Starting phenix.real_space_refine on Sat Sep 12 22:10:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ap1_8887/09_2026/6ap1_8887.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ap1_8887/09_2026/6ap1_8887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ap1_8887/09_2026/6ap1_8887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ap1_8887/09_2026/6ap1_8887.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ap1_8887/09_2026/6ap1_8887.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ap1_8887/09_2026/6ap1_8887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ap1_8887/09_2026/6ap1_8887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ap1_8887/09_2026/6ap1_8887.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 54 5.16 5 Be 3 3.05 5 C 11831 2.51 5 N 3185 2.21 5 O 3742 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 18838 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2427 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "E" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2360 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 287} Chain breaks: 1 Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2387 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 1 Chain: "H" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "I" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "J" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "K" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "L" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "M" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "N" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "P" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "R" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "S" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.40, per 1000 atoms: 0.23 Number of scatterers: 18838 At special positions: 0 Unit cell: (156.742, 103.033, 157.838, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 54 16.00 P 10 15.00 Mg 4 11.99 F 9 9.00 O 3742 8.00 N 3185 7.00 C 11831 6.00 Be 3 4.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 779.6 milliseconds 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4530 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 14 sheets defined 60.7% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 138 through 155 removed outlier: 5.329A pdb=" N LEU A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 178 through 190 Processing helix chain 'A' and resid 208 through 224 removed outlier: 4.213A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.539A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.936A pdb=" N LEU A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 335 through 356 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 138 through 155 removed outlier: 3.688A pdb=" N LYS B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Proline residue: B 152 - end of helix Processing helix chain 'B' and resid 178 through 190 Processing helix chain 'B' and resid 208 through 224 removed outlier: 4.505A pdb=" N VAL B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 245 through 261 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.935A pdb=" N LEU B 282 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 335 through 356 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'C' and resid 113 through 119 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.912A pdb=" N VAL C 135 " --> pdb=" O TRP C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 155 removed outlier: 5.330A pdb=" N LEU C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 211 through 224 Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.713A pdb=" N ALA C 236 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.934A pdb=" N LEU C 282 " --> pdb=" O PRO C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 335 through 348 Processing helix chain 'C' and resid 348 through 356 removed outlier: 3.934A pdb=" N ARG C 352 " --> pdb=" O MET C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 402 through 413 removed outlier: 3.829A pdb=" N PHE C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 138 through 155 removed outlier: 5.329A pdb=" N LEU D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Proline residue: D 152 - end of helix Processing helix chain 'D' and resid 178 through 190 Processing helix chain 'D' and resid 210 through 222 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 245 through 261 Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.935A pdb=" N LEU D 282 " --> pdb=" O PRO D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 335 through 348 Processing helix chain 'D' and resid 348 through 356 removed outlier: 3.635A pdb=" N ARG D 352 " --> pdb=" O MET D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 403 through 413 Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'E' and resid 138 through 154 Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 178 through 189 removed outlier: 3.561A pdb=" N LEU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 223 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 245 through 261 Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.935A pdb=" N LEU E 282 " --> pdb=" O PRO E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 