Starting phenix.real_space_refine on Mon Sep 14 06:38:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pig_20350/09_2026/6pig_20350.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pig_20350/09_2026/6pig_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6pig_20350/09_2026/6pig_20350.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pig_20350/09_2026/6pig_20350.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pig_20350/09_2026/6pig_20350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pig_20350/09_2026/6pig_20350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pig_20350/09_2026/6pig_20350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pig_20350/09_2026/6pig_20350.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 60} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 14, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 23, 'rna3p': 36} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 5.81, per 1000 atoms: 0.20 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.21 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: 5.09 Time building geometry restraints manager: 3.13 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: 26766 1.65 - 3.30: 11069 3.30 - 4.95: 2460 4.95 - 6.60: 288 6.60 - 8.25: 44 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 - 17.54: 15131 17.54 - 35.08: 1840 35.08 - 52.61: 403 52.61 - 70.15: 133 70.15 - 87.69: 38 Dihedral angle restraints: 17545 sinusoidal: 7460 harmonic: 10085 Sorted by residual: dihedral pdb=" C4' G 1 53 " pdb=" C3' G 1 53 " pdb=" C2' G 1 53 " pdb=" C1' G 1 53 " ideal model delta sinusoidal sigma weight residual 36.34 -38.87 75.21 1 3.10e+00 1.04e-01 7.44e+02 dihedral pdb=" C4' G 1 3 " pdb=" C3' G 1 3 " pdb=" C2' G 1 3 " pdb=" C1' G 1 3 " ideal model delta sinusoidal sigma weight residual 36.34 -38.85 75.20 1 3.10e+00 1.04e-01 7.44e+02 dihedral pdb=" C4' C 1 38 " pdb=" C3' C 1 38 " pdb=" C2' C 1 38 " pdb=" C1' C 1 38 " ideal model delta sinusoidal sigma weight residual 36.34 -38.83 75.18 1 3.10e+00 1.04e-01 7.43e+02 ... (remaining 17542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2134 0.061 - 0.122: 1585 0.122 - 0.184: 585 0.184 - 0.245: 165 0.245 - 0.306: 20 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' U 1 9 " pdb=" C3' U 1 9 " pdb=" O2' U 1 9 " pdb=" C1' U 1 9 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' G 1 3 " pdb=" C3' G 1 3 " pdb=" O2' G 1 3 " pdb=" C1' G 1 3 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.03e+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: 1.950 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 27.310 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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= 1.037 Angle : 1.768 8.247 40627 Z= 1.234 Chirality : 0.091 0.306 4489 Planarity : 0.004 0.063 4986 Dihedral : 16.697 87.688 10993 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 are 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/Z covalent geometry : bond 0.01367 / 1.04 (29728) covalent geometry : angle 1.76824 / 1.23 (40627) hydrogen bonds : bond 0.20229 / 10.42 ( 760) hydrogen bonds : angle 8.85847 / 3.54 ( 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 : 0.733 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: 0.1894 time to fit residues: 137.1323 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 : 1.054 ------------------------------------------------------------------------------- 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... 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 I 225 HIS J 23 ASN J 46 HIS J 84 ASN J 95 ASN J 345 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.168226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.134097 restraints weight = 43504.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133322 restraints weight = 58085.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134236 restraints weight = 58876.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134975 restraints weight = 34623.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135546 restraints weight = 30125.445| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29728 Z= 0.165 Angle : 0.926 17.582 40627 Z= 0.444 Chirality : 0.061 0.802 4489 Planarity : 0.005 0.078 4986 Dihedral : 13.487 166.665 4455 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.77 % Allowed : 14.13 % Favored : 85.11 % Rotamer: Outliers : 2.97 % Allowed : 11.99 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.77 % Twisted Proline : 5.45 % Twisted General : 1.