Starting phenix.real_space_refine on Sat Jun 21 01:17:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzw_22582/06_2025/7jzw_22582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzw_22582/06_2025/7jzw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jzw_22582/06_2025/7jzw_22582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzw_22582/06_2025/7jzw_22582.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzw_22582/06_2025/7jzw_22582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzw_22582/06_2025/7jzw_22582.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 760 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 15.29, per 1000 atoms: 0.63 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: 5.34 Conformation dependent library (CDL) restraints added in 3.0 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: 8.07 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: 8.92 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5046 1.32 - 1.44: 5968 1.44 - 1.56: 13702 1.56 - 1.68: 120 1.68 - 1.80: 44 Bond restraints: 24880 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.382 -0.046 9.80e-03 1.04e+04 2.16e+01 bond pdb=" O3' A M 36 " pdb=" P C M 37 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.26e+01 bond pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.32e-02 5.74e+03 8.10e+00 bond pdb=" N GLN H 186 " pdb=" CA GLN H 186 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.19e+00 bond pdb=" CG LEU D 229 " pdb=" CD1 LEU D 229 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.90e+00 ... (remaining 24875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 32451 2.02 - 4.05: 1378 4.05 - 6.07: 181 6.07 - 8.10: 53 8.10 - 10.12: 13 Bond angle restraints: 34076 Sorted by residual: angle pdb=" O ARG H 185 " pdb=" C ARG H 185 " pdb=" N GLN H 186 " ideal model delta sigma weight residual 122.23 129.29 -7.06 1.33e+00 5.65e-01 2.82e+01 angle pdb=" C ARG F 185 " pdb=" N GLN F 186 " pdb=" CA GLN F 186 " ideal model delta sigma weight residual 120.82 128.71 -7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.79 127.65 -6.86 1.39e+00 5.18e-01 2.44e+01 angle pdb=" C ARG I 185 " pdb=" N GLN I 186 " pdb=" CA GLN I 186 " ideal model delta sigma weight residual 120.38 126.93 -6.55 1.37e+00 5.33e-01 2.28e+01 angle pdb=" C ARG H 185 " pdb=" N GLN H 186 " pdb=" CA GLN H 186 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 ... (remaining 34071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 14498 35.59 - 71.19: 468 71.19 - 106.78: 39 106.78 - 142.37: 1 142.37 - 177.96: 5 Dihedral angle restraints: 15011 sinusoidal: 6419 harmonic: 8592 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 53.90 146.10 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 65.69 134.31 1 1.50e+01 4.44e-03 7.25e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual -128.00 49.96 -177.96 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3034 0.063 - 0.127: 682 0.127 - 0.190: 113 0.190 - 0.254: 6 0.254 - 0.317: 4 Chirality restraints: 3839 Sorted by residual: chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE B 219 " pdb=" CA ILE B 219 " pdb=" CG1 ILE B 219 " pdb=" CG2 ILE B 219 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1' U M 33 " pdb=" O4' U M 33 " pdb=" C2' U M 33 " pdb=" N1 U M 33 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3836 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.95e+00 pdb=" N PRO A 72 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 73 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO C 74 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 103 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO D 104 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 104 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 104 " 0.038 5.00e-02 4.00e+02 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4954 2.77 - 3.30: 21528 3.30 - 3.83: 42348 3.83 - 4.37: 51903 4.37 - 4.90: 87079 Nonbonded interactions: 207812 Sorted by model distance: nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR E 324 " pdb=" O SER F 73 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.256 3.040 nonbonded pdb=" O SER E 73 " pdb=" OH TYR D 324 " model vdw 2.266 3.040 ... (remaining 