300 through 312 removed outlier: 3.540A pdb=" N ARG E 304 " --> pdb=" O ASP E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 331 Processing helix chain 'E' and resid 335 through 356 Proline residue: E 350 - end of helix removed outlier: 3.502A pdb=" N SER E 356 " --> pdb=" O ARG E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 402 through 413 removed outlier: 3.809A pdb=" N PHE E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 433 Processing helix chain 'F' and resid 131 through 135 Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 149 through 155 Processing helix chain 'F' and resid 156 through 159 Processing helix chain 'F' and resid 178 through 191 Processing helix chain 'F' and resid 199 through 204 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 209 through 224 Processing helix chain 'F' and resid 245 through 261 removed outlier: 4.162A pdb=" N LEU F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 258 " --> pdb=" O THR F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 266 removed outlier: 4.231A pdb=" N ASN F 265 " --> pdb=" O ASN F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 Processing helix chain 'F' and resid 283 through 290 removed outlier: 3.578A pdb=" N ARG F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE F 290 " --> pdb=" O ILE F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 335 through 347 Processing helix chain 'F' and resid 348 through 356 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 402 through 413 removed outlier: 3.743A pdb=" N PHE F 406 " --> pdb=" O THR F 402 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 433 Processing helix chain 'H' and resid 292 through 309 removed outlier: 4.030A pdb=" N GLN H 298 " --> pdb=" O ILE H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 330 removed outlier: 3.838A pdb=" N THR H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU H 324 " --> pdb=" O LEU H 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 309 Processing helix chain 'I' and resid 312 through 330 removed outlier: 3.837A pdb=" N THR I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU I 324 " --> pdb=" O LEU I 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 309 removed outlier: 4.029A pdb=" N GLN J 298 " --> pdb=" O ILE J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 330 removed outlier: 3.839A pdb=" N THR J 321 " --> pdb=" O LYS J 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU J 324 " --> pdb=" O LEU J 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 309 Processing helix chain 'K' and resid 312 through 330 removed outlier: 3.839A pdb=" N THR K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU K 324 " --> pdb=" O LEU K 320 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 309 removed outlier: 4.030A pdb=" N GLN L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 330 removed outlier: 3.840A pdb=" N THR L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU L 324 " --> pdb=" O LEU L 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 309 Processing helix chain 'M' and resid 312 through 330 removed outlier: 3.839A pdb=" N THR M 321 " --> pdb=" O LYS M 317 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU M 324 " --> pdb=" O LEU M 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 309 removed outlier: 4.032A pdb=" N GLN N 298 " --> pdb=" O ILE N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 312 through 330 removed outlier: 3.838A pdb=" N THR N 321 " --> pdb=" O LYS N 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU N 324 " --> pdb=" O LEU N 320 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 309 Processing helix chain 'O' and resid 312 through 330 removed outlier: 3.839A pdb=" N THR O 321 " --> pdb=" O LYS O 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU O 324 " --> pdb=" O LEU O 320 " (cutoff:3.500A) Processing helix chain 'P' and resid 292 through 309 removed outlier: 4.030A pdb=" N GLN P 298 " --> pdb=" O ILE P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 312 through 330 removed outlier: 3.840A pdb=" N THR P 321 " --> pdb=" O LYS P 317 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU P 324 " --> pdb=" O LEU P 320 " (cutoff:3.500A) Processing helix chain 'Q' and resid 290 through 309 Processing helix chain 'Q' and resid 312 through 330 removed outlier: 3.840A pdb=" N THR Q 321 " --> pdb=" O LYS Q 317 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU Q 324 " --> pdb=" O LEU Q 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 309 removed outlier: 4.030A pdb=" N GLN R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 330 removed outlier: 3.838A pdb=" N THR R 321 " --> pdb=" O LYS R 317 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU R 324 " --> pdb=" O LEU R 320 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 309 Processing helix chain 'S' and resid 312 through 330 removed outlier: 3.839A pdb=" N THR S 321 " --> pdb=" O LYS S 317 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU S 324 " --> pdb=" O LEU S 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 removed outlier: 6.837A pdb=" N LEU A 171 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 195 removed outlier: 5.784A pdb=" N THR A 193 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE A 230 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE A 195 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER A 227 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 273 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 373 through 375 Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 197 removed outlier: 6.262A pdb=" N THR B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE B 230 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE B 195 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASP B 232 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL B 197 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 271 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 231 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 275 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU B 170 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 373 through 375 Processing sheet with id=AA6, first strand: chain 'C' and resid 193 through 194 removed outlier: 6.221A pdb=" N THR C 193 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE C 230 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER C 227 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU C 273 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ALA C 275 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE C 231 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LEU C 170 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AA8, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.973A pdb=" N ILE D 231 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 275 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 170 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 373 through 375 Processing sheet with id=AB1, first strand: chain 'E' and resid 170 through 172 removed outlier: 6.229A pdb=" N LEU E 170 " --> pdb=" O ILE E 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 193 through 195 Processing sheet with id=AB3, first strand: chain 'E' and resid 373 through 375 Processing sheet with id=AB4, first strand: chain 'F' and resid 124 through 126 removed outlier: 6.563A pdb=" N GLY F 168 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE F 294 " --> pdb=" O GLY F 168 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU F 170 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 373 through 375 993 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3400 1.31 - 1.44: 4400 1.44 - 1.56: 11159 1.56 - 1.69: 54 1.69 - 1.82: 96 Bond restraints: 19109 Sorted by residual: bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.351 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C5 ADP C 701 " pdb=" C6 ADP C 701 " ideal model delta sigma weight residual 1.490 1.356 0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.359 0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C4 ADP B 701 " pdb=" C5 ADP B 701 " ideal model delta sigma weight residual 1.490 1.361 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C5 ADP B 701 " pdb=" C6 ADP B 701 " ideal model delta sigma weight residual 1.490 1.362 0.128 2.00e-02 2.50e+03 4.10e+01 ... (remaining 19104 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.11: 25362 5.11 - 10.22: 445 10.22 - 15.33: 12 15.33 - 20.44: 1 20.44 - 25.55: 3 Bond angle restraints: 25823 Sorted by residual: angle pdb=" O1B ADP B 701 " pdb=" PB ADP B 701 " pdb=" O3B ADP B 701 " ideal model delta sigma weight residual 119.90 94.35 25.55 3.00e+00 1.11e-01 7.25e+01 angle pdb=" C LEU F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.84 130.15 -10.31 1.25e+00 6.40e-01 6.81e+01 angle pdb=" C GLU D 398 " pdb=" N PRO D 399 " pdb=" CA PRO D 399 " ideal model delta sigma weight residual 119.84 129.97 -10.13 1.25e+00 6.40e-01 6.57e+01 angle pdb=" N GLY F 269 " pdb=" CA GLY F 269 " pdb=" C GLY F 269 " ideal model delta sigma weight residual 115.32 126.06 -10.74 1.38e+00 5.25e-01 6.05e+01 angle pdb=" O1B ADP A 701 " pdb=" PB ADP A 701 " pdb=" O3B ADP A 701 " ideal model delta sigma weight residual 119.90 96.89 23.01 3.00e+00 1.11e-01 5.88e+01 ... (remaining 25818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 11612 34.50 - 69.01: 198 69.01 - 103.51: 16 103.51 - 138.01: 2 138.01 - 172.52: 4 Dihedral angle restraints: 11832 sinusoidal: 4869 harmonic: 6963 Sorted by residual: dihedral pdb=" CA LYS B 205 " pdb=" C LYS B 205 " pdb=" N TRP B 206 " pdb=" CA TRP B 206 " ideal model delta harmonic sigma weight residual 180.00 -142.41 -37.59 0 5.00e+00 4.00e-02 5.65e+01 dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 112.51 -172.52 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA GLY A 269 " pdb=" C GLY A 269 " pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta harmonic sigma weight residual -180.00 -145.99 -34.01 0 5.00e+00 4.00e-02 4.63e+01 ... (remaining 11829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2312 0.110 - 0.221: 577 0.221 - 0.331: 87 0.331 - 0.441: 7 0.441 - 0.551: 1 Chirality restraints: 2984 Sorted by residual: chirality pdb=" CA GLU F 147 " pdb=" N GLU F 147 " pdb=" C GLU F 147 " pdb=" CB GLU F 147 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" CA GLU F 139 " pdb=" N GLU F 139 " pdb=" C GLU F 139 " pdb=" CB GLU F 139 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA ILE F 278 " pdb=" N ILE