues: 2959 helix: 1.27 (0.17), residues: 957 sheet: -0.32 (0.22), residues: 524 loop : -1.78 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 68 TYR 0.022 0.002 TYR A 179 PHE 0.010 0.001 PHE C 155 TRP 0.010 0.001 TRP G 49 HIS 0.006 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (24880) covalent geometry : angle 0.64029 / 0.30 (34073) hydrogen bonds : bond 0.02866 / 1.96 ( 988) hydrogen bonds : angle 4.16614 / 3.03 ( 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 250 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.889 Fit side-chains REVERT: A 177 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: A 178 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8802 (mp) REVERT: A 290 ASP cc_start: 0.8056 (m-30) cc_final: 0.7766 (m-30) REVERT: A 422 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8062 (mt) REVERT: C 84 GLN cc_start: 0.8364 (pt0) cc_final: 0.8113 (pt0) REVERT: B 76 LYS cc_start: 0.8891 (mttp) cc_final: 0.8536 (mttt) REVERT: B 143 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8726 (m) REVERT: E 117 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8652 (ttm170) REVERT: E 308 THR cc_start: 0.8636 (t) cc_final: 0.8424 (p) REVERT: E 314 TYR cc_start: 0.8303 (m-80) cc_final: 0.8023 (m-80) REVERT: D 139 GLN cc_start: 0.7980 (tt0) cc_final: 0.7761 (tt0) REVERT: D 212 ASP cc_start: 0.7898 (m-30) cc_final: 0.7480 (t0) REVERT: F 185 ARG cc_start: 0.8343 (tpp80) cc_final: 0.7974 (mmp80) REVERT: G 290 TYR cc_start: 0.9170 (p90) cc_final: 0.8890 (p90) REVERT: H 290 TYR cc_start: 0.8880 (p90) cc_final: 0.8667 (p90) REVERT: H 307 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8316 (m) REVERT: I 333 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8437 (ptp90) REVERT: J 26 TRP cc_start: 0.8418 (m100) cc_final: 0.7853 (m100) REVERT: J 68 MET cc_start: 0.8480 (tpp) cc_final: 0.8206 (tpp) outliers start: 50 outliers final: 40 residues processed: 237 average time/residue: 0.2079 time to fit residues: 72.0337 Evaluate side-chains 237 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU 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 143 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 241 VAL 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 E residue 117 ARG Chi-restraints excluded: chain D residue 250 LEU 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 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 247 SER Chi-restraints excluded: chain H residue 250 LEU 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 I residue 333 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 122 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 254 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 179 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 342 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 = 0.3635 r_free = 0.3635 target = 0.123800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093006 restraints weight = 46454.116| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.53 r_work: 0.2907 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24880 Z= 0.128 Angle : 0.634 12.944 34073 Z= 0.294 Chirality : 0.049 0.357 3839 Planarity : 0.003 0.053 4272 Dihedral : 12.279 176.873 3986 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.07 % Allowed : 17.15 % Favored : 80.78 % 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: -0.63 (0.15), residues: 2959 helix: 1.36 (0.17), residues: 957 sheet: -0.21 (0.22), residues: 518 loop : -1.76 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 68 TYR 0.021 0.001 TYR A 179 PHE 0.011 0.001 PHE C 155 TRP 0.009 0.001 TRP F 49 HIS 0.008 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (24880) covalent geometry : angle 0.63392 / 0.29 (34073) hydrogen bonds : bond 0.02824 / 1.93 ( 988) hydrogen bonds : angle 4.12496 / 3.00 ( 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 243 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 0.852 Fit side-chains REVERT: A 177 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: A 178 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8808 (mt) REVERT: A 290 ASP cc_start: 0.8047 (m-30) cc_final: 0.7747 (m-30) REVERT: A 422 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8027 (mt) REVERT: C 84 GLN cc_start: 0.8392 (pt0) cc_final: 0.8155 (pt0) REVERT: B 76 LYS cc_start: 0.8901 (mttp) cc_final: 0.8548 (mttt) REVERT: B 143 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8717 (m) REVERT: B 170 ARG cc_start: 0.7401 (mtp-110) cc_final: 0.6807 (tmm-80) REVERT: E 117 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8691 (ttm170) REVERT: D 139 GLN cc_start: 0.8022 (tt0) cc_final: 0.7803 (tt0) REVERT: D 212 ASP cc_start: 0.7922 (m-30) cc_final: 0.7503 (t0) REVERT: F 185 ARG cc_start: 0.8330 (tpp80) cc_final: 0.7970 (mmp80) REVERT: G 290 TYR cc_start: 0.9169 (p90) cc_final: 0.8896 (p90) REVERT: H 290 TYR cc_start: 0.8872 (p90) cc_final: 0.8671 (p90) REVERT: H 307 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8333 (m) REVERT: I 333 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8430 (ptp90) REVERT: J 26 TRP cc_start: 0.8417 (m100) cc_final: 0.7851 (m100) REVERT: J 68 MET cc_start: 0.8482 (tpp) cc_final: 0.8225 (tpp) outliers start: 48 outliers final: 38 residues processed: 230 