207807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 60.480 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 24880 Z= 0.411 Angle : 0.973 10.119 34076 Z= 0.541 Chirality : 0.055 0.317 3839 Planarity : 0.007 0.079 4272 Dihedral : 17.319 177.963 9463 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.003 TRP I 49 HIS 0.010 0.002 HIS E 275 PHE 0.027 0.003 PHE B 40 TYR 0.021 0.003 TYR F 290 ARG 0.014 0.001 ARG H 237 Details of bonding type rmsd hydrogen bonds : bond 0.16316 ( 988) hydrogen bonds : angle 7.64732 ( 2953) covalent geometry : bond 0.00959 (24880) covalent geometry : angle 0.97325 (34076) *********************** 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 : 2.733 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.7798 (m-30) cc_final: 0.7553 (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: 0.5020 time to fit residues: 203.1288 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 : 2.576 ------------------------------------------------------------------------------- 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 252 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 271 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 305 GLN C 29 HIS B 69 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS D 310 GLN F 242 GLN G 242 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 HIS I 342 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.120991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.090288 restraints weight = 36880.098| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.12 r_work: 0.2877 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24880 Z= 0.144 Angle : 0.574 11.783 34076 Z= 0.304 Chirality : 0.041 0.217 3839 Planarity : 0.005 0.056 4272 Dihedral : 15.430 179.455 4206 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.42 % Rotamer: Outliers : 1.30 % Allowed : 12.14 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.13), residues: 2959 helix: -0.89 (0.15), residues: 950 sheet: -0.57 (0.23), residues: 459 loop : -2.45 (0.13), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 49 HIS 0.004 0.001 HIS B 114 PHE 0.013 0.001 PHE C 155 TYR 0.013 0.002 TYR G 290 ARG 0.025 0.001 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 988) hydrogen bonds : angle 5.11855 ( 2953) covalent geometry : bond 0.00316 (24880) covalent geometry : angle 0.57412 (34076) *********************** 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 270 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 2.693 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: A 290 ASP cc_start: 0.8003 (m-30) cc_final: 0.7792 (m-30) REVERT: C 84 GLN cc_start: 0.8567 (pt0) cc_final: 0.8220 (pt0) REVERT: B 57 ASP cc_start: 0.7990 (t0) cc_final: 0.7752 (t0) REVERT: B 76 LYS cc_start: 0.8941 (mttp) cc_final: 0.8597 (mttt) REVERT: B 170 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7209 (mtp-110) REVERT: B 288 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8361 (tp30) REVERT: B 314 TYR cc_start: 0.8698 (m-80) cc_final: 0.8326 (m-80) REVERT: B 320 ARG cc_start: 0.7933 (ptp90) cc_final: 0.7192 (ptt180) REVERT: D 138 LEU cc_start: 0.8699 (mt) cc_final: 0.8374 (mt) REVERT: F 185 ARG cc_start: 0.8524 (tpp80) cc_final: 0.8022 (mmp80) REVERT: G 95 LEU cc_start: 0.9078 (mm) cc_final: 0.8831 (mt) REVERT: G 290 TYR cc_start: 0.9253 (p90) cc_final: 0.9023 (p90) REVERT: H 80 ASP cc_start: 0.8149 (m-30) cc_final: 0.7296 (t0) REVERT: H 290 TYR cc_start: 0.8978 (p90) cc_final: 0.8646 (p90) REVERT: J 26 TRP cc_start: 0.8503 (m100) cc_final: 0.7829 (m100) outliers start: 30 outliers final: 13 residues processed: 260 average time/residue: 0.4802 time to fit residues: 179.0948 Evaluate side-chains 219 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 2.657 ------------------------------------------------------------------------------- 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 281 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 319 GLN Chi-restraints excluded: chain I residue 203 ARG Chi-restraints excluded: chain I residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 154 optimal weight: 0.1980 chunk 185 optimal weight: 0.3980 chunk 280 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 112 optimal weight: 0.0980 chunk 