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.13), residues: 3391 helix: -1.74 (0.15), residues: 946 sheet: -1.57 (0.22), residues: 502 loop : -3.60 (0.12), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 110 TYR 0.028 0.001 TYR H 149 PHE 0.016 0.001 PHE I 238 TRP 0.035 0.001 TRP A 24 HIS 0.007 0.001 HIS D 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (29728) covalent geometry : angle 0.92633 / 0.44 (40627) hydrogen bonds : bond 0.04265 / 2.21 ( 760) hydrogen bonds : angle 5.63871 / 2.27 ( 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 422 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 332 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: C 99 GLN cc_start: 0.7692 (mt0) cc_final: 0.7427 (mp10) REVERT: C 210 ARG cc_start: 0.7657 (ptp-170) cc_final: 0.7440 (ptp90) REVERT: C 334 MET cc_start: 0.7733 (mmm) cc_final: 0.7466 (mmp) REVERT: D 268 ILE cc_start: 0.8311 (pt) cc_final: 0.7912 (mt) REVERT: F 294 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8477 (t) REVERT: H 18 GLU cc_start: 0.7241 (mp0) cc_final: 0.7004 (mp0) REVERT: I 75 PHE cc_start: 0.5686 (OUTLIER) cc_final: 0.5480 (t80) REVERT: I 92 LEU cc_start: 0.3305 (OUTLIER) cc_final: 0.3076 (pp) REVERT: I 294 LEU cc_start: 0.6493 (mt) cc_final: 0.5835 (mt) REVERT: J 261 PHE cc_start: 0.3382 (t80) cc_final: 0.2745 (m-10) outliers start: 90 outliers final: 39 residues processed: 398 average time/residue: 0.1893 time to fit residues: 122.2327 Evaluate side-chains 293 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 38 THR 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 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 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 270 THR Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 391 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 17 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 325 optimal weight: 30.0000 chunk 84 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN B 218 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 252 HIS ** 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 = 0.3956 r_free = 0.3956 target = 0.167682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133357 restraints weight = 43499.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131862 restraints weight = 59506.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133011 restraints weight = 58886.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133738 restraints weight = 34605.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134293 restraints weight = 30507.430| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29728 Z= 0.147 Angle : 0.821 14.594 40627 Z= 0.401 Chirality : 0.054 0.522 4489 Planarity : 0.005 0.080 4986 Dihedral : 13.293 168.676 4437 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.62 % Allowed : 15.78 % Favored : 83.60 % Rotamer: Outliers : 3.20 % Allowed : 14.04 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.77 % Twisted Proline : 5.45 % Twisted General : 0.95 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.13), residues: 3391 helix: -1.31 (0.16), residues: 950 sheet: -1.32 (0.22), residues: 502 loop : -3.48 (0.12), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 110 TYR 0.031 0.001 TYR G 622 PHE 0.016 0.001 PHE D 89 TRP 0.028 0.001 TRP A 24 HIS 0.008 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (29728) covalent geometry : angle 0.82074 / 0.40 (40627) hydrogen bonds : bond 0.03759 / 1.95 ( 760) hydrogen bonds : angle 5.18489 / 2.08 ( 2098) *********************** REFINEMENT MACRO_CYCLE 3 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 391 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 294 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 THR cc_start: 0.8926 (m) cc_final: 0.8579 (p) REVERT: B 338 MET cc_start: 0.8634 (mmt) cc_final: 0.8144 (mmt) REVERT: C 99 GLN cc_start: 0.7604 (mt0) cc_final: 0.7347 (mp10) REVERT: D 268 ILE cc_start: 0.8386 (pt) cc_final: 0.7979 (mt) REVERT: F 280 GLU cc_start: 0.7284 (tp30) cc_final: 0.6988 (tt0) REVERT: F 294 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8498 (t) REVERT: G 71 TRP cc_start: 0.4027 (OUTLIER) cc_final: 0.1853 (t60) REVERT: H 18 GLU cc_start: 0.7427 (mp0) cc_final: 0.7172 (mp0) REVERT: I 75 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5437 (t80) REVERT: I 294 LEU cc_start: 0.6538 (mt) cc_final: 0.5943 (mt) REVERT: J 238 PHE cc_start: 0.5823 (t80) cc_final: 0.5572 (m-10) REVERT: J 244 PHE cc_start: 0.5212 (OUTLIER) cc_final: 0.4212 (m-10) REVERT: J 296 HIS cc_start: 0.6139 (m-70) cc_final: 0.5707 (m-70) REVERT: J 385 PHE cc_start: 0.3699 (OUTLIER) cc_final: 0.3323 (t80) outliers start: 97 outliers final: 55 residues processed: 365 average time/residue: 0.1649 time to fit residues: 100.6142 Evaluate side-chains 305 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 48 LEU 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 F residue 346 