Starting phenix.real_space_refine on Mon Aug 25 14:48:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pig_20350/08_2025/6pig_20350.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pig_20350/08_2025/6pig_20350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pig_20350/08_2025/6pig_20350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pig_20350/08_2025/6pig_20350.map" model { file = "/net/cci-nas-00/data/ceres_data/6pig_20350/08_2025/6pig_20350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pig_20350/08_2025/6pig_20350.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 59 5.49 5 S 142 5.16 5 C 18143 2.51 5 N 4990 2.21 5 O 5533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28867 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 14, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 23, 'rna3p': 36} Chain: "A" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2742 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2714 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2509 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 Chain: "G" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4009 Classifications: {'peptide': 511} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 486} Chain breaks: 2 Chain: "H" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1606 Classifications: {'peptide': 197} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 187} Chain: "I" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2923 Classifications: {'peptide': 357} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 335} Chain breaks: 3 Chain: "J" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2978 Classifications: {'peptide': 368} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 347} Chain breaks: 2 Time building chain proxies: 7.35, per 1000 atoms: 0.25 Number of scatterers: 28867 At special positions: 0 Unit cell: (133, 161.5, 185.25, 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 142 16.00 P 59 15.00 O 5533 8.00 N 4990 7.00 C 18143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 36 sheets defined 26.7% alpha, 12.4% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.558A pdb=" N PHE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.783A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 309 through 313 Processing helix chain 'A' and resid 316 through 321 removed outlier: 4.112A pdb=" N LEU A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 removed outlier: 4.028A pdb=" N ASN A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.574A pdb=" N LEU B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.799A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.551A pdb=" N ILE B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.789A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 removed outlier: 3.560A pdb=" N GLU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.689A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.808A pdb=" N ALA C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.633A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.895A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 187 through 192 removed outlier: 4.061A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.854A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'C' and resid 305 through 311 removed outlier: 3.646A pdb=" N GLN C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.802A pdb=" N GLU C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.894A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.680A pdb=" N THR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.832A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 262 through 269 removed outlier: 3.939A pdb=" N ILE D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.637A pdb=" N TYR D 316 " --> pdb=" O GLN D 312 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 320 " --> pdb=" O TYR D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 343 removed outlier: 3.797A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.809A pdb=" N ALA E 49 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.683A pdb=" N GLN E 67 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 123 Processing helix chain 'E' and resid 125 through 137 removed outlier: 3.772A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 200 removed outlier: 3.549A pdb=" N SER