285 optimal weight: 0.8980 chunk 269 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN D 102 ASN D 148 GLN D 348 ASN G 148 GLN G 342 GLN H 148 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095186 restraints weight = 46555.274| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.56 r_work: 0.2932 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24880 Z= 0.101 Angle : 0.514 11.706 34076 Z= 0.267 Chirality : 0.039 0.197 3839 Planarity : 0.004 0.053 4272 Dihedral : 15.128 179.372 4206 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.52 % Rotamer: Outliers : 1.60 % Allowed : 13.52 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 2959 helix: 0.29 (0.16), residues: 950 sheet: -0.46 (0.23), residues: 486 loop : -2.12 (0.14), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 49 HIS 0.004 0.001 HIS C 29 PHE 0.009 0.001 PHE C 44 TYR 0.017 0.001 TYR C 176 ARG 0.010 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 988) hydrogen bonds : angle 4.49750 ( 2953) covalent geometry : bond 0.00219 (24880) covalent geometry : angle 0.51362 (34076) *********************** 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 265 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 2.624 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: A 422 LEU cc_start: 0.8319 (mm) cc_final: 0.8017 (mt) REVERT: C 84 GLN cc_start: 0.8453 (pt0) cc_final: 0.8145 (pt0) REVERT: B 76 LYS cc_start: 0.8873 (mttp) cc_final: 0.8535 (mttt) REVERT: B 143 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8661 (m) REVERT: B 288 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8229 (tp30) REVERT: B 320 ARG cc_start: 0.7704 (ptp90) cc_final: 0.7253 (ptt180) REVERT: E 85 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8541 (tppt) REVERT: D 138 LEU cc_start: 0.8633 (mt) cc_final: 0.8289 (mt) REVERT: D 139 GLN cc_start: 0.7975 (tt0) cc_final: 0.7762 (tt0) REVERT: D 155 ARG cc_start: 0.8249 (ttp80) cc_final: 0.8048 (ttp-110) REVERT: F 185 ARG cc_start: 0.8283 (tpp80) cc_final: 0.7915 (mmp80) REVERT: H 74 ASN cc_start: 0.8724 (p0) cc_final: 0.8502 (p0) REVERT: H 290 TYR cc_start: 0.8823 (p90) cc_final: 0.8561 (p90) REVERT: H 307 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8411 (m) REVERT: I 53 ASP cc_start: 0.8041 (m-30) cc_final: 0.7776 (m-30) REVERT: J 26 TRP cc_start: 0.8433 (m100) cc_final: 0.7881 (m100) outliers start: 37 outliers final: 18 residues processed: 257 average time/residue: 0.4506 time to fit residues: 169.6209 Evaluate side-chains 227 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain D residue 250 LEU 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 250 LEU Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 189 optimal weight: 0.0030 chunk 290 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS B 69 GLN E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN F 148 GLN H 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.092853 restraints weight = 48860.452| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.69 r_work: 0.2887 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.003 0.027 24880 Z= 0.129 Angle : 0.516 12.488 34076 Z= 0.268 Chirality : 0.039 0.196 3839 Planarity : 0.004 0.052 4272 Dihedral : 15.059 179.805 4204 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 1.64 % Allowed : 14.21 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 2959 helix: 0.72 (0.16), residues: 958 sheet: -0.40 (0.22), residues: 496 loop : -2.03 (0.14), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 414 HIS 0.004 0.001 HIS B 305 PHE 0.010 0.001 PHE C 155 TYR 0.013 0.001 TYR A 336 ARG 0.008 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.02989 ( 988) hydrogen bonds : angle 4.35284 ( 2953) covalent geometry : bond 0.00292 (24880) covalent geometry : angle 0.51618 (34076) *********************** 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 252 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 2.688 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: A 290 ASP cc_start: 0.8044 (m-30) cc_final: 0.7735 (m-30) REVERT: A 422 LEU cc_start: 0.8392 (mm) cc_final: 0.8098 (mt) REVERT: C 84 GLN cc_start: 0.8414 (pt0) cc_final: 0.8156 (pt0) REVERT: B 76 LYS cc_start: 0.8871 (mttp) cc_final: 0.8534 (mttt) REVERT: B 