MET Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 403 SER 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 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 549 ASN Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain I residue 30 VAL 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 44 ILE Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 239 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 319 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 333 optimal weight: 5.9990 chunk 308 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 307 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN G 85 HIS H 17 ASN I 338 GLN J 296 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127883 restraints weight = 43303.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126264 restraints weight = 54699.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127601 restraints weight = 55197.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127797 restraints weight = 32513.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130804 restraints weight = 28946.142| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 29728 Z= 0.244 Angle : 0.893 13.764 40627 Z= 0.435 Chirality : 0.060 0.678 4489 Planarity : 0.006 0.080 4986 Dihedral : 13.418 163.691 4435 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.74 % Allowed : 15.90 % Favored : 83.37 % Rotamer: Outliers : 3.82 % Allowed : 15.32 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 5.45 % Twisted General : 1.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.13), residues: 3391 helix: -1.35 (0.16), residues: 953 sheet: -1.29 (0.23), residues: 503 loop : -3.43 (0.12), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 220 TYR 0.027 0.002 TYR G 622 PHE 0.022 0.002 PHE E 89 TRP 0.021 0.002 TRP A 24 HIS 0.009 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (29728) covalent geometry : angle 0.89274 / 0.44 (40627) hydrogen bonds : bond 0.04264 / 2.21 ( 760) hydrogen bonds : angle 5.29204 / 2.12 ( 2098) *********************** REFINEMENT MACRO_CYCLE 4 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 368 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 252 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7335 (mtm110) REVERT: C 99 GLN cc_start: 0.7585 (mt0) cc_final: 0.7309 (mp10) REVERT: C 210 ARG cc_start: 0.7836 (ptm160) cc_final: 0.7398 (ptp90) REVERT: D 268 ILE cc_start: 0.8534 (pt) cc_final: 0.8159 (mt) REVERT: D 347 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8870 (p90) REVERT: F 280 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: F 294 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8627 (t) REVERT: G 71 TRP cc_start: 0.4304 (OUTLIER) cc_final: 0.1844 (t60) REVERT: G 177 MET cc_start: 0.4776 (tmm) cc_final: 0.3623 (ttm) REVERT: H 105 GLN cc_start: 0.7429 (tt0) cc_final: 0.6931 (tt0) REVERT: I 195 GLU cc_start: 0.5403 (OUTLIER) cc_final: 0.4917 (tt0) REVERT: J 238 PHE cc_start: 0.5952 (t80) cc_final: 0.5643 (m-10) REVERT: J 244 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.3996 (m-10) REVERT: J 385 PHE cc_start: 0.4171 (OUTLIER) cc_final: 0.3804 (t80) outliers start: 116 outliers final: 78 residues processed: 333 average time/residue: 0.1656 time to fit residues: 92.1348 Evaluate side-chains 318 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 232 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 48 LEU 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 123 ILE 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 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain G residue 17 THR 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 236 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 409 ILE 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 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 549 ASN Chi-restraints excluded: chain G residue 590 ILE Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 149 TYR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 247 TRP 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 44 ILE Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 318 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 305 optimal weight: 0.0670 chunk 311 optimal weight: 10.0000 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 HIS F 311 GLN I 135 ASN J 333 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132594 restraints weight = 43415.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130915 restraints weight = 64444.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132539 restraints weight = 57786.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132472 restraints weight = 36302.