E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.820A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 344 removed outlier: 3.513A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 123 removed outlier: 4.022A pdb=" N THR F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 135 removed outlier: 3.870A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.629A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 removed outlier: 3.995A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 183 through 188' Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 307 through 312 removed outlier: 3.512A pdb=" N GLN F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN F 312 " --> pdb=" O SER F 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 307 through 312' Processing helix chain 'F' and resid 312 through 320 removed outlier: 3.742A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 320 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 342 removed outlier: 3.749A pdb=" N PHE F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 17 through 24 Processing helix chain 'G' and resid 36 through 44 removed outlier: 4.003A pdb=" N THR G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 removed outlier: 4.266A pdb=" N ASP G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 77 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.736A pdb=" N ILE G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 153 removed outlier: 3.556A pdb=" N LEU G 153 " --> pdb=" O LEU G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 167 removed outlier: 3.918A pdb=" N LEU G 167 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 removed outlier: 3.735A pdb=" N MET G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 229 removed outlier: 4.023A pdb=" N SER G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 229 " --> pdb=" O PHE G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 Processing helix chain 'G' and resid 411 through 427 removed outlier: 3.892A pdb=" N PHE G 415 " --> pdb=" O SER G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 499 removed outlier: 3.919A pdb=" N SER G 499 " --> pdb=" O THR G 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 529 Processing helix chain 'G' and resid 550 through 557 Processing helix chain 'H' and resid 16 through 31 removed outlier: 3.798A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 70 removed outlier: 3.529A pdb=" N ASP H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 80 removed outlier: 3.593A pdb=" N GLN H 77 " --> pdb=" O HIS H 73 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.582A pdb=" N ARG H 117 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 128 No H-bonds generated for 'chain 'H' and resid 126 through 128' Processing helix chain 'I' and resid 16 through 21 Processing helix chain 'I' and resid 30 through 45 removed outlier: 4.299A pdb=" N LEU I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE I 44 " --> pdb=" O PHE I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 81 removed outlier: 4.386A pdb=" N LEU I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 201 removed outlier: 3.857A pdb=" N VAL I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER I 201 " --> pdb=" O ALA I 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 196 through 201' Processing helix chain 'I' and resid 216 through 228 removed outlier: 3.965A pdb=" N ARG I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP I 221 " --> pdb=" O LYS I 217 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 265 removed outlier: 3.863A pdb=" N PHE I 251 " --> pdb=" O TRP I 247 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N HIS I 252 " --> pdb=" O PRO I 248 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 285 removed outlier: 3.950A pdb=" N PHE I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 removed outlier: 3.901A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU I 302 " --> pdb=" O ILE I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 333 Processing helix chain 'I' and resid 336 through 345 removed outlier: 3.999A pdb=" N ALA I 340 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER I 341 " --> pdb=" O ASP I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 379 removed outlier: 3.502A pdb=" N ILE I 372 " --> pdb=" O HIS I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 24 removed outlier: 3.916A pdb=" N LYS J 24 " --> pdb=" O ARG J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 