Starting phenix.real_space_refine on Thu Mar 5 14:04:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kmf_22924/03_2026/7kmf_22924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kmf_22924/03_2026/7kmf_22924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kmf_22924/03_2026/7kmf_22924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kmf_22924/03_2026/7kmf_22924.map" model { file = "/net/cci-nas-00/data/ceres_data/7kmf_22924/03_2026/7kmf_22924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kmf_22924/03_2026/7kmf_22924.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 117 5.16 5 C 14575 2.51 5 N 3997 2.21 5 O 4184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22875 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2468 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 300} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 2414 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 325, 2406 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 309} Chain breaks: 4 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 325, 2406 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 309} Chain breaks: 4 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 2438 Chain: "E" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2466 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Chain breaks: 4 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 2151 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 280, 2140 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 280, 2140 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 2160 Chain: "G" Number of atoms: 2201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 287, 2190 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Conformer: "B" Number of residues, atoms: 287, 2190 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 bond proxies already assigned to first conformer: 2212 Chain: "B" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3165 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 4, 'HIS:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "I" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3192 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "J" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1159 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain breaks: 8 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 7, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "K" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1169 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain breaks: 8 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ASP:plan': 8, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'F6P': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'F6P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG H 136 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG H 136 " occ=0.50 residue: pdb=" N AARG G 136 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG G 136 " occ=0.50 Time building chain proxies: 6.69, per 1000 atoms: 0.29 Number of scatterers: 22875 At special positions: 0 Unit cell: (165.36, 144.56, 113.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 117 16.00 P 2 15.00 O 4184 8.00 N 3997 7.00 C 14575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS F 465 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.6 seconds 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5740 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 34 sheets defined 43.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 49 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.656A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 95 removed outlier: 3.973A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 142 removed outlier: 3.837A pdb=" N ILE C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 154 through 159 removed outlier: 3.841A pdb=" N HIS C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 183 Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.732A pdb=" N ASN C 206 " --> pdb=" O GLU C 202 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 removed outlier: 4.170A pdb=" N SER C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 228 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.762A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.535A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 30 through 49 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.668A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 93 removed outlier: 4.372A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 142 removed outlier: 3.861A pdb=" N ILE D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 removed outlier: 4.017A pdb=" N GLN D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 181 Processing helix chain 'D' and resid 199 through 210 removed outlier: 3.693A pdb=" N ALA D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.627A pdb=" N ALA D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 296 through 305 removed outlier: 3.683A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.843A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 217 Processing helix chain 'F' and resid 221 through 239 Processing helix chain 'F' and resid 249 through 267 removed outlier: 3.705A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 287 Processing helix chain 'F' and resid 295 through 313 removed outlier: 3.511A pdb=" N ASP F 305 " --> pdb=" O ARG F 301 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU F 310 " --> pdb=" O ARG F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 326 removed outlier: 3.921A pdb=" N GLN F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS F 326 " --> pdb=" O PHE F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 352 Processing helix chain 'F' and resid 368 through 380 removed outlier: 3.733A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER F 375 " --> pdb=" O HIS F 371 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA F 379 " --> pdb=" O SER F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 419 through 430 Processing helix chain 'F' and resid 439 through 443 removed outlier: 3.627A pdb=" N LYS F 442 " --> pdb=" O GLU F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 463 Processing helix chain 'F' and resid 511 through 519 removed outlier: 3.618A pdb=" N VAL F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 217 Processing helix chain 'E' and resid 221 through 233 removed outlier: 3.635A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.750A pdb=" N GLN E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP E 239 " --> pdb=" O GLN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 267 removed outlier: 3.746A pdb=" N ASN E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 287 Processing helix chain 'E' and resid 293 through 303 removed outlier: 3.542A pdb=" N ARG E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 312 Processing helix chain 'E' and resid 312 through 325 removed outlier: 3.596A pdb=" N ALA E 316 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG E 321 " --> pdb=" O GLN E 317 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 removed outlier: 3.766A pdb=" N SER E 375 " --> pdb=" O HIS E 371 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 392 removed