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134662 restraints weight = 32098.482| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29728 Z= 0.151 Angle : 0.796 13.428 40627 Z= 0.389 Chirality : 0.053 0.419 4489 Planarity : 0.005 0.079 4986 Dihedral : 13.075 168.031 4435 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.71 % Allowed : 15.42 % Favored : 83.87 % Rotamer: Outliers : 3.56 % Allowed : 16.18 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 4.24 % Twisted General : 0.86 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.13), residues: 3391 helix: -1.12 (0.17), residues: 956 sheet: -1.25 (0.22), residues: 516 loop : -3.32 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 292 TYR 0.027 0.001 TYR G 622 PHE 0.017 0.001 PHE D 89 TRP 0.027 0.001 TRP A 24 HIS 0.009 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (29728) covalent geometry : angle 0.79619 / 0.39 (40627) hydrogen bonds : bond 0.03550 / 1.83 ( 760) hydrogen bonds : angle 5.06478 / 2.02 ( 2098) *********************** REFINEMENT MACRO_CYCLE 5 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 371 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 263 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 157 THR cc_start: 0.8933 (m) cc_final: 0.8517 (p) REVERT: A 270 THR cc_start: 0.9048 (m) cc_final: 0.8522 (p) REVERT: C 210 ARG cc_start: 0.7784 (ptm160) cc_final: 0.7341 (ptp90) REVERT: F 280 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6891 (tp30) REVERT: F 294 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8575 (t) REVERT: G 436 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.6018 (pt0) REVERT: H 18 GLU cc_start: 0.6894 (mp0) cc_final: 0.6610 (mt-10) REVERT: H 25 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.7021 (tt) REVERT: H 158 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7106 (mm-40) REVERT: I 75 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.5437 (t80) REVERT: I 247 TRP cc_start: 0.5838 (OUTLIER) cc_final: 0.3163 (t-100) REVERT: J 238 PHE cc_start: 0.5796 (t80) cc_final: 0.5438 (p90) REVERT: J 240 PHE cc_start: 0.5615 (t80) cc_final: 0.4894 (t80) REVERT: J 244 PHE cc_start: 0.5080 (OUTLIER) cc_final: 0.3818 (m-10) REVERT: J 385 PHE cc_start: 0.3989 (OUTLIER) cc_final: 0.3673 (t80) outliers start: 108 outliers final: 71 residues processed: 342 average time/residue: 0.1622 time to fit residues: 93.6093 Evaluate side-chains 314 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 234 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 436 GLU 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 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 60 ASN 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 128 CYS Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 247 TRP 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 44 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 125 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS C 179 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.163537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129141 restraints weight = 43553.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127747 restraints weight = 60177.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128920 restraints weight = 59624.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129316 restraints weight = 34746.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131325 restraints weight = 30693.210| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29728 Z= 0.212 Angle : 0.848 13.605 40627 Z= 0.413 Chirality : 0.057 0.534 4489 Planarity : 0.006 0.079 4986 Dihedral : 13.153 165.310 4434 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.65 % Allowed : 16.48 % Favored : 82.87 % Rotamer: Outliers : 4.28 % Allowed : 16.31 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.80 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.13), residues: 3391 helix: -1.22 (0.16), residues: 967 sheet: -1.22 (0.22), residues: 522 loop : -3.32 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 117 TYR 0.025 0.002 TYR G 622 PHE 0.022 0.002 PHE D 89 TRP 0.025 0.002 TRP A 24 HIS 0.009 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (29728) covalent geometry : angle 0.84797 / 0.41 (40627) hydrogen bonds : bond 0.03954 / 2.05 ( 760) hydrogen bonds : angle 5.14513 / 2.05 ( 2098) *********************** REFINEMENT MACRO_CYCLE 6 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 370 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 240 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: C 210 ARG cc_start: 0.7894 (ptm160) cc_final: 0.7421 (ptp90) REVERT: F 280 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6934 (tp30) REVERT: F 294 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8645 (t) REVERT: G 436 