F 278 " pdb=" C ILE F 278 " pdb=" CB ILE F 278 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 2981 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C AACE G 0 " -0.014 2.00e-02 2.50e+03 5.76e-02 4.14e+01 pdb=" O AACE G 0 " -0.015 2.00e-02 2.50e+03 pdb=" CH3AACE G 0 " 0.051 2.00e-02 2.50e+03 pdb=" N ASP G 165 " -0.093 2.00e-02 2.50e+03 pdb=" CA ASP G 165 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 125 " -0.033 2.00e-02 2.50e+03 6.37e-02 4.06e+01 pdb=" C SER C 125 " 0.110 2.00e-02 2.50e+03 pdb=" O SER C 125 " -0.040 2.00e-02 2.50e+03 pdb=" N GLU C 126 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 310 " -0.081 2.00e-02 2.50e+03 4.26e-02 3.63e+01 pdb=" CG TYR L 310 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR L 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR L 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR L 310 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR L 310 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR L 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 310 " -0.060 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 12 1.94 - 2.68: 1014 2.68 - 3.42: 26493 3.42 - 4.16: 43758 4.16 - 4.90: 78867 Nonbonded interactions: 150144 Sorted by model distance: nonbonded pdb=" CD1 ILE F 354 " pdb=" CA GLU F 398 " model vdw 1.198 3.890 nonbonded pdb=" CD1 ILE F 354 " pdb=" CB GLU F 398 " model vdw 1.573 3.860 nonbonded pdb=" O VAL F 263 " pdb=" CA SER F 267 " model vdw 1.574 3.470 nonbonded pdb=" O VAL F 263 " pdb=" N SER F 267 " model vdw 1.612 3.120 nonbonded pdb=" CG2 THR F 238 " pdb=" CD1 ILE F 286 " model vdw 1.654 3.880 ... (remaining 150139 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 126 through 433) selection = (chain 'B' and resid 126 through 433) selection = (chain 'C' and resid 126 through 433) selection = (chain 'D' and resid 126 through 433) selection = (chain 'E' and resid 126 through 433) selection = (chain 'F' and resid 126 through 433) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.760 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 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 : 0.019 0.758 19114 Z= 1.218 Angle : 1.657 25.552 25823 Z= 0.948 Chirality : 0.094 0.551 2984 Planarity : 0.009 0.086 3304 Dihedral : 14.240 172.515 7302 Min Nonbonded Distance : 1.198 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 2.12 % Allowed : 10.88 % Favored : 87.00 % Rotamer: Outliers : 3.62 % Allowed : 6.65 % Favored : 89.74 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.53 (0.14), residues: 2354 helix: -2.82 (0.11), residues: 1296 sheet: -2.56 (0.36), residues: 204 loop : -3.13 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG B 222 TYR 0.082 0.015 TYR H 310 PHE 0.036 0.005 PHE C 195 TRP 0.051 0.006 TRP C 206 HIS 0.003 0.001 HIS F 157 Details of bonding type rmsd/Z covalent geometry : bond 0.01645 / 0.76 (19109) covalent geometry : angle 1.65663 / 0.95 (25823) hydrogen bonds : bond 0.20670 / 13.69 ( 993) hydrogen bonds : angle 9.34140 / 6.53 ( 2868) Misc. bond : bond 0.58634 / 33.27 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 391 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 ILE cc_start: 0.8376 (mt) cc_final: 0.8107 (mt) REVERT: D 113 LYS cc_start: 0.7187 (mttt) cc_final: 0.6564 (ptmm) REVERT: D 245 GLU cc_start: 0.6828 (pt0) cc_final: 0.6095 (pm20) REVERT: D 398 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6227 (pt0) REVERT: E 254 THR cc_start: 0.8202 (m) cc_final: 0.7862 (m) REVERT: E 280 TRP cc_start: 0.6494 (p90) cc_final: 0.6069 (p90) REVERT: F 163 ARG cc_start: 0.2433 (ttm170) cc_final: 0.1495 (mmt180) REVERT: F 291 GLU cc_start: 0.3280 (OUTLIER) cc_final: 0.2987 (tt0) REVERT: F 304 ARG cc_start: 0.5002 (mtm110) cc_final: 0.4792 (ptp90) REVERT: L 319 GLU cc_start: 0.0087 (OUTLIER) cc_final: -0.0951 (mt-10) outliers start: 74 outliers final: 17 residues processed: 463 average time/residue: 0.1678 time to fit residues: 112.6077 Evaluate side-chains 203 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 397 LYS Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain L residue 319 GLU Chi-restraints excluded: chain M residue 314 PRO Chi-restraints excluded: chain N residue 314 PRO Chi-restraints excluded: chain O residue 314 PRO Chi-restraints excluded: chain Q residue 314 PRO Chi-restraints excluded: chain S residue 314 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN A 259 GLN A 359 HIS B 265 ASN B 277 ASN C 162 ASN C 191 ASN C 359 HIS C 427 GLN D 216 GLN D 355 GLN ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN F 162 ASN F 265 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN I 328 ASN J 296 GLN L 296 GLN N 296 GLN P 296 GLN ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 GLN R 328 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.242970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.209556 restraints weight = 31259.568| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 4.20 r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4393 r_free = 0.4393 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4393 r_free = 0.4393 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.4393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19114 Z= 0.162 Angle : 0.767 10.289 25823 Z= 0.390 