143 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8664 (m) REVERT: B 152 PHE cc_start: 0.6761 (p90) cc_final: 0.6524 (p90) REVERT: E 85 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8534 (tppt) REVERT: E 186 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7138 (mp10) REVERT: D 138 LEU cc_start: 0.8596 (mt) cc_final: 0.8139 (mp) REVERT: D 139 GLN cc_start: 0.7930 (tt0) cc_final: 0.7720 (tt0) REVERT: F 185 ARG cc_start: 0.8291 (tpp80) cc_final: 0.7912 (mmp80) REVERT: G 290 TYR cc_start: 0.9210 (p90) cc_final: 0.9005 (p90) REVERT: H 290 TYR cc_start: 0.8856 (p90) cc_final: 0.8597 (p90) REVERT: H 307 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8416 (m) REVERT: J 26 TRP cc_start: 0.8424 (m100) cc_final: 0.7872 (m100) outliers start: 38 outliers final: 23 residues processed: 244 average time/residue: 0.4772 time to fit residues: 171.8610 Evaluate side-chains 227 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 319 GLN Chi-restraints excluded: chain I residue 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 270 optimal weight: 0.7980 chunk 264 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 chunk 44 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** 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 = 0.3620 r_free = 0.3620 target = 0.122917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092863 restraints weight = 39374.912| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.17 r_work: 0.2923 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24880 Z= 0.112 Angle : 0.505 12.281 34076 Z= 0.262 Chirality : 0.039 0.194 3839 Planarity : 0.003 0.053 4272 Dihedral : 15.008 179.576 4203 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 2.03 % Allowed : 15.21 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 2959 helix: 1.03 (0.17), residues: 956 sheet: -0.20 (0.23), residues: 486 loop : -1.93 (0.14), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 49 HIS 0.005 0.001 HIS A 283 PHE 0.010 0.001 PHE C 44 TYR 0.014 0.001 TYR A 336 ARG 0.008 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 988) hydrogen bonds : angle 4.19803 ( 2953) covalent geometry : bond 0.00249 (24880) covalent geometry : angle 0.50513 (34076) *********************** 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 259 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8087 (pt0) REVERT: A 422 LEU cc_start: 0.8353 (mm) cc_final: 0.8075 (mt) REVERT: C 84 GLN cc_start: 0.8415 (pt0) cc_final: 0.8186 (pt0) REVERT: B 76 LYS cc_start: 0.8817 (mttp) cc_final: 0.8473 (mttt) REVERT: B 143 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8602 (m) REVERT: B 152 PHE cc_start: 0.6722 (p90) cc_final: 0.6501 (p90) REVERT: B 170 ARG cc_start: 0.7216 (mtp-110) cc_final: 0.6684 (tmm-80) REVERT: E 186 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7113 (mp10) REVERT: E 314 TYR cc_start: 0.8166 (m-80) cc_final: 0.7805 (m-80) REVERT: D 102 ASN cc_start: 0.8507 (m110) cc_final: 0.8189 (m110) REVERT: D 138 LEU cc_start: 0.8596 (mt) cc_final: 0.8238 (mt) REVERT: D 139 GLN cc_start: 0.7954 (tt0) cc_final: 0.7748 (tt0) REVERT: D 212 ASP cc_start: 0.7903 (m-30) cc_final: 0.7385 (t0) REVERT: F 185 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7888 (mmp80) REVERT: G 290 TYR cc_start: 0.9138 (p90) cc_final: 0.8935 (p90) REVERT: H 290 TYR cc_start: 0.8831 (p90) cc_final: 0.8582 (p90) REVERT: H 307 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8376 (m) REVERT: J 26 TRP cc_start: 0.8414 (m100) cc_final: 0.7870 (m100) outliers start: 47 outliers final: 27 residues processed: 249 average time/residue: 0.4480 time to fit residues: 164.2875 Evaluate side-chains 228 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain 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 E residue 43 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 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 105 SER 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 296 LEU Chi-restraints excluded: chain J residue 17 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 214 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 180 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 213 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 289 