outlier: 4.278A pdb=" N SER E 392 " --> pdb=" O PRO E 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 389 through 392' Processing helix chain 'E' and resid 394 through 398 Processing helix chain 'E' and resid 418 through 430 removed outlier: 4.634A pdb=" N GLN E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 464 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 493 through 497 removed outlier: 3.548A pdb=" N VAL E 497 " --> pdb=" O PRO E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 519 removed outlier: 3.511A pdb=" N ARG E 517 " --> pdb=" O PRO E 513 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 16 removed outlier: 3.571A pdb=" N GLU H 8 " --> pdb=" O LYS H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 35 Processing helix chain 'H' and resid 44 through 60 removed outlier: 4.113A pdb=" N ASN H 48 " --> pdb=" O GLY H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 76 removed outlier: 3.739A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU H 70 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE H 76 " --> pdb=" O PHE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 80 removed outlier: 3.569A pdb=" N SER H 80 " --> pdb=" O SER H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 77 through 80' Processing helix chain 'H' and resid 89 through 103 Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 159 through 169 removed outlier: 3.654A pdb=" N LYS H 163 " --> pdb=" O LEU H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'H' and resid 211 through 222 Processing helix chain 'H' and resid 231 through 235 removed outlier: 3.521A pdb=" N PHE H 235 " --> pdb=" O SER H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.702A pdb=" N TYR H 252 " --> pdb=" O ASP H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 294 No H-bonds generated for 'chain 'H' and resid 292 through 294' Processing helix chain 'H' and resid 295 through 302 removed outlier: 3.940A pdb=" N GLU H 299 " --> pdb=" O ALA H 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 43 through 61 removed outlier: 3.714A pdb=" N ALA G 47 " --> pdb=" O GLN G 43 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 76 removed outlier: 3.600A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU G 70 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE G 76 " --> pdb=" O PHE G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 83 removed outlier: 3.590A pdb=" N GLU G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 103 removed outlier: 3.874A pdb=" N LEU G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 133 through 143 Processing helix chain 'G' and resid 159 through 169 removed outlier: 3.639A pdb=" N LYS G 163 " --> pdb=" O LEU G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 172 No H-bonds generated for 'chain 'G' and resid 170 through 172' Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 211 through 222 Processing helix chain 'G' and resid 231 through 235 Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.789A pdb=" N TYR G 252 " --> pdb=" O ASP G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 292 through 304 removed outlier: 4.319A pdb=" N SER G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 63 removed outlier: 4.188A pdb=" N ASP B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.530A pdb=" N TYR B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.732A pdb=" N ILE B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.822A pdb=" N CYS B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 113 " --> pdb=" O LYS B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 113' Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.763A pdb=" N ASP B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.561A pdb=" N LEU B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 262 removed outlier: 4.186A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 277 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 74 through 87 removed outlier: 3.763A pdb=" N TYR I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 108 Processing helix chain 'I' and resid 109 through 113 removed outlier: 3.705A pdb=" N CYS I 112 " --> pdb=" O SER I 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG I 113 " --> pdb=" O LYS I 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 109 through 113' Processing helix chain 'I' and resid 130 through 137 removed outlier: 3.656A pdb=" N VAL I 134 " --> pdb=" O SER I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 174 Processing helix chain 'I' and resid 253 through 263 removed outlier: 4.116A pdb=" N ALA I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN I 263 " --> pdb=" O LEU I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 277 Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 318 through 326 Proline residue: I 323 - end of helix removed outlier: 3.542A pdb=" N ASN I 326 " --> pdb=" O PRO I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 341 No H-bonds generated for 'chain 'I' and resid 339 through 341' Processing helix chain 'J' and resid 37 through 47 Processing helix chain 'J' and resid 88 through 93 removed outlier: 3.886A pdb=" N TYR J 92 " --> pdb=" O ASP J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 removed outlier: 3.934A pdb=" N VAL J 117 " --> pdb=" O ALA J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 228 through 233 removed outlier: 3.913A pdb=" N VAL J 233 " --> pdb=" O ILE J 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 41 Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 114 through 119 removed outlier: 3.571A pdb=" N ASP K 119 " --> pdb=" O HIS K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 190 Processing helix chain 'K' and resid 210 through 217 removed outlier: 3.603A pdb=" N MET K 216 " --> pdb=" O VAL K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 236 removed outlier: 3.609A pdb=" N VAL K 233 " --> pdb=" O ILE K 229 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG K 234 " --> pdb=" O PRO K 230 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.827A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 216 " --> pdb=" O LEU F 485 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AA3, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.189A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 323 through 325 removed outlier: 6.755A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N THR D 214 " --> pdb=" O ARG E 483 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AA6, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.151A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'E' and resid 500 through 501 Processing sheet with id=AB1, first strand: chain 'H' and resid 289 through 291 removed outlier: 3.581A pdb=" N GLY H 289 " --> pdb=" O THR H 286 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR H 286 " --> pdb=" O GLY H 289 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR H 153 " --> pdb=" O THR H 127 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS G 267 " --> pdb=" O VAL H 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AB3, first strand: chain 'G' and resid 175 through 178 removed outlier: 6.493A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR G 286 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY G 289 " --> pdb=" O THR