Chirality : 0.045 0.401 2984 Planarity : 0.007 0.133 3304 Dihedral : 10.629 179.928 2664 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.95 % Favored : 93.59 % Rotamer: Outliers : 2.10 % Allowed : 12.17 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.17), residues: 2354 helix: -0.56 (0.14), residues: 1367 sheet: -2.00 (0.39), residues: 181 loop : -2.28 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 241 TYR 0.017 0.001 TYR B 295 PHE 0.021 0.002 PHE D 218 TRP 0.017 0.002 TRP B 206 HIS 0.013 0.002 HIS F 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (19109) covalent geometry : angle 0.76738 / 0.39 (25823) hydrogen bonds : bond 0.04306 / 2.89 ( 993) hydrogen bonds : angle 5.62239 / 3.92 ( 2868) Misc. bond : bond 0.00297 / 0.16 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.6347 (mm) cc_final: 0.6124 (mt) REVERT: A 224 ASN cc_start: 0.7657 (m-40) cc_final: 0.7445 (m110) REVERT: B 292 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7303 (mmt-90) REVERT: C 158 LEU cc_start: 0.8225 (mt) cc_final: 0.7924 (mt) REVERT: C 220 MET cc_start: 0.8366 (mtm) cc_final: 0.8101 (mtp) REVERT: D 113 LYS cc_start: 0.7222 (mttt) cc_final: 0.6946 (ptmm) REVERT: D 207 MET cc_start: 0.8217 (tpt) cc_final: 0.7570 (tpt) REVERT: D 245 GLU cc_start: 0.6858 (pt0) cc_final: 0.6540 (pm20) REVERT: D 397 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5347 (mmtt) REVERT: E 184 LYS cc_start: 0.7312 (mttt) cc_final: 0.7108 (pttt) REVERT: E 280 TRP cc_start: 0.6628 (p90) cc_final: 0.6402 (p90) REVERT: E 300 ASP cc_start: 0.4701 (p0) cc_final: 0.4383 (p0) outliers start: 43 outliers final: 16 residues processed: 270 average time/residue: 0.1581 time to fit residues: 64.2060 Evaluate side-chains 179 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 169 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 183 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 119 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 202 optimal weight: 50.0000 chunk 88 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 overall best weight: 1.0738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 434 GLN D 157 HIS D 265 ASN D 281 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.239725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.205840 restraints weight = 31237.800| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 4.25 r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4359 r_free = 0.4359 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4359 r_free = 0.4359 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19114 Z= 0.151 Angle : 0.679 8.222 25823 Z= 0.342 Chirality : 0.043 0.250 2984 Planarity : 0.006 0.094 3304 Dihedral : 9.344 171.001 2628 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.12 % Favored : 93.42 % Rotamer: Outliers : 2.00 % Allowed : 13.78 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.18), residues: 2354 helix: 0.65 (0.15), residues: 1365 sheet: -1.66 (0.39), residues: 188 loop : -2.00 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 241 TYR 0.020 0.001 TYR B 295 PHE 0.021 0.002 PHE D 218 TRP 0.015 0.002 TRP F 132 HIS 0.005 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (19109) covalent geometry : angle 0.67894 / 0.34 (25823) hydrogen bonds : bond 0.03837 / 2.56 ( 993) hydrogen bonds : angle 5.03621 / 3.50 ( 2868) Misc. bond : bond 0.00233 / 0.12 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASN cc_start: 0.7694 (m-40) cc_final: 0.7364 (m110) REVERT: D 113 LYS cc_start: 0.7294 (mttt) cc_final: 0.7018 (ptmm) REVERT: D 386 MET cc_start: 0.3006 (mtp) cc_final: 0.2706 (mtm) REVERT: E 280 TRP cc_start: 0.6567 (p90) cc_final: 0.6319 (p90) REVERT: E 300 ASP cc_start: 0.4755 (p0) cc_final: 0.4392 (p0) REVERT: E 355 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6140 (pm20) outliers start: 41 outliers final: 22 residues processed: 219 average time/residue: 0.1513 time to fit residues: 51.0389 Evaluate side-chains 182 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 373 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 133 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 191 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 277 ASN D 281 GLN F 162 ASN F 311 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.239244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.204783 restraints weight = 30983.608| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 4.40 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19114 Z= 0.140 Angle : 0.636 8.086 25823 Z= 0.320 Chirality : 0.042 0.207 2984 Planarity : 0.005 0.088 3304 Dihedral : 8.854 165.274 2624 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.33 % Favored : 93.20 % Rotamer: Outliers : 2.69 % Allowed : 14.81 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2354 helix: 0.99 (0.15), residues: 1373 sheet: -1.55 (0.38), residues: 202 loop : -1.55 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 241 TYR 0.018 0.001 TYR B 295 PHE 0.019 0.002 PHE D 218 TRP 0.018 0.001 TRP F 206 HIS 0.003 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (19109) covalent geometry : angle 0.63551 / 0.32 (25823) hydrogen bonds : bond 0.03457 / 2.30 ( 993) hydrogen bonds : angle 4.81730 / 3.35 ( 2868) Misc. bond : bond 0.00170 