average time/residue: 0.2191 time to fit residues: 73.0464 Evaluate side-chains 235 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU 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 143 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain D residue 250 LEU 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 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 247 SER Chi-restraints excluded: chain H residue 250 LEU 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 I residue 333 ARG Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 49 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 200 optimal weight: 0.0970 chunk 242 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 0.0570 chunk 70 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 260 GLN ** 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 = 0.3666 r_free = 0.3666 target = 0.125920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096167 restraints weight = 39097.680| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.15 r_work: 0.3004 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24880 Z= 0.102 Angle : 0.617 13.254 34073 Z= 0.287 Chirality : 0.048 0.343 3839 Planarity : 0.003 0.054 4272 Dihedral : 12.173 177.683 3986 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.81 % Allowed : 17.49 % Favored : 80.69 % 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: -0.48 (0.15), residues: 2959 helix: 1.52 (0.17), residues: 957 sheet: -0.06 (0.23), residues: 504 loop : -1.72 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 68 TYR 0.016 0.001 TYR A 235 PHE 0.010 0.001 PHE C 155 TRP 0.009 0.001 TRP F 193 HIS 0.009 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (24880) covalent geometry : angle 0.61739 / 0.29 (34073) hydrogen bonds : bond 0.02655 / 1.82 ( 988) hydrogen bonds : angle 3.99604 / 2.90 ( 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 250 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.912 Fit side-chains REVERT: A 177 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: A 178 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8735 (mt) REVERT: A 422 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8045 (mt) REVERT: C 84 GLN cc_start: 0.8425 (pt0) cc_final: 0.8212 (pt0) REVERT: B 76 LYS cc_start: 0.8908 (mttp) cc_final: 0.8587 (mttt) REVERT: B 170 ARG cc_start: 0.7328 (mtp-110) cc_final: 0.6755 (tmm-80) REVERT: E 314 TYR cc_start: 0.8345 (m-80) cc_final: 0.8064 (m-80) REVERT: D 139 GLN cc_start: 0.8131 (tt0) cc_final: 0.7909 (tt0) REVERT: D 212 ASP cc_start: 0.8064 (m-30) cc_final: 0.7548 (t0) REVERT: F 185 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7975 (mmp80) REVERT: G 290 TYR cc_start: 0.9111 (p90) cc_final: 0.8901 (p90) REVERT: H 251 ILE cc_start: 0.7967 (mp) cc_final: 0.7261 (mp) REVERT: H 290 TYR cc_start: 0.8874 (p90) cc_final: 0.8654 (p90) REVERT: H 304 TYR cc_start: 0.7978 (m-80) cc_final: 0.7729 (m-80) REVERT: H 307 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8398 (m) REVERT: I 307 VAL cc_start: 0.8761 (t) cc_final: 0.8468 (t) REVERT: J 26 TRP cc_start: 0.8418 (m100) cc_final: 0.7847 (m100) outliers start: 42 outliers final: 30 residues processed: 238 average time/residue: 0.2071 time to fit residues: 72.2004 Evaluate side-chains 227 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 422 LEU 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 241 VAL Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain D residue 250 LEU 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 105 SER Chi-restraints excluded: chain G residue 250 LEU 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 250 LEU 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 18 VAL Chi-restraints excluded: chain J residue 46 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 248 optimal weight: 0.3980 chunk 48 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 221 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 203 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 D 163 ASN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 342 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 = 0.3649 r_free = 0.3649 target = 0.124783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.094119 restraints weight = 39640.533| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.23 r_work: 0.2959 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24880 Z= 0.125 Angle : 0.623 12.880 34073 Z= 0.289 Chirality : 0.048 0.351 3839 Planarity : 0.003 0.053 4272 Dihedral : 12.165 178.052 3986 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.43 % Allowed : 17.88 % Favored : 80.69 % 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: -0.46 (0.15), residues: 2959 helix: 1.54 (0.17), residues: 957 sheet: -0.02 (0.23), residues: 504 loop : -1.72 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 68 TYR 0.019 0.001 TYR A 179 PHE 0.011 0.001 PHE C 155 TRP 0.008 0.001 TRP H 49 HIS 0.014 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (24880) covalent geometry : angle 0.62307 / 0.29 (34073) hydrogen bonds : bond 0.02734 / 1.87 ( 988) hydrogen bonds : angle 4.02746 / 2.92 ( 2953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5899.92 seconds wall clock time: 101 minutes 58.10 seconds (6118.10 seconds total)