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN G 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092671 restraints weight = 48478.698| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.72 r_work: 0.2882 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24880 Z= 0.152 Angle : 0.524 12.590 34076 Z= 0.272 Chirality : 0.040 0.195 3839 Planarity : 0.003 0.053 4272 Dihedral : 15.008 179.917 4203 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.35 % Rotamer: Outliers : 1.77 % Allowed : 15.85 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 2959 helix: 1.11 (0.17), residues: 956 sheet: -0.21 (0.23), residues: 488 loop : -1.89 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 49 HIS 0.005 0.001 HIS C 29 PHE 0.010 0.001 PHE C 155 TYR 0.014 0.002 TYR A 336 ARG 0.006 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 988) hydrogen bonds : angle 4.23082 ( 2953) covalent geometry : bond 0.00347 (24880) covalent geometry : angle 0.52428 (34076) *********************** 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 255 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 2.487 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: A 422 LEU cc_start: 0.8375 (mm) cc_final: 0.8108 (mt) REVERT: C 84 GLN cc_start: 0.8443 (pt0) cc_final: 0.8196 (pt0) REVERT: B 76 LYS cc_start: 0.8897 (mttp) cc_final: 0.8543 (mttt) REVERT: B 143 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8654 (m) REVERT: B 152 PHE cc_start: 0.6683 (p90) cc_final: 0.6483 (p90) REVERT: B 170 ARG cc_start: 0.7213 (mtp-110) cc_final: 0.6676 (tmm-80) REVERT: E 82 ASP cc_start: 0.8195 (m-30) cc_final: 0.7909 (t0) REVERT: E 186 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7223 (mp10) REVERT: D 102 ASN cc_start: 0.8529 (m-40) cc_final: 0.8287 (m-40) REVERT: D 138 LEU cc_start: 0.8635 (mt) cc_final: 0.8149 (mp) REVERT: D 212 ASP cc_start: 0.7898 (m-30) cc_final: 0.7431 (t0) REVERT: F 185 ARG cc_start: 0.8331 (tpp80) cc_final: 0.7996 (mmp80) REVERT: G 290 TYR cc_start: 0.9190 (p90) cc_final: 0.8969 (p90) REVERT: H 290 TYR cc_start: 0.8876 (p90) cc_final: 0.8635 (p90) REVERT: H 307 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8418 (m) REVERT: I 203 ARG cc_start: 0.8094 (mtp-110) cc_final: 0.7567 (mtp85) REVERT: I 307 VAL cc_start: 0.8791 (t) cc_final: 0.8467 (t) REVERT: I 333 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8469 (ptp90) REVERT: J 26 TRP cc_start: 0.8448 (m100) cc_final: 0.7888 (m100) outliers start: 41 outliers final: 32 residues processed: 242 average time/residue: 0.4798 time to fit residues: 167.8786 Evaluate side-chains 240 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain 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 E residue 43 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 105 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 146 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 241 optimal weight: 0.0770 chunk 275 optimal weight: 0.0970 chunk 102 optimal weight: 0.7980 chunk 290 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 246 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3633 r_free = 0.3633 target = 0.123800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094113 restraints weight = 39400.792| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.15 r_work: 0.2950 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24880 Z= 0.098 Angle : 0.484 12.192 34076 Z= 0.252 Chirality : 0.038 0.193 3839 Planarity : 0.003 0.053 4272 Dihedral : 14.932 178.852 4203 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 1.90 % Allowed : 16.37 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 2959 helix: 1.36 (0.17), residues: 958 sheet: 0.01 (0.23), residues: 466 loop : -1.80 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 49 HIS 0.010 0.001 HIS C 29 PHE 0.012 0.001 PHE C 44 TYR 0.012 0.001 TYR A 235 ARG 0.005 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.02720 ( 988) hydrogen bonds : angle 4.03497 ( 2953) covalent geometry : bond 0.00215 (24880) covalent geometry : angle 0.48418 (34076) *********************** 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 254 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 2.685 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8130 (pt0) REVERT: A 290 ASP cc_start: 0.8063 (m-30) cc_final: 0.7697 (m-30) REVERT: A 422 LEU cc_start: 0.8413 (mm) cc_final: 0.8136 (mt) REVERT: B 76 LYS cc_start: 0.8916 (mttp) cc_final: 0.8590 (mttt) REVERT: B 170 ARG cc_start: 0.7335 (mtp-110) cc_final: 0.6730 (tmm-80) REVERT: E 186 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7288 (mp10) REVERT: E 308 THR cc_start: 0.8577 (t) cc_final: 0.8371 (p) REVERT: D 212 ASP cc_start: 0.8088 (m-30) cc_final: 0.7571 (t0) REVERT: F 185 ARG cc_start: 0.8491 (tpp80) cc_final: 0.8165 (mmp80) REVERT: G 53 ASP cc_start: 0.8850 (m-30) cc_final: 0.8646 (m-30) REVERT: H 251 ILE cc_start: 0.7989 (mp) cc_final: 0.7273 (mp) REVERT: H 290 TYR cc_start: 0.8902 (p90) cc_final: 0.8632 (p90) REVERT: H 307 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8437 (m) REVERT: I 203 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7606 (mtp85) REVERT: I 307 VAL cc_start: 0.8795 (t) cc_final: 0.8488 (t) REVERT: J 26 TRP cc_start: 0.8421 (m100) cc_final: 0.7864 (m100) outliers start: 44 outliers final: 28 residues processed: 244 average time/residue: 0.4598 time to fit residues: 165.0781 Evaluate side-chains 224 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 2.429 ------------------------------------------------------------------------------- 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 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 219 ILE Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 94 ASN 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 78 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain H residue 307 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 247 optimal weight: 3.9990 chunk 288 optimal weight: 0.5980 chunk 211 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 198 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN D 102 ASN D 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091452 restraints weight = 41981.476| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.28 r_work: 0.2893 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24880 Z= 0.150 Angle : 0.519 12.519 34076 Z= 0.267 Chirality : 0.040 0.194 3839 Planarity : 0.003 0.053 4272 Dihedral : 14.940 179.516 4203 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.51 % Allowed : 17.67 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 2959 helix: 1.37 (0.17), residues: 957 sheet: -0.26 (0.22), residues: 508 loop : -1.76 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 49 HIS 0.014 0.001 HIS C 29 PHE 0.012 0.001 PHE C 44 TYR 0.017 0.002 TYR C 176 ARG 0.004 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 988) hydrogen bonds : angle 4.12807 ( 2953) covalent geometry : bond 0.00347 (24880) covalent geometry : angle 0.51872 (34076) *********************** 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 232 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 2.461 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: A 422 LEU cc_start: 0.8454 (mm) cc_final: 0.8187 (mt) REVERT: B 76 LYS cc_start: 0.8934 (mttp) cc_final: 0.8584 (mttt) REVERT: E 82 ASP cc_start: 0.8240 (m-30) cc_final: 0.7968 (t0) REVERT: E 186 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7348 (mp10) REVERT: D 102 ASN cc_start: 0.8636 (m-40) cc_final: 0.8395 (m-40) REVERT: F 185 ARG cc_start: 0.8567 (tpp80) cc_final: 0.8123 (mmp80) REVERT: G 53 ASP cc_start: 0.8965 (m-30) cc_final: 0.8755 (m-30) REVERT: G 250 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8109 (pt) REVERT: G 290 TYR cc_start: 0.9291 (p90) cc_final: 0.8975 (p90) REVERT: H 251 ILE cc_start: 0.8035 (mp) cc_final: 0.7294 (mp) REVERT: H 290 TYR cc_start: 0.8942 (p90) cc_final: 0.8676 (p90) REVERT: H 307 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8471 (m) REVERT: I 307 VAL cc_start: 0.8803 (t) cc_final: 0.8491 (t) REVERT: J 26 TRP cc_start: 0.8456 (m100) cc_final: 0.7873 (m100) outliers start: 35 outliers final: 28 residues processed: 225 average time/residue: 0.4761 time to fit residues: 156.9312 Evaluate side-chains 224 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 3.039 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain E residue 91 GLN 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 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 