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.6055 (pt0) REVERT: G 506 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7163 (mtt-85) REVERT: H 18 GLU cc_start: 0.6896 (mp0) cc_final: 0.6620 (mt-10) REVERT: H 25 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7083 (tt) REVERT: H 105 GLN cc_start: 0.7418 (tt0) cc_final: 0.6779 (tt0) REVERT: H 158 GLN cc_start: 0.7371 (mp10) cc_final: 0.7143 (mm-40) REVERT: I 75 PHE cc_start: 0.5921 (OUTLIER) cc_final: 0.5562 (t80) REVERT: I 195 GLU cc_start: 0.5239 (OUTLIER) cc_final: 0.4828 (tt0) REVERT: I 247 TRP cc_start: 0.5874 (OUTLIER) cc_final: 0.3424 (t-100) REVERT: J 244 PHE cc_start: 0.5190 (OUTLIER) cc_final: 0.4021 (m-10) REVERT: J 323 MET cc_start: 0.3995 (mmm) cc_final: 0.3724 (mmm) REVERT: J 385 PHE cc_start: 0.4098 (OUTLIER) cc_final: 0.3739 (t80) outliers start: 130 outliers final: 101 residues processed: 337 average time/residue: 0.1621 time to fit residues: 92.0391 Evaluate side-chains 343 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 232 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 402 SER Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 436 GLU 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 497 VAL Chi-restraints excluded: chain G residue 506 ARG Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 590 ILE Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 149 TYR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 60 ASN 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 128 CYS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 237 HIS Chi-restraints excluded: chain I residue 247 TRP Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 250 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 290 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 300 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.167361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133001 restraints weight = 43568.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131577 restraints weight = 55884.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132642 restraints weight = 58507.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133187 restraints weight = 34553.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133723 restraints weight = 31061.448| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29728 Z= 0.137 Angle : 0.775 13.491 40627 Z= 0.379 Chirality : 0.052 0.399 4489 Planarity : 0.005 0.079 4986 Dihedral : 12.852 169.401 4434 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.13 % Favored : 84.34 % Rotamer: Outliers : 3.92 % Allowed : 16.84 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.80 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.14), residues: 3391 helix: -0.94 (0.17), residues: 940 sheet: -1.10 (0.22), residues: 527 loop : -3.20 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 292 TYR 0.025 0.001 TYR G 622 PHE 0.015 0.001 PHE D 89 TRP 0.033 0.001 TRP A 24 HIS 0.009 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (29728) covalent geometry : angle 0.77531 / 0.38 (40627) hydrogen bonds : bond 0.03326 / 1.72 ( 760) hydrogen bonds : angle 4.92552 / 1.97 ( 2098) *********************** REFINEMENT MACRO_CYCLE 7 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 382 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 263 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8506 (p) REVERT: A 270 THR cc_start: 0.9026 (m) cc_final: 0.8632 (p) REVERT: C 179 GLN cc_start: 0.7583 (tp40) cc_final: 0.7331 (mp10) REVERT: C 210 ARG cc_start: 0.7815 (ptm160) cc_final: 0.7400 (ptp90) REVERT: D 171 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8505 (mp) REVERT: F 280 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6812 (tp30) REVERT: F 294 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8521 (t) REVERT: G 177 MET cc_start: 0.4389 (tmm) cc_final: 0.3193 (ttt) REVERT: G 436 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5989 (pt0) REVERT: H 6 LYS cc_start: 0.7061 (mttm) cc_final: 0.6818 (mmtt) REVERT: H 18 GLU cc_start: 0.6976 (mp0) cc_final: 0.6726 (mt-10) REVERT: H 25 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7027 (tt) REVERT: H 158 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.7079 (mm-40) REVERT: I 1 MET cc_start: 0.0230 (ttt) cc_final: -0.0165 (tpp) REVERT: I 75 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.5386 (t80) REVERT: I 92 LEU cc_start: 0.2247 (OUTLIER) cc_final: 0.2040 (pp) REVERT: I 195 GLU cc_start: 0.5107 (OUTLIER) cc_final: 0.4680 (tt0) REVERT: J 24 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5630 (ptmt) REVERT: J 238 PHE cc_start: 0.5716 (t80) cc_final: 0.5415 (p90) REVERT: J 240 PHE cc_start: 0.5632 (t80) cc_final: 0.5037 (t80) REVERT: J 244 PHE cc_start: 