43 Processing helix chain 'J' and resid 68 through 81 removed outlier: 3.806A pdb=" N LEU J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 206 removed outlier: 3.626A pdb=" N ALA J 205 " --> pdb=" O SER J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 231 removed outlier: 4.151A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 244 removed outlier: 3.861A pdb=" N VAL J 241 " --> pdb=" O HIS J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 260 removed outlier: 3.644A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 285 Processing helix chain 'J' and resid 297 through 310 Processing helix chain 'J' and resid 328 through 333 removed outlier: 3.982A pdb=" N LEU J 332 " --> pdb=" O ALA J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 345 Processing helix chain 'J' and resid 369 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.556A pdb=" N HIS A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 206 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A 151 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 272 Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.909A pdb=" N HIS A 290 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 295 " --> pdb=" O HIS A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.848A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 15 removed outlier: 3.718A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AB3, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.719A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 156 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AB7, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB8, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AB9, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AC1, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.893A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AC3, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AC4, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.606A pdb=" N VAL F 166 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 38 Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AC9, first strand: chain 'G' and resid 201 through 204 Processing sheet with id=AD1, first strand: chain 'G' and resid 438 through 444 removed outlier: 6.590A pdb=" N VAL G 478 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU G 481 " --> pdb=" O PRO G 391 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU G 483 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL G 389 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 398 through 399 Processing sheet with id=AD3, first strand: chain 'G' and resid 539 through 541 Processing sheet with id=AD4, first strand: chain 'G' and resid 569 through 572 removed outlier: 3.878A pdb=" N GLY G 569 " --> pdb=" O ILE G 594 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 615 through 616 Processing sheet with id=AD6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'H' and resid 55 through 56 removed outlier: 3.535A pdb=" N THR H 9 " --> pdb=" O HIS H 85 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS H 85 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 99 through 100 Processing sheet with id=AD9, first strand: chain 'J' and resid 322 through 324 753 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5482 1.33 - 1.46: 7938 1.46 - 1.58: 15985 1.58 - 1.70: 118 1.70 - 1.82: 205 Bond restraints: 29728 Sorted by residual: bond pdb=" N ILE J 125 " pdb=" CA ILE J 125 " ideal model delta sigma weight residual 1.460 1.495 -0.035 7.50e-03 1.78e+04 2.22e+01 bond pdb=" N ILE E 190 " pdb=" CA ILE E 190 " ideal model delta sigma weight residual 1.459 1.500 -0.042 9.10e-03 1.21e+04 2.10e+01 bond pdb=" N VAL G 497 " pdb=" CA VAL G 497 " ideal model delta sigma weight residual 1.458 1.498 -0.040 9.00e-03 1.23e+04 2.01e+01 bond pdb=" N ILE A 271 " pdb=" CA ILE A 271 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.50e-03 1.11e+04 1.99e+01 bond pdb=" N LEU H 11 " pdb=" CA LEU H 11 " ideal model delta sigma weight residual 1.463 1.494 -0.031 6.90e-03 2.10e+04 1.96e+01 ... (remaining 29723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 26911 1.65 - 3.30: 10987 3.30 - 4.95: 2410 4.95 - 6.60: 276 6.60 - 8.25: 43 Bond angle restraints: 40627 Sorted by residual: angle pdb=" N PRO G 533 " pdb=" CA PRO G 533 " pdb=" CB PRO G 533 " ideal model delta sigma weight residual 103.25 