G 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AB5, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.175A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 48 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 245 removed outlier: 5.635A pdb=" N GLN B 286 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N MET B 181 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 212 through 216 removed outlier: 6.141A pdb=" N ALA B 204 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE B 215 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B 202 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE J 157 " --> pdb=" O MET J 170 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET J 170 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY J 159 " --> pdb=" O LEU J 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 223 through 227 Processing sheet with id=AC1, first strand: chain 'B' and resid 343 through 344 removed outlier: 6.670A pdb=" N TYR B 343 " --> pdb=" O LEU B 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.489A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 384 through 387 removed outlier: 5.950A pdb=" N ALA B 404 " --> pdb=" O GLY B 386 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLU B 421 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ALA B 403 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 412 through 413 removed outlier: 6.571A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 122 through 124 removed outlier: 7.830A pdb=" N ILE I 123 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL I 93 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA I 45 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE I 94 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU I 47 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL I 151 " --> pdb=" O GLN I 44 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL I 46 " --> pdb=" O VAL I 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AC7, first strand: chain 'I' and resid 244 through 245 removed outlier: 6.398A pdb=" N GLN I 286 " --> pdb=" O SER I 179 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET I 181 " --> pdb=" O GLN I 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 212 through 217 removed outlier: 6.758A pdb=" N PHE K 157 " --> pdb=" O MET K 170 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET K 170 " --> pdb=" O PHE K 157 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY K 159 " --> pdb=" O LEU K 168 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 223 through 227 removed outlier: 3.553A pdb=" N PHE I 226 " --> pdb=" O LEU K 180 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 336 through 337 removed outlier: 3.657A pdb=" N ARG I 344 " --> pdb=" O THR I 336 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR I 343 " --> pdb=" O LEU I 362 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 373 through 375 removed outlier: 3.733A pdb=" N LEU I 391 " --> pdb=" O PHE I 373 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 384 through 387 removed outlier: 5.871A pdb=" N ALA I 404 " --> pdb=" O GLY I 386 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ARG I 401 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU I 418 " --> pdb=" O VAL I 437 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 411 through 413 removed outlier: 6.368A pdb=" N LEU I 412 " --> pdb=" O LEU I 431 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL I 430 " --> pdb=" O ILE I 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.565A pdb=" N ILE J 52 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU J 204 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU J 131 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU J 128 " --> pdb=" O TYR J 264 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE J 266 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET J 130 " --> pdb=" O PHE J 266 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.386A pdb=" N GLN K 4 " --> pdb=" O LEU K 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'K' and resid 128 through 131 removed outlier: 6.328A pdb=" N LEU K 128 " --> pdb=" O TYR K 264 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE K 266 " --> pdb=" O LEU K 128 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET K 130 " --> pdb=" O PHE K 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 886 hydrogen bonds defined for protein. 2470 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: 3.92 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6961 1.33 - 1.45: 3723 1.45 - 1.57: 12396 1.57 - 1.69: 6 1.69 - 1.81: 176 Bond restraints: 23262 Sorted by residual: bond pdb=" CB VAL F 332 " pdb=" CG2 VAL F 332 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.85e+00 bond pdb=" CG LEU D 254 " pdb=" CD1 LEU D 254 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.46e+00 bond pdb=" CB ILE B 408 " pdb=" CG2 ILE B 408 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.35e+00 bond pdb=" CB VAL E 381 " pdb=" CG1 VAL E 381 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.58e+00 bond pdb=" CB VAL E 434 " pdb=" CG1 VAL E 434 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.52e+00 ... (remaining 23257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 30992 3.20 - 6.40: 520 6.40 - 9.60: 70 9.60 - 12.81: 14 12.81 - 16.01: 4 Bond angle restraints: 31600 Sorted by residual: angle pdb=" C THR C 218 " pdb=" N ASP C 219 " pdb=" CA ASP C 219 " ideal model delta sigma weight residual 126.32 138.13 -11.81 1.74e+00 3.30e-01 4.60e+01 angle pdb=" N PHE K 121 " pdb=" CA PHE K 121 " pdb=" C PHE K 121 " ideal model delta sigma weight residual 114.56 108.37 6.19 1.27e+00 6.20e-01 2.38e+01 angle pdb=" N ILE C 151 " pdb=" CA ILE C 151 " pdb=" C ILE C 151 " ideal model delta sigma weight residual 111.58 106.42 5.16 1.06e+00 8.90e-01 2.37e+01 angle pdb=" CB MET G 187 " pdb=" CG MET G 187 " pdb=" SD MET G 187 " ideal model delta sigma weight residual 112.70 98.19 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CA LEU E 346 " pdb=" CB LEU E 346 " pdb=" CG LEU E 346 " ideal model delta sigma weight residual 116.30 132.31 -16.01 3.50e+00 8.16e-02 2.09e+01 ... (remaining 31595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12795 17.81 - 35.62: 1050 35.62 - 53.42: 162 53.42 - 71.23: 45 71.23 - 89.04: 25 Dihedral angle restraints: 14077 sinusoidal: 5290 harmonic: 8787 Sorted by residual: dihedral pdb=" CB CYS C 198 " pdb=" SG CYS C 198 " pdb=" SG CYS F 465 " pdb=" CB CYS F 465 " ideal model delta sinusoidal sigma weight residual 93.00 155.40 -62.40 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CA HIS G 128 " pdb=" C HIS G 128 " pdb=" N ALA G 129 " pdb=" CA ALA G 129 " ideal model delta harmonic sigma weight residual -180.00 -147.31 -32.69 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA THR I 208 " pdb=" C THR I 208 " pdb=" N THR I 209 " pdb=" CA THR I 209 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 14074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3336 0.095 - 0.189: 412 0.189 - 0.284: 33 0.284 - 0.378: 5 0.378 - 0.473: 4 Chirality restraints: 3790 Sorted by residual: chirality pdb=" CB THR G 124 " pdb=" CA THR G 124 " pdb=" OG1 THR G 124 " pdb=" CG2 THR G 124 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CB