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASN cc_start: 0.7593 (m-40) cc_final: 0.7300 (m110) REVERT: B 332 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7551 (tp30) REVERT: D 113 LYS cc_start: 0.7096 (mttt) cc_final: 0.6885 (ptmm) outliers start: 55 outliers final: 32 residues processed: 224 average time/residue: 0.1400 time to fit residues: 49.3752 Evaluate side-chains 195 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 36 optimal weight: 0.0270 chunk 199 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 234 optimal weight: 40.0000 chunk 156 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.4844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 277 ASN C 162 ASN C 359 HIS D 281 GLN E 261 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.236800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.202800 restraints weight = 31010.263| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 4.27 r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4322 r_free = 0.4322 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4322 r_free = 0.4322 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19114 Z= 0.165 Angle : 0.674 8.572 25823 Z= 0.337 Chirality : 0.043 0.199 2984 Planarity : 0.006 0.077 3304 Dihedral : 8.678 157.475 2619 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.88 % Favored : 92.74 % Rotamer: Outliers : 3.08 % Allowed : 16.03 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2354 helix: 1.22 (0.15), residues: 1363 sheet: -1.46 (0.38), residues: 202 loop : -1.47 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 241 TYR 0.023 0.001 TYR B 295 PHE 0.019 0.002 PHE D 218 TRP 0.019 0.002 TRP F 132 HIS 0.005 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (19109) covalent geometry : angle 0.67359 / 0.34 (25823) hydrogen bonds : bond 0.03842 / 2.56 ( 993) hydrogen bonds : angle 4.82058 / 3.34 ( 2868) Misc. bond : bond 0.00184 / 0.10 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASN cc_start: 0.7657 (m-40) cc_final: 0.7331 (m110) REVERT: B 332 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: B 397 LYS cc_start: 0.7126 (tptt) cc_final: 0.6918 (mtpt) REVERT: D 123 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7836 (tt) REVERT: F 325 ARG cc_start: 0.6257 (tpm170) cc_final: 0.6001 (mmp-170) outliers start: 63 outliers final: 36 residues processed: 233 average time/residue: 0.1480 time to fit residues: 52.9596 Evaluate side-chains 206 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 65 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 277 ASN D 261 ASN D 281 GLN E 261 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.237057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.201189 restraints weight = 30644.499| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 4.40 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4300 r_free = 0.4300 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4300 r_free = 0.4300 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19114 Z= 0.144 Angle : 0.635 7.984 25823 Z= 0.317 Chirality : 0.042 0.187 2984 Planarity : 0.006 0.129 3304 Dihedral : 8.481 152.442 2619 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.03 % Favored : 93.59 % Rotamer: Outliers : 2.35 % Allowed : 17.06 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.18), residues: 2354 helix: 1.38 (0.15), residues: 1379 sheet: -1.30 (0.39), residues: 202 loop : -1.38 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 241 TYR 0.018 0.001 TYR B 295 PHE 0.020 0.002 PHE A 155 TRP 0.023 0.002 TRP F 206 HIS 0.005 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (19109) covalent geometry : angle 0.63473 / 0.32 (25823) hydrogen bonds : bond 0.03414 / 2.28 ( 993) hydrogen bonds : angle 4.65792 / 3.22 ( 2868) Misc. bond : bond 0.00164 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASN cc_start: 0.7600 (m-40) cc_final: 0.7312 (m110) REVERT: B 332 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: B 397 LYS cc_start: 0.7537 (tptt) cc_final: 0.7237 (mtpt) REVERT: D 123 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7724 (tt) REVERT: E 270 VAL cc_start: 0.7943 (OUTLIER) cc_final: 0.7652 (p) REVERT: E 351 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.5015 (mm) REVERT: E 355 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6276 (pm20) REVERT: E 388 TRP cc_start: 0.4599 (p-90) cc_final: 0.3969 (p-90) REVERT: F 325 ARG cc_start: 0.6345 (tpm170) cc_final: 0.6061 (mmp-170) outliers start: 48 outliers final: 33 residues processed: 224 average time/residue: 0.1544 time to fit residues: 52.8869 Evaluate side-chains 210 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 70 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 277 ASN D 281 GLN E 261 ASN E 311 ASN F 427 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.235258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.200527 restraints weight = 30607.872| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 4.31 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4293 r_free = 0.4293 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4293 r_free = 0.4293 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19114 Z= 0.167 Angle : 0.669 8.695 25823 Z= 0.334 Chirality : 0.043 0.187 2984 Planarity : 0.006 0.105 