96.50 6.75 1.05e+00 9.07e-01 4.13e+01 angle pdb=" N PRO C 276 " pdb=" CA PRO C 276 " pdb=" CB PRO C 276 " ideal model delta sigma weight residual 103.25 96.88 6.37 1.05e+00 9.07e-01 3.68e+01 angle pdb=" C GLN B 67 " pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta sigma weight residual 119.92 125.43 -5.51 9.60e-01 1.09e+00 3.29e+01 angle pdb=" CA ILE G 201 " pdb=" C ILE G 201 " pdb=" O ILE G 201 " ideal model delta sigma weight residual 121.68 117.44 4.24 7.90e-01 1.60e+00 2.88e+01 angle pdb=" C LYS D 343 " pdb=" N GLY D 344 " pdb=" CA GLY D 344 " ideal model delta sigma weight residual 120.44 126.25 -5.81 1.09e+00 8.42e-01 2.84e+01 ... (remaining 40622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 17217 35.97 - 71.94: 504 71.94 - 107.91: 38 107.91 - 143.88: 2 143.88 - 179.85: 2 Dihedral angle restraints: 17763 sinusoidal: 7678 harmonic: 10085 Sorted by residual: dihedral pdb=" CA TRP A 24 " pdb=" C TRP A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta harmonic sigma weight residual 180.00 -100.77 -79.23 0 5.00e+00 4.00e-02 2.51e+02 dihedral pdb=" CA ILE I 125 " pdb=" C ILE I 125 " pdb=" N PRO I 126 " pdb=" CA PRO I 126 " ideal model delta harmonic sigma weight residual 180.00 110.99 69.01 0 5.00e+00 4.00e-02 1.91e+02 dihedral pdb=" CA LYS J 7 " pdb=" C LYS J 7 " pdb=" N PRO J 8 " pdb=" CA PRO J 8 " ideal model delta harmonic sigma weight residual -180.00 -125.64 -54.36 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 17760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2212 0.061 - 0.122: 1583 0.122 - 0.184: 588 0.184 - 0.245: 105 0.245 - 0.306: 1 Chirality restraints: 4489 Sorted by residual: chirality pdb=" CA HIS A 349 " pdb=" N HIS A 349 " pdb=" C HIS A 349 " pdb=" CB HIS A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2' G 1 41 " pdb=" C3' G 1 41 " pdb=" O2' G 1 41 " pdb=" C1' G 1 41 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE B 85 " pdb=" N ILE B 85 " pdb=" C ILE B 85 " pdb=" CB ILE B 85 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4486 not shown) Planarity restraints: 4986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 48 " -0.017 2.00e-02 2.50e+03 1.47e-02 6.52e+00 pdb=" N9 G 1 48 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G 1 48 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 1 48 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 1 48 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 1 48 " 0.016 2.00e-02 2.50e+03 pdb=" O6 G 1 48 " -0.029 2.00e-02 2.50e+03 pdb=" N1 G 1 48 " 0.026 2.00e-02 2.50e+03 pdb=" C2 G 1 48 " -0.013 2.00e-02 2.50e+03 pdb=" N2 G 1 48 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G 1 48 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G 1 48 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 125 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO I 126 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO I 126 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 126 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 67 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C ASP H 67 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP H 67 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU H 68 " 0.015 2.00e-02 2.50e+03 ... (remaining 4983 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1033 2.72 - 3.26: 26356 3.26 - 3.81: 42513 3.81 - 4.35: 57282 4.35 - 4.90: 94986 Nonbonded interactions: 222170 Sorted by model distance: nonbonded pdb=" O GLU H 154 " pdb=" O PHE H 163 " model vdw 2.173 3.040 nonbonded pdb=" O LEU H 152 " pdb=" NH1 ARG H 164 " model vdw 2.327 3.120 nonbonded pdb=" O ASP A 14 " pdb=" NZ LYS G 510 " model vdw 2.348 3.120 nonbonded pdb=" O LYS G 517 " pdb=" N ILE G 519 " model vdw 2.356 3.120 nonbonded pdb=" O ASP G 608 " pdb=" OG1 THR G 611 " model vdw 2.377 3.040 ... (remaining 222165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'B' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'C' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'D' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'E' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 1 through 193 or resid 195 through 232 or resid 236 throug \ h 351 or resid 361 through 378 or resid 380 through 393)) selection = (chain 'J' and (resid 1 through 162 or resid 164 or resid 166 or resid 196 throu \ gh 351 or resid 361 through 378 or resid 380 through 393)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.050 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.014 0.047 29728 Z= 1.038 Angle : 1.756 8.247 40627 Z= 1.238 Chirality : 0.085 0.306 4489 Planarity : 0.004 0.063 4986 Dihedral : 16.960 179.853 11211 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 3.45 % Allowed : 15.16 % Favored : 81.39 % Rotamer: Outliers : 1.58 % Allowed : 8.37 % Favored : 90.