ILE I 374 " pdb=" CA ILE I 374 " pdb=" CG1 ILE I 374 " pdb=" CG2 ILE I 374 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CB THR H 124 " pdb=" CA THR H 124 " pdb=" OG1 THR H 124 " pdb=" CG2 THR H 124 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.80e+00 ... (remaining 3787 not shown) Planarity restraints: 4011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 380 " -0.089 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO I 381 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO I 381 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO I 381 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 183 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO E 184 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO E 184 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO E 184 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 300 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C VAL B 300 " 0.058 2.00e-02 2.50e+03 pdb=" O VAL B 300 " -0.022 2.00e-02 2.50e+03 pdb=" N SER B 301 " -0.019 2.00e-02 2.50e+03 ... (remaining 4008 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2441 2.74 - 3.28: 22644 3.28 - 3.82: 38583 3.82 - 4.36: 46533 4.36 - 4.90: 81541 Nonbonded interactions: 191742 Sorted by model distance: nonbonded pdb=" OG1 THR C 76 " pdb=" OG1 THR C 238 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR D 76 " pdb=" OG1 THR D 238 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN E 223 " pdb=" OH TYR E 441 " model vdw 2.229 3.040 nonbonded pdb=" O GLY G 196 " pdb=" OD1 ASN G 208 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU D 193 " pdb=" NE2 HIS D 201 " model vdw 2.285 3.120 ... (remaining 191737 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 'B' and (resid 41 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 218 or (resid 219 and (name N o \ r name CA or name C or name O or name CB )) or resid 220 or (resid 221 through 2 \ 23 and (name N or name CA or name C or name O or name CB )) or resid 224 through \ 456 or (resid 457 through 458 and (name N or name CA or name C or name O or nam \ e CB )) or resid 459 through 464)) selection = (chain 'I' and (resid 41 through 176 or (resid 177 through 178 and (name N or na \ me CA or name C or name O or name CB )) or resid 179 through 196 or (resid 197 a \ nd (name N or name CA or name C or name O or name CB )) or resid 198 through 231 \ or resid 238 through 279 or (resid 285 and (name N or name CA or name C or name \ O or name CB )) or resid 286 through 433 or (resid 434 and (name N or name CA o \ r name C or name O or name CB )) or resid 435 through 459 or (resid 460 through \ 461 and (name N or name CA or name C or name O or name CB )) or resid 462 throug \ h 464)) } ncs_group { reference = (chain 'C' and (resid 9 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 26 or resid 29 through 138 or (resi \ d 139 and (name N or name CA or name C or name O or name CB )) or resid 140 thro \ ugh 142 or (resid 143 and (name N or name CA or name C or name O or name CB )) o \ r resid 144 or (resid 145 and (name N or name CA or name C or name O or name CB \ )) or resid 146 through 148 or (resid 149 and (name N or name CA or name C or na \ me O or name CB )) or resid 150 through 281 or (resid 282 through 283 and (name \ N or name CA or name C or name O or name CB )) or resid 284 through 351)) selection = (chain 'D' and (resid 9 through 97 or resid 126 through 351)) } ncs_group { reference = (chain 'E' and (resid 179 through 180 or (resid 181 and (name N or name CA or na \ me C or name O or name CB )) or resid 182 through 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 or (resid 192 through \ 198 and (name N or name CA or name C or name O or name CB )) or resid 199 throug \ h 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or \ resid 204 through 240 or (resid 241 and (name N or name CA or name C or name O o \ r name CB )) or resid 242 through 256 or (resid 257 and (name N or name CA or na \ me C or name O or name CB )) or resid 258 through 263 or (resid 264 through 265 \ and (name N or name CA or name C or name O or name CB )) or resid 266 through 28 \ 9 or (resid 294 through 300 and (name N or name CA or name C or name O or name C \ B )) or resid 301 through 320 or resid 322 through 339 or (resid 340 and (name N \ or name CA or name C or name O or name CB )) or resid 341 through 452 or (resid \ 453 through 454 and (name N or name CA or name C or name O or name CB )) or res \ id 455 through 457 or (resid 458 and (name N or name CA or name C or name O or n \ ame CB )) or resid 459 through 460 or (resid 461 and (name N or name CA or name \ C or name O or name CB )) or resid 462 through 466 or resid 471 through 520)) selection = (chain 'F' and (resid 179 through 214 or (resid 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 through 320 or resid 322 through 327 o \ r (resid 328 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 29 through 449 or (resid 450 through 454 and (name N or name CA or name C or nam \ e O or name CB )) or resid 455 through 477 or (resid 478 and (name N or name CA \ or name C or name O or name CB )) or resid 479 through 518 or (resid 519 and (na \ me N or name CA or name C or name O or name CB )) or resid 520)) } ncs_group { reference = (chain 'G' and (resid 3 through 36 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 80 or resid 88 through \ 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or res \ id 96 through 135 or resid 137 through 304 or resid 401)) selection = (chain 'H' and (resid 3 through 36 or resid 42 through 135 or resid 137 through \ 254 or (resid 266 and (name N or name CA or name C or name O or name CB )) or re \ sid 267 through 401)) } ncs_group { reference = (chain 'J' and (resid 1 through 44 or resid 48 through 53 or resid 75 through 78 \ or resid 87 through 95 or (resid 96 through 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 212 or (resid 213 through 214 and \ (name N or name CA or name C or name O or name CB )) or resid 226 through 233 or \ (resid 234 through 235 and (name N or name CA or name C or name O or name CB )) \ or resid 236 through 267)) selection = (chain 'K' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 48 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 98 or (resid 99 and (n \ ame N or name CA or name C or name O or name CB )) or resid 100 through 113 or ( \ resid 114 and (name N or name CA or name C or name O or name CB )) or resid 115 \ through 116 or (resid 117 and (name N or name CA or name C or name O or name CB \ )) or resid 118 through 171 or resid 174 through 214 or resid 226 or (resid 227 \ through 229 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 0 through 236 or (resid 237 through 240 and (name N or name CA or name C or name \ O or name CB )) or resid 241 through 243 or resid 260 through 267)) } 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=0.50 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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 23.110 Find NCS groups from input model: 0.480 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:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.009 0.086 23263 Z= 0.371 Angle : 1.056 16.008 31602 Z= 0.554 Chirality : 0.064 0.473 