105 SER 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 296 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 270 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 197 optimal weight: 0.0270 chunk 178 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 282 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3633 r_free = 0.3633 target = 0.123781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.095210 restraints weight = 47785.046| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.59 r_work: 0.2935 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- 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: 5 | |-----------------------------------------------------------------------------| |-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: 5 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24880 Z= 0.104 Angle : 0.489 12.343 34076 Z= 0.253 Chirality : 0.039 0.192 3839 Planarity : 0.003 0.053 4272 Dihedral : 14.883 178.856 4203 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.64 % Allowed : 17.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2959 helix: 1.52 (0.17), residues: 958 sheet: -0.10 (0.23), residues: 484 loop : -1.72 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 49 HIS 0.012 0.001 HIS C 29 PHE 0.014 0.001 PHE C 44 TYR 0.012 0.001 TYR I 304 ARG 0.005 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.02698 ( 988) hydrogen bonds : angle 3.99594 ( 2953) covalent geometry : bond 0.00232 (24880) covalent geometry : angle 0.48904 (34076) *********************** 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 238 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 2.660 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: A 422 LEU cc_start: 0.8421 (mm) cc_final: 0.8167 (mt) REVERT: B 76 LYS cc_start: 0.8857 (mttp) cc_final: 0.8517 (mttt) REVERT: E 82 ASP cc_start: 0.8133 (m-30) cc_final: 0.7905 (t0) REVERT: E 85 LYS cc_start: 0.8726 (tppt) cc_final: 0.8513 (tppp) REVERT: E 186 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7228 (mp10) REVERT: E 308 THR cc_start: 0.8528 (t) cc_final: 0.8320 (p) REVERT: D 212 ASP cc_start: 0.7852 (m-30) cc_final: 0.7404 (t0) REVERT: F 185 ARG cc_start: 0.8317 (tpp80) cc_final: 0.8070 (mmp80) REVERT: G 290 TYR cc_start: 0.9167 (p90) cc_final: 0.8782 (p90) REVERT: H 251 ILE cc_start: 0.7938 (mp) cc_final: 0.7239 (mp) REVERT: H 290 TYR cc_start: 0.8815 (p90) cc_final: 0.8605 (p90) REVERT: H 307 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8353 (m) REVERT: I 307 VAL cc_start: 0.8722 (t) cc_final: 0.8415 (t) REVERT: J 26 TRP cc_start: 0.8379 (m100) cc_final: 0.7812 (m100) outliers start: 38 outliers final: 30 residues processed: 228 average time/residue: 0.4680 time to fit residues: 156.7006 Evaluate side-chains 224 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 2.566 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain 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 333 ARG Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain H residue 307 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 266 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 281 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 11 optimal weight: 0.0970 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN J 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.090319 restraints weight = 46601.438| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.48 r_work: 0.2857 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24880 Z= 0.185 Angle : 0.551 12.807 34076 Z= 0.283 Chirality : 0.041 0.194 3839 Planarity : 0.004 0.053 4272 Dihedral : 14.945 179.110 4203 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.38 % Allowed : 18.10 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 2959 helix: 1.35 (0.17), residues: 959 sheet: -0.24 (0.22), residues: 508 loop : -1.76 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 49 HIS 0.018 0.001 HIS C 29 PHE 0.012 0.002 PHE C 155 TYR 0.023 0.002 TYR A 235 ARG 0.010 0.000 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 988) hydrogen bonds : angle 4.23053 ( 2953) covalent geometry : bond 0.00435 (24880) covalent geometry : angle 0.55073 (34076) ********************** 