0.5137 (OUTLIER) cc_final: 0.3882 (m-10) REVERT: J 385 PHE cc_start: 0.4100 (OUTLIER) cc_final: 0.3745 (t80) outliers start: 119 outliers final: 77 residues processed: 349 average time/residue: 0.1758 time to fit residues: 102.4633 Evaluate side-chains 333 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 243 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 436 GLU 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 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL 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 128 CYS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 215 LEU 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 24 LYS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 242 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 339 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 251 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 208 optimal weight: 0.2980 chunk 276 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN I 237 HIS I 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132492 restraints weight = 43489.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130998 restraints weight = 61298.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.132275 restraints weight = 57861.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132532 restraints weight = 35073.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133284 restraints weight = 31564.034| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29728 Z= 0.150 Angle : 0.787 13.681 40627 Z= 0.384 Chirality : 0.053 0.394 4489 Planarity : 0.005 0.078 4986 Dihedral : 12.747 168.378 4433 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.92 % Favored : 83.57 % Rotamer: Outliers : 3.76 % Allowed : 17.46 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.03 % Twisted General : 0.80 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.14), residues: 3391 helix: -0.91 (0.17), residues: 945 sheet: -1.02 (0.23), residues: 523 loop : -3.17 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 292 TYR 0.035 0.001 TYR H 149 PHE 0.017 0.001 PHE D 89 TRP 0.025 0.001 TRP A 24 HIS 0.011 0.001 HIS I 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (29728) covalent geometry : angle 0.78719 / 0.38 (40627) hydrogen bonds : bond 0.03477 / 1.80 ( 760) hydrogen bonds : angle 4.93305 / 1.97 ( 2098) *********************** REFINEMENT MACRO_CYCLE 8 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 367 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 253 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8499 (p) REVERT: A 270 THR cc_start: 0.9019 (m) cc_final: 0.8634 (p) REVERT: B 193 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7413 (ptm) REVERT: C 52 VAL cc_start: 0.6109 (OUTLIER) cc_final: 0.5865 (m) REVERT: C 210 ARG cc_start: 0.7838 (ptm160) cc_final: 0.7402 (ptp90) REVERT: D 171 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8502 (mp) REVERT: F 280 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6842 (tp30) REVERT: F 294 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8559 (t) REVERT: G 177 MET cc_start: 0.4508 (tmm) cc_final: 0.3302 (ttm) REVERT: G 436 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.6018 (pt0) REVERT: H 18 GLU cc_start: 0.6960 (mp0) cc_final: 0.6661 (mt-10) REVERT: H 25 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7043 (tt) REVERT: H 158 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6997 (mm-40) REVERT: I 1 MET cc_start: 0.0104 (ttt) cc_final: -0.0194 (tpp) REVERT: I 75 PHE cc_start: 0.5675 (OUTLIER) cc_final: 0.5403 (t80) REVERT: I 195 GLU cc_start: 0.5075 (OUTLIER) cc_final: 0.4660 (tt0) REVERT: I 247 TRP cc_start: 0.5804 (OUTLIER) cc_final: 0.3184 (t-100) REVERT: J 24 LYS cc_start: 0.6143 (OUTLIER) cc_final: 0.5636 (ptmt) REVERT: J 238 PHE cc_start: 0.5816 (t80) cc_final: 0.5520 (p90) REVERT: J 244 PHE cc_start: 0.5190 (OUTLIER) cc_final: 0.4313 (m-10) REVERT: J 385 PHE cc_start: 0.4149 (OUTLIER) cc_final: 0.3795 (t80) outliers start: 114 outliers final: 90 residues processed: 335 average time/residue: 0.1741 time to fit residues: 98.4871 Evaluate side-chains 339 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 234 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 436 GLU 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 490 HIS Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 247 TRP Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 331 MET Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 24 LYS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 9.9990 chunk 184 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 321 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 278 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN J 31 HIS ** J 252 HIS ** 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 = 0.3943 r_free = 0.3943 target = 0.166746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131785 restraints weight = 43740.