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.77 % Twisted Proline : 6.06 % Twisted General : 1.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.85 (0.12), residues: 3391 helix: -2.89 (0.13), residues: 868 sheet: -2.09 (0.21), residues: 484 loop : -3.87 (0.11), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 393 TYR 0.027 0.002 TYR H 149 PHE 0.017 0.002 PHE B 246 TRP 0.033 0.002 TRP A 24 HIS 0.010 0.002 HIS A 349 Details of bonding type rmsd covalent geometry : bond 0.01366 (29728) covalent geometry : angle 1.75597 (40627) hydrogen bonds : bond 0.20229 ( 760) hydrogen bonds : angle 8.85847 ( 2098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 414 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8002 (tp30) cc_final: 0.7787 (tp30) REVERT: A 122 LYS cc_start: 0.7184 (tptt) cc_final: 0.6893 (tttp) REVERT: A 165 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7220 (mptt) REVERT: A 202 ASP cc_start: 0.6072 (m-30) cc_final: 0.5791 (m-30) REVERT: A 297 TYR cc_start: 0.8139 (m-80) cc_final: 0.7700 (m-10) REVERT: A 342 ILE cc_start: 0.8500 (mt) cc_final: 0.8216 (mm) REVERT: B 117 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7893 (mm-30) REVERT: B 195 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7947 (mtmm) REVERT: B 338 MET cc_start: 0.8802 (mmt) cc_final: 0.8389 (mmt) REVERT: C 99 GLN cc_start: 0.8144 (mt0) cc_final: 0.7520 (mp10) REVERT: C 107 LYS cc_start: 0.7554 (tptt) cc_final: 0.7113 (tttt) REVERT: C 210 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7031 (ptp90) REVERT: D 107 LYS cc_start: 0.7996 (pttm) cc_final: 0.7546 (tmtt) REVERT: D 210 ARG cc_start: 0.7654 (tpp80) cc_final: 0.7259 (ttp-110) REVERT: D 268 ILE cc_start: 0.8309 (pt) cc_final: 0.7718 (mt) REVERT: E 254 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7832 (mt-10) REVERT: F 74 ASP cc_start: 0.8815 (m-30) cc_final: 0.8501 (m-30) REVERT: F 122 LYS cc_start: 0.7908 (tptt) cc_final: 0.7516 (tptp) REVERT: F 210 ARG cc_start: 0.7783 (ttm-80) cc_final: 0.7243 (ttm170) REVERT: F 294 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8369 (t) REVERT: F 311 GLN cc_start: 0.7757 (mt0) cc_final: 0.7445 (pp30) REVERT: G 177 MET cc_start: 0.5077 (ttt) cc_final: 0.4829 (tmm) REVERT: G 200 GLN cc_start: 0.7821 (mt0) cc_final: 0.7563 (mt0) REVERT: H 4 TYR cc_start: 0.6939 (m-80) cc_final: 0.6545 (m-80) REVERT: H 65 GLU cc_start: 0.7665 (tp30) cc_final: 0.7307 (tp30) REVERT: I 257 ASP cc_start: 0.6737 (p0) cc_final: 0.5875 (p0) REVERT: I 276 LYS cc_start: 0.5591 (mtmm) cc_final: 0.5220 (mttm) REVERT: I 294 LEU cc_start: 0.7529 (mt) cc_final: 0.6642 (mt) REVERT: I 322 LYS cc_start: 0.7604 (mtpt) cc_final: 0.7252 (mtpt) REVERT: I 338 GLN cc_start: 0.8433 (mt0) cc_final: 0.8061 (mt0) REVERT: I 365 TYR cc_start: 0.7727 (m-80) cc_final: 0.7509 (m-80) REVERT: J 2 PHE cc_start: 0.8226 (t80) cc_final: 0.7783 (t80) REVERT: J 238 PHE cc_start: 0.6309 (t80) cc_final: 0.5920 (p90) REVERT: J 261 PHE cc_start: 0.3242 (t80) cc_final: 0.2323 (m-10) outliers start: 48 outliers final: 17 residues processed: 460 average time/residue: 0.2168 time to fit residues: 155.6499 Evaluate side-chains 300 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 282 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 276 PRO Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 276 PRO Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 533 PRO Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 ASN A 312 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 145 ASN B 174 ASN B 183 ASN B 218 ASN C 104 ASN C 174 ASN C 179 GLN C 214 HIS C 311 GLN D 135 ASN D 183 ASN D 328 GLN E 99 GLN E 311 GLN E 349 HIS F 174 ASN F 183 ASN G 227 GLN G 230 GLN G 246 ASN G 518 HIS G 618 ASN H 162 ASN H 166 ASN I 60 ASN I 95 ASN I 154 ASN I 207 HIS J 23 ASN J 46 HIS J 84 ASN J 95 ASN J 345 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.166862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131634 restraints weight = 43430.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129525 restraints weight = 58166.