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 226 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 2.369 Fit side-chains revert: symmetry clash REVERT: A 177 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.7847 (pt0) REVERT: A 290 ASP cc_start: 0.8045 (m-30) cc_final: 0.7746 (m-30) REVERT: A 422 LEU cc_start: 0.8459 (mm) cc_final: 0.8123 (mt) REVERT: B 76 LYS cc_start: 0.8920 (mttp) cc_final: 0.8546 (mttt) REVERT: B 314 TYR cc_start: 0.8517 (m-80) cc_final: 0.8250 (m-80) REVERT: E 82 ASP cc_start: 0.8169 (m-30) cc_final: 0.7929 (t0) REVERT: E 85 LYS cc_start: 0.8697 (tppt) cc_final: 0.8481 (tppp) REVERT: E 186 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7260 (mp10) REVERT: F 185 ARG cc_start: 0.8387 (tpp80) cc_final: 0.8036 (mmp80) REVERT: H 290 TYR cc_start: 0.8905 (p90) cc_final: 0.8643 (p90) REVERT: H 307 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8402 (m) REVERT: I 203 ARG cc_start: 0.8185 (mtp-110) cc_final: 0.7909 (mtp85) REVERT: I 307 VAL cc_start: 0.8792 (t) cc_final: 0.8476 (t) REVERT: J 26 TRP cc_start: 0.8440 (m100) cc_final: 0.7887 (m100) outliers start: 32 outliers final: 28 residues processed: 219 average time/residue: 0.4679 time to fit residues: 148.4665 Evaluate side-chains 220 residues out of total 2406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 2.579 ------------------------------------------------------------------------------- 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 297 VAL 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 159 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain D residue 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 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 304 TYR Chi-restraints excluded: chain G residue 333 ARG Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 105 SER 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 296 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.1195 > 50: distance: 88 - 111: 30.565 distance: 106 - 111: 29.204 distance: 111 - 112: 37.327 distance: 112 - 113: 49.430 distance: 112 - 115: 28.933 distance: 113 - 116: 39.043 distance: 116 - 117: 5.261 distance: 117 - 118: 45.596 distance: 117 - 120: 17.348 distance: 118 - 119: 26.440 distance: 118 - 127: 41.308 distance: 120 - 121: 49.894 distance: 121 - 122: 14.704 distance: 122 - 123: 17.725 distance: 123 - 124: 12.301 distance: 124 - 125: 31.654 distance: 124 - 126: 20.828 distance: 127 - 128: 15.765 distance: 128 - 129: 25.293 distance: 128 - 131: 41.745 distance: 129 - 130: 40.398 distance: 129 - 132: 12.141 distance: 132 - 133: 40.349 distance: 133 - 134: 3.981 distance: 133 - 136: 16.142 distance: 134 - 135: 20.270 distance: 134 - 146: 40.420 distance: 136 - 137: 42.488 distance: 137 - 138: 6.938 distance: 137 - 139: 6.219 distance: 138 - 140: 18.290 distance: 139 - 141: 31.351 distance: 139 - 142: 16.347 distance: 140 - 141: 4.530 distance: 141 - 143: 34.931 distance: 142 - 144: 30.798 distance: 143 - 145: 31.978 distance: 144 - 145: 22.459 distance: 146 - 147: 9.704 distance: 147 - 148: 18.911 distance: 147 - 150: 40.339 distance: 148 - 149: 39.516 distance: 148 - 157: 52.905 distance: 150 - 151: 24.617 distance: 151 - 152: 17.200 distance: 152 - 153: 41.956 distance: 153 - 154: 14.403 distance: 154 - 155: 37.120 distance: 154 - 156: 19.251 distance: 157 - 158: 5.215 distance: 158 - 159: 11.003 distance: 158 - 161: 4.490 distance: 159 - 160: 20.265 distance: 159 - 168: 5.860 distance: 161 - 162: 3.893 distance: 162 - 163: 58.644 distance: 163 - 165: 27.351 distance: 164 - 166: 6.456 distance: 165 - 167: 39.624 distance: 166 - 167: 39.819 distance: 168 - 169: 30.370 distance: 169 - 170: 40.484 distance: 169 - 172: 17.256 distance: 170 - 171: 17.959 distance: 170 - 176: 46.519 distance: 172 - 173: 39.284 distance: 173 - 174: 44.749 distance: 173 - 175: 41.229 distance: 176 - 177: 40.772 distance: 177 - 180: 69.306 distance: 181 - 182: 24.525 distance: 182 - 183: 37.112 distance: 182 - 185: 44.929 distance: 183 - 184: 24.014 distance: 183 - 189: 40.096 distance: 185 - 186: 43.867 distance: 186 - 187: 42.557 distance: 186 - 188: 19.114 distance: 189 - 190: 7.955 distance: 190 - 191: 56.073 distance: 190 - 193: 28.797 distance: 191 - 192: 8.358 distance: 191 - 194: 30.288