3790 Planarity : 0.007 0.135 4011 Dihedral : 14.190 89.040 8334 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.21 % Allowed : 0.59 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.14), residues: 2920 helix: -1.75 (0.13), residues: 1168 sheet: -1.55 (0.27), residues: 365 loop : -1.59 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 428 TYR 0.041 0.003 TYR G 9 PHE 0.032 0.003 PHE G 239 TRP 0.018 0.002 TRP D 51 HIS 0.010 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00915 (23262) covalent geometry : angle 1.05547 (31600) SS BOND : bond 0.00452 ( 1) SS BOND : angle 4.63773 ( 2) hydrogen bonds : bond 0.20357 ( 886) hydrogen bonds : angle 7.86250 ( 2470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.835 Fit side-chains REVERT: C 16 GLU cc_start: 0.7613 (mp0) cc_final: 0.7394 (mp0) REVERT: C 130 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8518 (tm-30) REVERT: D 16 GLU cc_start: 0.7825 (mp0) cc_final: 0.7547 (mp0) REVERT: D 128 GLN cc_start: 0.8590 (pm20) cc_final: 0.8342 (pm20) REVERT: F 363 SER cc_start: 0.8830 (p) cc_final: 0.8425 (t) REVERT: F 415 MET cc_start: 0.8397 (ttp) cc_final: 0.7942 (ttm) REVERT: F 459 ASP cc_start: 0.7588 (p0) cc_final: 0.7260 (p0) REVERT: F 506 MET cc_start: 0.8846 (mtm) cc_final: 0.8548 (mtm) REVERT: E 300 LEU cc_start: 0.8278 (mm) cc_final: 0.8043 (mm) REVERT: E 415 MET cc_start: 0.8251 (ttp) cc_final: 0.7849 (ttm) REVERT: G 48 ASN cc_start: 0.8344 (m110) cc_final: 0.8143 (m110) REVERT: J 263 ILE cc_start: 0.6825 (mt) cc_final: 0.6595 (mt) REVERT: K 100 ASP cc_start: 0.7444 (m-30) cc_final: 0.7029 (m-30) REVERT: K 192 ARG cc_start: 0.8642 (mtp180) cc_final: 0.8026 (mtp180) outliers start: 0 outliers final: 1 residues processed: 318 average time/residue: 0.6302 time to fit residues: 228.6666 Evaluate side-chains 233 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 329 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 GLN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 130 GLN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN E 234 GLN E 431 ASN E 455 ASN ** H 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.123821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087914 restraints weight = 63372.940| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.51 r_work: 0.3104 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23263 Z= 0.152 Angle : 0.675 11.287 31602 Z= 0.344 Chirality : 0.047 0.228 3790 Planarity : 0.005 0.094 4011 Dihedral : 7.020 62.948 3265 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.47 % Allowed : 9.22 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.68 (0.15), residues: 2920 helix: -0.60 (0.15), residues: 1164 sheet: -1.57 (0.26), residues: 403 loop : -1.32 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 234 TYR 0.017 0.002 TYR F 240 PHE 0.030 0.001 PHE B 264 TRP 0.010 0.001 TRP I 97 HIS 0.007 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00359 (23262) covalent geometry : angle 0.67436 (31600) SS BOND : bond 0.00085 ( 1) SS BOND : angle 2.45263 ( 2) hydrogen bonds : bond 0.04057 ( 886) hydrogen bonds : angle 5.03254 ( 2470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 283 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8255 (tm-30) REVERT: C 219 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8317 (p0) REVERT: D 128 GLN cc_start: 0.8826 (pm20) cc_final: 0.8498 (pm20) REVERT: F 415 MET cc_start: 0.8651 (ttp) cc_final: 0.8211 (ttm) REVERT: E 192 LEU cc_start: 0.7556 (tp) cc_final: 0.7289 (tp) REVERT: E 235 GLN cc_start: 0.7012 (tp-100) cc_final: 0.6227 (tp-100) REVERT: E 415 MET cc_start: 0.8770 (ttp) cc_final: 0.8082 (ttm) REVERT: G 48 ASN cc_start: 0.8470 (m110) cc_final: 0.8208 (m110) REVERT: I 276 LEU cc_start: 0.7823 (tt) cc_final: 0.7619 (tm) REVERT: I 296 TYR cc_start: 0.9112 (t80) cc_final: 0.8834 (t80) REVERT: K 100 ASP cc_start: 0.7097 (m-30) cc_final: 0.6804 (m-30) REVERT: K 192 ARG cc_start: 0.8773 (mtp180) cc_final: 0.8242 (mtp180) outliers start: 30 outliers final: 9 residues processed: 298 average time/residue: 0.5708 time to fit residues: 196.2818 Evaluate side-chains 246 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 130 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 247 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 227 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN H 48 ASN ** H 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN I 177 ASN I 288 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.123678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088443 restraints weight = 51777.309| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.13 r_work: 0.3122 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23263 Z= 0.150 Angle : 0.628 10.951 31602 Z= 0.321 Chirality : 0.046 0.233 3790 Planarity : 0.005 0.066 4011 Dihedral : 6.258 55.286 3263 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.31 % Allowed : 12.62 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.26 (0.16), residues: 2920 helix: -0.03 (0.15), residues: 1162 sheet: -1.45 (0.26), residues: 405 loop : -1.27 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 234 TYR 0.018 0.001 TYR G 185 PHE 0.017 0.001 PHE D 272 TRP 0.006 0.001 TRP F 476 HIS 0.005 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00361 (23262) covalent geometry : angle 0.62839 (31600) SS BOND : bond 0.00076 ( 1) SS BOND : angle 1.58669 ( 2) hydrogen bonds : bond 0.03546 ( 886) hydrogen bonds : angle 4.56748 ( 2470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 219 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8349 (p0) REVERT: D 128 GLN cc_start: 0.8774 (pm20) cc_final: 0.8399 (pm20) REVERT: F 306 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6795 (ttm110) REVERT: F 459 ASP cc_start: 0.7293 (p0) cc_final: 0.6895 (p0) REVERT: E 415 MET cc_start: 0.8833 (ttp) cc_final: 0.8127 (ttm) REVERT: H 16 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: H 20 MET cc_start: 0.9009 (ttm) cc_final: 0.8761 (ptp) REVERT: H 185 TYR cc_start: 0.9228 (t80) cc_final: 0.9024 (t80) REVERT: G 48 ASN cc_start: 0.8473 (m110) cc_final: 0.8241 (m110) REVERT: I 177 ASN cc_start: 0.7653 (m110) cc_final: 0.7431 (m-40) REVERT: I 296 TYR cc_start: 0.9113 (t80) cc_final: 0.8836 (t80) REVERT: K 100 ASP cc_start: 0.7252 (m-30) cc_final: 0.6907 (m-30) REVERT: K 121 PHE cc_start: 0.7425 (t80) cc_final: 0.7200 (t80) REVERT: K 190 HIS cc_start: 0.8540 (m90) cc_final: 0.8212 (m90) REVERT: K 192 ARG cc_start: 0.8787 (mtp180) cc_final: 0.8321 (mtp180) outliers start: 50 outliers final: 18 residues processed: 285 average time/residue: 0.5739 time to fit residues: 188.5220 Evaluate side-chains 258 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain G residue 89 CYS Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 130 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 chunk 117 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 223 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** H 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.123158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087911 restraints weight = 53322.362| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.18 r_work: 0.3106 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23263 Z= 0.163 Angle : 0.628 10.946 31602 