3304 Dihedral : 8.574 154.621 2619 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.80 % Favored : 92.95 % Rotamer: Outliers : 2.79 % Allowed : 17.06 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2354 helix: 1.47 (0.15), residues: 1379 sheet: -1.19 (0.40), residues: 202 loop : -1.38 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 163 TYR 0.022 0.001 TYR B 295 PHE 0.016 0.002 PHE B 218 TRP 0.025 0.002 TRP E 280 HIS 0.007 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (19109) covalent geometry : angle 0.66900 / 0.33 (25823) hydrogen bonds : bond 0.03825 / 2.56 ( 993) hydrogen bonds : angle 4.70859 / 3.24 ( 2868) Misc. bond : bond 0.00160 / 0.08 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASN cc_start: 0.7371 (m-40) cc_final: 0.7095 (m-40) REVERT: B 332 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7654 (tp30) REVERT: B 334 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: B 397 LYS cc_start: 0.7736 (tptt) cc_final: 0.7219 (mttt) REVERT: B 402 THR cc_start: 0.7544 (OUTLIER) cc_final: 0.7323 (p) REVERT: C 322 GLU cc_start: 0.7426 (tp30) cc_final: 0.7074 (mp0) REVERT: D 123 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7823 (tt) REVERT: D 373 LEU cc_start: 0.3040 (OUTLIER) cc_final: 0.2562 (pp) REVERT: D 386 MET cc_start: 0.4876 (tmm) cc_final: 0.4545 (ttp) REVERT: E 270 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7727 (p) REVERT: E 351 ILE cc_start: 0.5600 (OUTLIER) cc_final: 0.5161 (mm) REVERT: E 355 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6230 (pm20) REVERT: E 388 TRP cc_start: 0.4693 (p-90) cc_final: 0.4298 (p-90) REVERT: F 292 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6835 (mtp85) REVERT: F 359 HIS cc_start: 0.3784 (OUTLIER) cc_final: 0.2746 (m-70) outliers start: 57 outliers final: 32 residues processed: 215 average time/residue: 0.1443 time to fit residues: 48.3029 Evaluate side-chains 204 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 334 TYR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 178 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 40.0000 chunk 86 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN B 277 ASN D 281 GLN E 259 GLN E 261 ASN E 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.229829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.202009 restraints weight = 30421.568| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 3.86 r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4321 r_free = 0.4321 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4321 r_free = 0.4321 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 19114 Z= 0.318 Angle : 0.862 10.560 25823 Z= 0.437 Chirality : 0.050 0.224 2984 Planarity : 0.007 0.107 3304 Dihedral : 9.362 173.350 2619 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.03 % Favored : 91.72 % Rotamer: Outliers : 3.23 % Allowed : 17.25 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.18), residues: 2354 helix: 0.99 (0.14), residues: 1376 sheet: -1.11 (0.40), residues: 183 loop : -1.81 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 163 TYR 0.033 0.003 TYR B 295 PHE 0.026 0.003 PHE B 432 TRP 0.030 0.003 TRP B 206 HIS 0.007 0.002 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.32 (19109) covalent geometry : angle 0.86240 / 0.44 (25823) hydrogen bonds : bond 0.05504 / 3.68 ( 993) hydrogen bonds : angle 5.29404 / 3.65 ( 2868) Misc. bond : bond 0.00271 / 0.15 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 172 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 224 ASN cc_start: 0.7372 (m-40) cc_final: 0.7074 (m110) REVERT: B 131 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7918 (mtpp) REVERT: B 334 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.8528 (m-80) REVERT: B 402 THR cc_start: 0.7504 (OUTLIER) cc_final: 0.7291 (p) REVERT: C 322 GLU cc_start: 0.7723 (tp30) cc_final: 0.7123 (mp0) REVERT: C 347 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8738 (mp) REVERT: D 123 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7998 (tt) REVERT: D 373 LEU cc_start: 0.3038 (OUTLIER) cc_final: 0.2617 (pp) REVERT: E 207 MET cc_start: 0.6591 (tpp) cc_final: 0.6364 (tpp) REVERT: E 334 TYR cc_start: 0.5017 (OUTLIER) cc_final: 0.4578 (m-10) REVERT: E 355 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6703 (pt0) REVERT: E 388 TRP cc_start: 0.5075 (p-90) cc_final: 0.4689 (p-90) REVERT: F 292 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6789 (mtp85) REVERT: F 359 HIS cc_start: 0.3209 (OUTLIER) cc_final: 0.2398 (m-70) outliers start: 66 outliers final: 37 residues processed: 227 average time/residue: 0.1519 time to fit residues: 52.7309 Evaluate side-chains 200 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 334 TYR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 308 PHE Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 22 optimal weight: 0.5980 chunk 217 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 211 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN C 265 ASN D 281 GLN E 261 ASN E 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.234680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.199886 restraints weight = 30466.166| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 4.39 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4293 