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.129583 restraints weight = 60189.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130829 restraints weight = 54744.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.131800 restraints weight = 33581.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.132105 restraints weight = 31003.421| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29728 Z= 0.151 Angle : 0.789 15.451 40627 Z= 0.385 Chirality : 0.052 0.398 4489 Planarity : 0.005 0.078 4986 Dihedral : 12.687 168.295 4431 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.75 % Favored : 83.75 % Rotamer: Outliers : 3.82 % Allowed : 17.76 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 3.64 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.14), residues: 3391 helix: -0.86 (0.17), residues: 943 sheet: -1.01 (0.23), residues: 523 loop : -3.14 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 292 TYR 0.024 0.001 TYR G 622 PHE 0.017 0.001 PHE D 89 TRP 0.040 0.001 TRP A 24 HIS 0.009 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (29728) covalent geometry : angle 0.78943 / 0.38 (40627) hydrogen bonds : bond 0.03447 / 1.78 ( 760) hydrogen bonds : angle 4.92596 / 1.96 ( 2098) *********************** REFINEMENT MACRO_CYCLE 9 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 365 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 249 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8505 (p) REVERT: A 270 THR cc_start: 0.8985 (m) cc_final: 0.8584 (p) REVERT: B 193 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7389 (ptm) REVERT: C 52 VAL cc_start: 0.6115 (OUTLIER) cc_final: 0.5890 (m) REVERT: C 210 ARG cc_start: 0.7795 (ptm160) cc_final: 0.7342 (ptp90) REVERT: D 171 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8480 (mp) REVERT: F 280 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6785 (tp30) REVERT: F 294 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8573 (t) REVERT: G 177 MET cc_start: 0.4601 (tmm) cc_final: 0.3351 (ttt) REVERT: G 436 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.6016 (pt0) REVERT: H 18 GLU cc_start: 0.6949 (mp0) cc_final: 0.6642 (mt-10) REVERT: H 25 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6992 (tt) REVERT: I 1 MET cc_start: 0.0161 (ttt) cc_final: -0.0119 (tpp) REVERT: I 195 GLU cc_start: 0.5124 (OUTLIER) cc_final: 0.4698 (tt0) REVERT: I 247 TRP cc_start: 0.5847 (OUTLIER) cc_final: 0.3074 (t-100) REVERT: J 24 LYS cc_start: 0.6081 (OUTLIER) cc_final: 0.5543 (ptmt) REVERT: J 238 PHE cc_start: 0.5924 (t80) cc_final: 0.5542 (p90) REVERT: J 244 PHE cc_start: 0.5182 (OUTLIER) cc_final: 0.4352 (m-10) REVERT: J 281 ARG cc_start: 0.6200 (ttp-170) cc_final: 0.3112 (mtt-85) REVERT: J 385 PHE cc_start: 0.3938 (OUTLIER) cc_final: 0.3636 (t80) outliers start: 116 outliers final: 88 residues processed: 330 average time/residue: 0.1707 time to fit residues: 95.7282 Evaluate side-chains 345 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 244 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 236 SER Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 409 ILE Chi-restraints excluded: chain G residue 436 GLU 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 490 HIS Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 593 CYS Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 247 TRP 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 3 LEU Chi-restraints excluded: chain J residue 24 LYS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 244 PHE Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 308 optimal weight: 0.0020 chunk 125 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 307 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 288 optimal weight: 0.0470 chunk 18 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 301 optimal weight: 0.0570 chunk 270 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 overall best weight: 0.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 HIS C 179 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 290 HIS ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 HIS F 218 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN I 252 HIS ** J 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.173971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139306 restraints weight = 43423.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137038 restraints weight = 61728.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138758 restraints weight = 51660.