Z= 0.318 Chirality : 0.046 0.217 3790 Planarity : 0.005 0.057 4011 Dihedral : 5.735 46.594 3263 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.43 % Allowed : 14.17 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.03 (0.16), residues: 2920 helix: 0.28 (0.15), residues: 1163 sheet: -1.37 (0.26), residues: 414 loop : -1.25 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 183 TYR 0.017 0.001 TYR F 240 PHE 0.021 0.001 PHE I 264 TRP 0.006 0.001 TRP I 111 HIS 0.006 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00393 (23262) covalent geometry : angle 0.62816 (31600) SS BOND : bond 0.00163 ( 1) SS BOND : angle 1.31888 ( 2) hydrogen bonds : bond 0.03319 ( 886) hydrogen bonds : angle 4.36231 ( 2470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.8881 (mmp) cc_final: 0.8616 (mmp) REVERT: C 130 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8084 (tm-30) REVERT: D 59 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7516 (tm-30) REVERT: D 128 GLN cc_start: 0.8812 (pm20) cc_final: 0.8404 (pm20) REVERT: F 306 ARG cc_start: 0.7128 (mtm-85) cc_final: 0.6774 (ttm110) REVERT: F 311 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8476 (mttp) REVERT: F 459 ASP cc_start: 0.7284 (p0) cc_final: 0.7031 (p0) REVERT: E 192 LEU cc_start: 0.7725 (tp) cc_final: 0.7512 (tp) REVERT: E 415 MET cc_start: 0.8838 (ttp) cc_final: 0.8155 (ttm) REVERT: H 185 TYR cc_start: 0.9232 (t80) cc_final: 0.9002 (t80) REVERT: G 48 ASN cc_start: 0.8509 (m110) cc_final: 0.8244 (m110) REVERT: I 177 ASN cc_start: 0.7670 (m110) cc_final: 0.7427 (m-40) REVERT: J 183 LYS cc_start: 0.8252 (ttpt) cc_final: 0.8030 (mtpm) REVERT: K 100 ASP cc_start: 0.7106 (m-30) cc_final: 0.6740 (m-30) REVERT: K 121 PHE cc_start: 0.7343 (t80) cc_final: 0.7127 (t80) REVERT: K 190 HIS cc_start: 0.8499 (m90) cc_final: 0.8193 (m90) REVERT: K 192 ARG cc_start: 0.8758 (mtp180) cc_final: 0.8278 (mtp180) outliers start: 53 outliers final: 24 residues processed: 284 average time/residue: 0.5727 time to fit residues: 187.8842 Evaluate side-chains 262 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain G residue 89 CYS Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 130 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 173 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 274 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 255 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN ** I 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.123896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087425 restraints weight = 76503.389| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.80 r_work: 0.3090 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23263 Z= 0.144 Angle : 0.602 10.854 31602 Z= 0.305 Chirality : 0.045 0.202 3790 Planarity : 0.004 0.058 4011 Dihedral : 5.283 34.254 3263 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.81 % Allowed : 15.01 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.87 (0.16), residues: 2920 helix: 0.46 (0.16), residues: 1171 sheet: -1.33 (0.26), residues: 415 loop : -1.20 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 234 TYR 0.017 0.001 TYR G 185 PHE 0.017 0.001 PHE D 272 TRP 0.005 0.001 TRP I 111 HIS 0.005 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00346 (23262) covalent geometry : angle 0.60226 (31600) SS BOND : bond 0.00147 ( 1) SS BOND : angle 1.09600 ( 2) hydrogen bonds : bond 0.03108 ( 886) hydrogen bonds : angle 4.22487 ( 2470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 260 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 14 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7707 (ttt90) REVERT: C 50 ARG cc_start: 0.6885 (mmp-170) cc_final: 0.6671 (mmp-170) REVERT: C 130 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7972 (tm-30) REVERT: D 81 MET cc_start: 0.8892 (mmp) cc_final: 0.8619 (mmp) REVERT: D 128 GLN cc_start: 0.8807 (pm20) cc_final: 0.8420 (pm20) REVERT: F 306 ARG cc_start: 0.7181 (mtm-85) cc_final: 0.6863 (ttm110) REVERT: F 311 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8529 (mttp) REVERT: F 459 ASP cc_start: 0.7203 (p0) cc_final: 0.6985 (p0) REVERT: E 415 MET cc_start: 0.8878 (ttp) cc_final: 0.8384 (ttm) REVERT: H 91 LYS cc_start: 0.8941 (mmpt) cc_final: 0.8407 (mptt) REVERT: G 48 ASN cc_start: 0.8532 (m110) cc_final: 0.8292 (m110) REVERT: I 145 ARG cc_start: 0.7797 (ptp-110) cc_final: 0.7501 (ptm-80) REVERT: I 177 ASN cc_start: 0.7705 (m110) cc_final: 0.7452 (m-40) REVERT: J 8 MET cc_start: 0.7670 (mmm) cc_final: 0.7390 (mmm) REVERT: J 183 LYS cc_start: 0.8268 (ttpt) cc_final: 0.8048 (mtpm) REVERT: K 100 ASP cc_start: 0.7139 (m-30) cc_final: 0.6765 (m-30) REVERT: K 121 PHE cc_start: 0.7387 (t80) cc_final: 0.7178 (t80) REVERT: K 132 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6602 (mtt) REVERT: K 183 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7855 (mtpm) REVERT: K 190 HIS cc_start: 0.8512 (m90) cc_final: 0.8269 (m90) REVERT: K 192 ARG cc_start: 0.8763 (mtp180) cc_final: 0.8557 (mtp180) outliers start: 62 outliers final: 28 residues processed: 301 average time/residue: 0.5915 time to fit residues: 204.7057 Evaluate side-chains 268 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 132 MET Chi-restraints excluded: chain K residue 183 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 267 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 215 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 147 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN E 422 GLN E 431 ASN G 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.125218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088959 restraints weight = 74739.056| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.77 r_work: 0.3114 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23263 Z= 0.122 Angle : 0.592 10.674 31602 Z= 0.298 Chirality : 0.045 0.194 3790 Planarity : 0.004 0.058 4011 Dihedral : 4.891 28.213 3263 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.06 % Allowed : 15.93 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2920 helix: 0.66 (0.16), residues: 1167 sheet: -1.29 (0.26), residues: 415 loop : -1.16 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 234 TYR 0.017 0.001 TYR F 240 PHE 0.019 0.001 PHE C 272 TRP 0.005 0.001 TRP F 476 HIS 0.004 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00288 (23262) covalent geometry : angle 0.59159 (31600) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.93755 ( 2) hydrogen bonds : bond 0.02914 ( 886) hydrogen bonds : angle 4.10489 ( 2470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 252 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 219 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8242 (p0) REVERT: D 128 GLN cc_start: 0.8779 (pm20) cc_final: 0.8410 (pm20) REVERT: F 306 ARG cc_start: 0.7137 (mtm-85) cc_final: 0.6819 (ttm110) REVERT: F 311 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8528 (mttp) REVERT: F 445 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: F 459 ASP cc_start: 0.7168 (p0) cc_final: 0.6810 (p0) REVERT: E 415 MET cc_start: 0.8877 (ttp) cc_final: 0.8389 (ttm) REVERT: H 91 LYS cc_start: 0.8957 (mmpt) cc_final: 0.8427 (mptt) REVERT: H 244 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7860 (mp10) REVERT: G 48 ASN cc_start: 