r_free = 0.4293 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4293 r_free = 0.4293 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19114 Z= 0.140 Angle : 0.650 10.229 25823 Z= 0.326 Chirality : 0.041 0.206 2984 Planarity : 0.005 0.056 3304 Dihedral : 8.397 151.355 2617 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.99 % Favored : 93.80 % Rotamer: Outliers : 2.35 % Allowed : 18.91 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2354 helix: 1.43 (0.15), residues: 1379 sheet: -1.00 (0.42), residues: 177 loop : -1.54 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 371 TYR 0.015 0.001 TYR B 295 PHE 0.015 0.002 PHE B 218 TRP 0.019 0.002 TRP A 388 HIS 0.006 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19109) covalent geometry : angle 0.65033 / 0.33 (25823) hydrogen bonds : bond 0.03461 / 2.31 ( 993) hydrogen bonds : angle 4.71302 / 3.26 ( 2868) Misc. bond : bond 0.00110 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8016 (tt) REVERT: A 224 ASN cc_start: 0.7331 (m-40) cc_final: 0.7040 (m110) REVERT: B 402 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.7144 (p) REVERT: C 259 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8468 (mm-40) REVERT: C 322 GLU cc_start: 0.7606 (tp30) cc_final: 0.7157 (mp0) REVERT: D 373 LEU cc_start: 0.3010 (OUTLIER) cc_final: 0.2683 (pp) REVERT: E 334 TYR cc_start: 0.4770 (OUTLIER) cc_final: 0.4406 (m-10) REVERT: E 351 ILE cc_start: 0.6272 (OUTLIER) cc_final: 0.5783 (tp) REVERT: E 388 TRP cc_start: 0.5274 (p-90) cc_final: 0.4955 (p-90) REVERT: F 292 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7035 (mtp85) outliers start: 48 outliers final: 26 residues processed: 213 average time/residue: 0.1522 time to fit residues: 49.6077 Evaluate side-chains 196 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 123 optimal weight: 1.9990 chunk 231 optimal weight: 30.0000 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 281 GLN E 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.235785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.201931 restraints weight = 30478.648| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 4.16 r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4311 r_free = 0.4311 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4311 r_free = 0.4311 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19114 Z= 0.127 Angle : 0.638 9.900 25823 Z= 0.316 Chirality : 0.041 0.314 2984 Planarity : 0.005 0.058 3304 Dihedral : 7.951 150.622 2617 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.37 % Rotamer: Outliers : 1.66 % Allowed : 19.70 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2354 helix: 1.64 (0.15), residues: 1381 sheet: -0.94 (0.42), residues: 177 loop : -1.35 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 352 TYR 0.013 0.001 TYR B 295 PHE 0.015 0.002 PHE A 155 TRP 0.035 0.002 TRP E 280 HIS 0.006 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (19109) covalent geometry : angle 0.63796 / 0.32 (25823) hydrogen bonds : bond 0.03273 / 2.18 ( 993) hydrogen bonds : angle 4.55658 / 3.13 ( 2868) Misc. bond : bond 0.00105 / 0.06 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7896 (tt) REVERT: A 224 ASN cc_start: 0.7344 (m-40) cc_final: 0.6981 (m110) REVERT: A 388 TRP cc_start: 0.5451 (p-90) cc_final: 0.5004 (p-90) REVERT: B 402 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7207 (p) REVERT: C 322 GLU cc_start: 0.7549 (tp30) cc_final: 0.7176 (mp0) REVERT: D 373 LEU cc_start: 0.3079 (OUTLIER) cc_final: 0.2794 (pp) REVERT: E 388 TRP cc_start: 0.5272 (p-90) cc_final: 0.4987 (p-90) REVERT: F 359 HIS cc_start: 0.2502 (OUTLIER) cc_final: 0.1688 (m-70) outliers start: 34 outliers final: 23 residues processed: 195 average time/residue: 0.1371 time to fit residues: 42.3285 Evaluate side-chains 187 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 207 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 176 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 281 GLN E 261 ASN E 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.231572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.199764 restraints weight = 30267.068| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 4.07 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4294 r_free = 0.4294 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19114 Z= 0.230 Angle : 0.761 9.668 25823 Z= 0.382 Chirality : 0.046 0.428 2984 Planarity : 0.006 0.061 3304 Dihedral : 8.704 156.118 2617 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.86 % Favored : 91.93 % Rotamer: Outliers : 2.10 % Allowed : 19.50 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2354 helix: 1.38 (0.15), residues: 1377 sheet: -1.01 (0.42), residues: 177 loop : -1.56 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 325 TYR 0.026 0.002 TYR B 295 PHE 0.020 0.003 PHE B 159 TRP 0.040 0.003 TRP E 280 HIS 0.005 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (19109) covalent geometry : angle 0.76119 / 0.38 (25823) hydrogen bonds : bond 0.04573 / 3.06 ( 993) hydrogen bonds : angle 4.90862 / 3.38 ( 2868) Misc. bond : bond 0.00195 / 0.10 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3503.74 seconds wall clock time: 61 minutes 26.78 seconds (3686.78 seconds total)