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131206 restraints weight = 55697.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131509 restraints weight = 33556.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134317 restraints weight = 29915.239| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29728 Z= 0.148 Angle : 0.777 13.582 40627 Z= 0.409 Chirality : 0.046 0.231 4489 Planarity : 0.005 0.079 4986 Dihedral : 15.689 179.053 4673 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.74 % Allowed : 14.24 % Favored : 85.02 % Rotamer: Outliers : 2.83 % Allowed : 12.09 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.77 % Twisted Proline : 5.45 % Twisted General : 1.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.97 (0.13), residues: 3391 helix: -1.71 (0.15), residues: 946 sheet: -1.60 (0.22), residues: 494 loop : -3.59 (0.12), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 110 TYR 0.031 0.001 TYR H 149 PHE 0.017 0.001 PHE I 238 TRP 0.034 0.001 TRP A 24 HIS 0.007 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00306 (29728) covalent geometry : angle 0.77678 (40627) hydrogen bonds : bond 0.04246 ( 760) hydrogen bonds : angle 5.58662 ( 2098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6782 Ramachandran restraints generated. 3391 Oldfield, 0 Emsley, 3391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 332 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: C 99 GLN cc_start: 0.7634 (mt0) cc_final: 0.7394 (mp10) REVERT: C 210 ARG cc_start: 0.7640 (ptp-170) cc_final: 0.7432 (ptp90) REVERT: C 334 MET cc_start: 0.7636 (mmm) cc_final: 0.7377 (mmp) REVERT: D 268 ILE cc_start: 0.8280 (pt) cc_final: 0.7908 (mt) REVERT: F 294 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8500 (t) REVERT: H 18 GLU cc_start: 0.7257 (mp0) cc_final: 0.7005 (mp0) REVERT: I 75 PHE cc_start: 0.5520 (OUTLIER) cc_final: 0.5303 (t80) REVERT: I 92 LEU cc_start: 0.3287 (OUTLIER) cc_final: 0.3001 (pp) REVERT: I 292 ARG cc_start: 0.7938 (ptp90) cc_final: 0.7737 (ptp90) REVERT: I 294 LEU cc_start: 0.6699 (mt) cc_final: 0.6010 (mt) REVERT: J 261 PHE cc_start: 0.3406 (t80) cc_final: 0.2732 (m-10) outliers start: 86 outliers final: 40 residues processed: 396 average time/residue: 0.1963 time to fit residues: 124.7864 Evaluate side-chains 297 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 403 SER Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 530 GLU Chi-restraints excluded: chain G residue 549 ASN Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8067 > 50: distance: 11 - 94: 29.120 distance: 14 - 91: 28.545 distance: 36 - 39: 9.374 distance: 39 - 40: 9.007 distance: 40 - 41: 20.020 distance: 40 - 43: 24.046 distance: 41 - 42: 23.734 distance: 41 - 46: 20.925 distance: 43 - 44: 8.859 distance: 43 - 45: 12.555 distance: 46 - 47: 6.940 distance: 47 - 48: 32.276 distance: 47 - 50: 16.034 distance: 48 - 49: 24.289 distance: 48 - 51: 39.596 distance: 51 - 52: 23.687 distance: 52 - 53: 10.064 distance: 52 - 55: 11.025 distance: 53 - 54: 29.033 distance: 53 - 60: 13.898 distance: 55 - 56: 13.154 distance: 56 - 57: 25.611 distance: 57 - 58: 3.775 distance: 57 - 59: 9.053 distance: 60 - 61: 16.221 distance: 61 - 62: 13.229 distance: 61 - 64: 26.097 distance: 62 - 63: 23.087 distance: 62 - 65: 19.539 distance: 65 - 66: 13.275 distance: 66 - 67: 14.492 distance: 66 - 69: 10.695 distance: 67 - 68: 30.849 distance: 67 - 73: 23.599 distance: 69 - 70: 22.373 distance: 70 - 71: 21.558 distance: 70 - 72: 28.435 distance: 73 - 74: 15.785 distance: 74 - 75: 14.679 distance: 74 - 77: 29.006 distance: 75 - 76: 7.808 distance: 75 - 78: 20.043 distance: 78 - 79: 21.028 distance: 79 - 80: 24.354 distance: 79 - 82: 8.044 distance: 80 - 81: 22.021 distance: 80 - 87: 11.686 distance: 82 - 83: 30.854 distance: 83 - 84: 10.236 distance: 84 - 85: 13.909 distance: 84 - 86: 15.620 distance: 87 - 88: 34.337 distance: 88 - 89: 6.527 distance: 89 - 90: 20.223 distance: 89 - 91: 39.346 distance: 91 - 92: 8.557 distance: 92 - 93: 35.785 distance: 92 - 95: 22.281 distance: 93 - 94: 25.529 distance: 93 - 99: 23.419 distance: 95 - 96: 21.430 distance: 96 - 97: 17.141 distance: 96 - 98: 5.400 distance: 99 - 100: 15.885 distance: 99 - 105: 10.721 distance: 100 - 101: 11.006 distance: 100 - 103: 5.721 distance: 101 - 102: 7.329 distance: 101 - 106: 14.550 distance: 103 - 104: 25.163 distance: 104 - 105: 21.395