0.8533 (m110) cc_final: 0.8290 (m110) REVERT: B 175 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: I 145 ARG cc_start: 0.7825 (ptp-110) cc_final: 0.7543 (ptm-80) REVERT: I 177 ASN cc_start: 0.7712 (m110) cc_final: 0.7460 (m-40) REVERT: J 8 MET cc_start: 0.7692 (mmm) cc_final: 0.7373 (mmm) REVERT: J 52 ILE cc_start: 0.6453 (OUTLIER) cc_final: 0.5985 (pp) REVERT: J 183 LYS cc_start: 0.8238 (ttpt) cc_final: 0.8015 (mtpm) REVERT: K 100 ASP cc_start: 0.7142 (m-30) cc_final: 0.6772 (m-30) REVERT: K 183 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7899 (mtpm) REVERT: K 190 HIS cc_start: 0.8501 (m90) cc_final: 0.8270 (m90) outliers start: 68 outliers final: 32 residues processed: 294 average time/residue: 0.5780 time to fit residues: 196.2182 Evaluate side-chains 276 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 183 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 156 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** I 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088167 restraints weight = 82840.964| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.94 r_work: 0.3109 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23263 Z= 0.144 Angle : 0.605 10.885 31602 Z= 0.305 Chirality : 0.045 0.194 3790 Planarity : 0.004 0.060 4011 Dihedral : 4.811 28.175 3263 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.10 % Allowed : 16.60 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2920 helix: 0.68 (0.16), residues: 1181 sheet: -1.30 (0.26), residues: 430 loop : -1.19 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 234 TYR 0.016 0.001 TYR G 9 PHE 0.018 0.001 PHE D 272 TRP 0.006 0.001 TRP I 97 HIS 0.004 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00346 (23262) covalent geometry : angle 0.60477 (31600) SS BOND : bond 0.00172 ( 1) SS BOND : angle 0.87103 ( 2) hydrogen bonds : bond 0.02967 ( 886) hydrogen bonds : angle 4.06799 ( 2470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 245 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.7554 (pp20) cc_final: 0.7179 (pp20) REVERT: C 50 ARG cc_start: 0.6909 (mmp-170) cc_final: 0.6695 (mmp-170) REVERT: C 130 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 219 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8213 (p0) REVERT: D 128 GLN cc_start: 0.8800 (pm20) cc_final: 0.8433 (pm20) REVERT: F 306 ARG cc_start: 0.7026 (mtm-85) cc_final: 0.6757 (ttm110) REVERT: F 311 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8422 (mttp) REVERT: F 445 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: F 459 ASP cc_start: 0.7042 (p0) cc_final: 0.6779 (p0) REVERT: E 415 MET cc_start: 0.8763 (ttp) cc_final: 0.8249 (ttm) REVERT: E 490 ASP cc_start: 0.8320 (t0) cc_final: 0.8083 (t0) REVERT: H 13 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7957 (tp40) REVERT: H 91 LYS cc_start: 0.8943 (mmpt) cc_final: 0.8423 (mptt) REVERT: H 244 GLN cc_start: 0.8552 (mm-40) cc_final: 0.7850 (mp10) REVERT: G 48 ASN cc_start: 0.8543 (m110) cc_final: 0.8304 (m110) REVERT: G 215 MET cc_start: 0.8859 (ttm) cc_final: 0.8644 (ttm) REVERT: I 145 ARG cc_start: 0.7834 (ptp-110) cc_final: 0.7572 (ptm-80) REVERT: I 177 ASN cc_start: 0.7739 (m110) cc_final: 0.7434 (m-40) REVERT: I 296 TYR cc_start: 0.9067 (t80) cc_final: 0.8840 (t80) REVERT: J 8 MET cc_start: 0.7629 (mmm) cc_final: 0.7365 (mmm) REVERT: J 52 ILE cc_start: 0.6465 (OUTLIER) cc_final: 0.5989 (pp) REVERT: J 183 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7934 (mtpm) REVERT: K 44 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5936 (pt0) REVERT: K 100 ASP cc_start: 0.6946 (m-30) cc_final: 0.6673 (m-30) REVERT: K 183 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7810 (mtpm) REVERT: K 190 HIS cc_start: 0.8525 (m90) cc_final: 0.8224 (m90) outliers start: 69 outliers final: 35 residues processed: 287 average time/residue: 0.5731 time to fit residues: 189.7140 Evaluate side-chains 277 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 89 CYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 183 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 126 optimal weight: 1.9990 chunk 272 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 chunk 138 optimal weight: 0.0270 chunk 18 optimal weight: 0.8980 chunk 279 optimal weight: 0.9990 chunk 134 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.126091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089951 restraints weight = 73225.647| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.73 r_work: 0.3096 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23263 Z= 0.122 Angle : 0.600 10.640 31602 Z= 0.299 Chirality : 0.045 0.301 3790 Planarity : 0.004 0.060 4011 Dihedral : 4.689 29.014 3263 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.68 % Allowed : 17.57 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.59 (0.16), residues: 2920 helix: 0.78 (0.16), residues: 1178 sheet: -1.16 (0.26), residues: 421 loop : -1.16 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 234 TYR 0.018 0.001 TYR F 240 PHE 0.020 0.001 PHE D 272 TRP 0.006 0.001 TRP I 97 HIS 0.004 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00291 (23262) covalent geometry : angle 0.59964 (31600) SS BOND : bond 0.00104 ( 1) SS BOND : angle 0.78771 ( 2) hydrogen bonds : bond 0.02821 ( 886) hydrogen bonds : angle 4.04821 ( 2470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 261 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 ARG cc_start: 0.6893 (mmp-170) cc_final: 0.6690 (mmp-170) REVERT: C 130 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7763 (tm-30) REVERT: C 219 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8100 (p0) REVERT: D 128 GLN cc_start: 0.8787 (pm20) cc_final: 0.8422 (pm20) REVERT: D 130 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7648 (tp-100) REVERT: F 311 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8420 (mttp) REVERT: F 445 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: E 415 MET cc_start: 0.8754 (ttp) cc_final: 0.8233 (ttm) REVERT: H 91 LYS cc_start: 0.8945 (mmpt) cc_final: 0.8411 (mptt) REVERT: H 244 GLN cc_start: 0.8521 (mm-40) cc_final: 0.7828 (mp10) REVERT: G 48 ASN cc_start: 0.8546 (m110) cc_final: 0.8304 (m110) REVERT: G 164 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7177 (ttp) REVERT: G 215 MET cc_start: 0.8811 (ttm) cc_final: 0.8605 (ttm) REVERT: B 175 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: B 296 TYR cc_start: 0.9038 (t80) cc_final: 0.8834 (t80) REVERT: I 145 ARG cc_start: 0.7855 (ptp-110) cc_final: 0.7610 (ptm-80) REVERT: I 296 TYR cc_start: 0.9055 (t80) cc_final: 0.8814 (t80) REVERT: J 8 MET cc_start: 0.7636 (mmm) cc_final: 0.7373 (mmm) REVERT: J 52 ILE cc_start: 0.6387 (OUTLIER) cc_final: 0.5972 (pp) REVERT: J 183 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7890 (mtpm) REVERT: K 100 ASP cc_start: 0.6943 (m-30) cc_final: 0.6680 (m-30) REVERT: K 183 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7932 (mtpm) REVERT: K 185 SER cc_start: 0.8539 (m) cc_final: 0.8008 (p) REVERT: K 190 HIS cc_start: 0.8511 (m90) cc_final: 0.8216 (m90) outliers start: 59 outliers final: 33 residues processed: 297 average time/residue: 0.5570 time to fit residues: 192.3310 Evaluate side-chains 282 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 183 