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139250 restraints weight = 32691.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.139819 restraints weight = 30483.810| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29728 Z= 0.121 Angle : 0.759 15.539 40627 Z= 0.369 Chirality : 0.049 0.408 4489 Planarity : 0.005 0.078 4986 Dihedral : 12.340 175.604 4431 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.13 % Favored : 85.37 % Rotamer: Outliers : 2.73 % Allowed : 18.88 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 4.85 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.14), residues: 3391 helix: -0.70 (0.17), residues: 962 sheet: -0.80 (0.23), residues: 512 loop : -3.05 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 292 TYR 0.026 0.001 TYR G 622 PHE 0.019 0.001 PHE G 516 TRP 0.029 0.001 TRP A 24 HIS 0.009 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (29728) covalent geometry : angle 0.75909 / 0.37 (40627) hydrogen bonds : bond 0.03001 / 1.55 ( 760) hydrogen bonds : angle 4.71897 / 1.87 ( 2098) ********************** REFINEMENT MACRO_CYCLE 10 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 400 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 317 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ILE cc_start: 0.6517 (OUTLIER) cc_final: 0.6104 (mt) REVERT: A 157 THR cc_start: 0.8836 (m) cc_final: 0.8529 (p) REVERT: B 338 MET cc_start: 0.8547 (mmt) cc_final: 0.8107 (mmt) REVERT: C 52 VAL cc_start: 0.5936 (OUTLIER) cc_final: 0.5656 (m) REVERT: C 210 ARG cc_start: 0.7846 (ptm160) cc_final: 0.7444 (ptp90) REVERT: F 11 ARG cc_start: 0.8402 (ptt180) cc_final: 0.8161 (ptt90) REVERT: F 294 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8202 (t) REVERT: F 346 MET cc_start: 0.7298 (ptp) cc_final: 0.6975 (mtm) REVERT: G 177 MET cc_start: 0.4407 (tmm) cc_final: 0.3077 (ttt) REVERT: H 18 GLU cc_start: 0.6796 (mp0) cc_final: 0.6561 (mt-10) REVERT: I 195 GLU cc_start: 0.4991 (OUTLIER) cc_final: 0.4548 (tt0) REVERT: J 24 LYS cc_start: 0.5671 (OUTLIER) cc_final: 0.5309 (ptmt) REVERT: J 31 HIS cc_start: 0.4456 (m-70) cc_final: 0.4154 (m-70) REVERT: J 238 PHE cc_start: 0.5759 (t80) cc_final: 0.5518 (p90) REVERT: J 281 ARG cc_start: 0.6044 (ttp-170) cc_final: 0.3119 (mtt-85) REVERT: J 326 LEU cc_start: 0.8112 (mt) cc_final: 0.7495 (mt) REVERT: J 342 MET cc_start: 0.3586 (mmp) cc_final: 0.3324 (mmt) REVERT: J 385 PHE cc_start: 0.4102 (OUTLIER) cc_final: 0.3740 (t80) outliers start: 83 outliers final: 51 residues processed: 372 average time/residue: 0.1806 time to fit residues: 111.6465 Evaluate side-chains 321 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 264 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 226 VAL 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 F residue 347 PHE Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 274 ARG Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 24 LYS Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 385 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 240 optimal weight: 2.9990 chunk 250 optimal weight: 7.9990 chunk 231 optimal weight: 0.0970 chunk 80 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 218 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN F 135 ASN F 311 GLN F 315 HIS ** J 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.170551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135639 restraints weight = 43790.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133190 restraints weight = 60660.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134766 restraints weight = 54299.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135361 restraints weight = 33271.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135939 restraints weight = 31213.525| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29728 Z= 0.133 Angle : 0.771 14.668 40627 Z= 0.374 Chirality : 0.051 0.394 4489 Planarity : 0.005 0.089 4986 Dihedral : 12.268 168.516 4431 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.66 % Favored : 84.90 % Rotamer: Outliers : 2.50 % Allowed : 19.60 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 4.85 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.14), residues: 3391 helix: -0.57 (0.17), residues: 954 sheet: -0.86 (0.23), residues: 524 loop : -3.03 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 220 TYR 0.022 0.001 TYR G 622 PHE 0.021 0.001 PHE G 516 TRP 0.023 0.001 TRP A 24 HIS 0.009 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (29728) covalent geometry : angle 0.77097 / 0.37 (40627) hydrogen bonds : bond 0.03209 / 1.66 ( 760) hydrogen bonds : angle 4.67066 / 1.86 ( 2098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4274.53 seconds wall clock time: 75 minutes 16.41 seconds (4516.41 seconds total)