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 286 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 199 optimal weight: 0.4980 chunk 89 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 283 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.089391 restraints weight = 66262.682| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.57 r_work: 0.3143 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23263 Z= 0.139 Angle : 0.614 10.742 31602 Z= 0.306 Chirality : 0.045 0.296 3790 Planarity : 0.004 0.059 4011 Dihedral : 4.694 28.999 3263 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.60 % Allowed : 18.03 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.60 (0.16), residues: 2920 helix: 0.77 (0.16), residues: 1178 sheet: -1.16 (0.26), residues: 431 loop : -1.16 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 234 TYR 0.016 0.001 TYR G 9 PHE 0.021 0.001 PHE J 169 TRP 0.006 0.001 TRP I 97 HIS 0.004 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00333 (23262) covalent geometry : angle 0.61356 (31600) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.77605 ( 2) hydrogen bonds : bond 0.02937 ( 886) hydrogen bonds : angle 4.05361 ( 2470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 243 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.7629 (pp20) cc_final: 0.7279 (pp20) REVERT: C 219 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8156 (p0) REVERT: D 128 GLN cc_start: 0.8772 (pm20) cc_final: 0.8423 (pm20) REVERT: D 130 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7894 (tp40) REVERT: F 306 ARG cc_start: 0.6874 (ttm110) cc_final: 0.6468 (ttp-110) REVERT: F 311 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8428 (mttp) REVERT: F 445 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: E 415 MET cc_start: 0.8750 (ttp) cc_final: 0.8232 (ttm) REVERT: E 490 ASP cc_start: 0.8283 (t0) cc_final: 0.7967 (t0) REVERT: H 91 LYS cc_start: 0.8930 (mmpt) cc_final: 0.8419 (mptt) REVERT: H 244 GLN cc_start: 0.8540 (mm-40) cc_final: 0.7840 (mp10) REVERT: G 48 ASN cc_start: 0.8551 (m110) cc_final: 0.8306 (m110) REVERT: G 164 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7194 (ttp) REVERT: B 175 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: B 296 TYR cc_start: 0.9054 (t80) cc_final: 0.8842 (t80) REVERT: I 145 ARG cc_start: 0.7833 (ptp-110) cc_final: 0.7564 (ptm-80) REVERT: I 177 ASN cc_start: 0.7692 (m110) cc_final: 0.7383 (m-40) REVERT: I 296 TYR cc_start: 0.9069 (t80) cc_final: 0.8818 (t80) REVERT: J 8 MET cc_start: 0.7573 (mmm) cc_final: 0.7323 (mmm) REVERT: J 52 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.6007 (pp) REVERT: J 183 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7956 (mtpm) REVERT: K 100 ASP cc_start: 0.6976 (m-30) cc_final: 0.6717 (m-30) REVERT: K 183 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7862 (mtpm) REVERT: K 190 HIS cc_start: 0.8485 (m90) cc_final: 0.8195 (m90) outliers start: 57 outliers final: 38 residues processed: 278 average time/residue: 0.5495 time to fit residues: 177.7318 Evaluate side-chains 288 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 89 CYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 18 optimal weight: 0.6980 chunk 266 optimal weight: 0.1980 chunk 214 optimal weight: 4.9990 chunk 277 optimal weight: 10.0000 chunk 112 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.126713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.090641 restraints weight = 71940.780| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.70 r_work: 0.3149 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23263 Z= 0.120 Angle : 0.606 10.607 31602 Z= 0.302 Chirality : 0.045 0.354 3790 Planarity : 0.004 0.060 4011 Dihedral : 4.625 31.368 3263 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.47 % Allowed : 18.28 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.51 (0.16), residues: 2920 helix: 0.86 (0.16), residues: 1169 sheet: -1.06 (0.26), residues: 427 loop : -1.13 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 234 TYR 0.018 0.001 TYR F 240 PHE 0.022 0.001 PHE J 169 TRP 0.007 0.001 TRP I 97 HIS 0.003 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00285 (23262) covalent geometry : angle 0.60648 (31600) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.74261 ( 2) hydrogen bonds : bond 0.02778 ( 886) hydrogen bonds : angle 4.01746 ( 2470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.7631 (pp20) cc_final: 0.7305 (pp20) REVERT: C 56 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: C 130 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7940 (tm-30) REVERT: D 128 GLN cc_start: 0.8761 (pm20) cc_final: 0.8413 (pm20) REVERT: F 306 ARG cc_start: 0.6968 (ttm110) cc_final: 0.6680 (ttp-110) REVERT: F 311 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8431 (mttp) REVERT: F 445 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: E 415 MET cc_start: 0.8744 (ttp) cc_final: 0.8139 (ttm) REVERT: E 490 ASP cc_start: 0.8222 (t0) cc_final: 0.7883 (t0) REVERT: H 91 LYS cc_start: 0.8905 (mmpt) cc_final: 0.8442 (mptt) REVERT: H 244 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7847 (mp10) REVERT: G 48 ASN cc_start: 0.8553 (m110) cc_final: 0.8313 (m110) REVERT: G 164 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7123 (ttp) REVERT: B 175 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: B 296 TYR cc_start: 0.9062 (t80) cc_final: 0.8821 (t80) REVERT: I 145 ARG cc_start: 0.7857 (ptp-110) cc_final: 0.7602 (ptm-80) REVERT: I 177 ASN cc_start: 0.7708 (m110) cc_final: 0.7384 (m-40) REVERT: I 296 TYR cc_start: 0.9094 (t80) cc_final: 0.8815 (t80) REVERT: J 8 MET cc_start: 0.7606 (mmm) cc_final: 0.7355 (mmm) REVERT: J 52 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6041 (pp) REVERT: J 183 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7978 (mtpm) REVERT: K 183 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7963 (mtpm) REVERT: K 190 HIS cc_start: 0.8521 (m90) cc_final: 0.8246 (m90) REVERT: K 192 ARG cc_start: 0.8548 (mtp180) cc_final: 0.8225 (mmm-85) outliers start: 54 outliers final: 33 residues processed: 287 average time/residue: 0.5799 time to fit residues: 192.3212 Evaluate side-chains 281 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 495 GLU Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 252 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 264 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 ASN ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.124609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089096 restraints weight = 58832.014| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.34 r_work: 0.3143 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23263 Z= 0.165 Angle : 0.635 12.764 31602 Z= 0.317 Chirality : 0.046 0.360 3790 Planarity : 0.004 0.059 4011 Dihedral : 4.698 29.131 3263 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.35 % Allowed : 18.83 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.59 (0.16), residues: 2920 helix: 0.77 (0.16), residues: 1177 sheet: -1.07 (0.26), residues: 437 loop : -1.19 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 234 TYR 0.019 0.001 TYR G 9 PHE 0.021 0.001 PHE J 169 TRP 0.007 0.001 TRP E 350 HIS 0.005 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00401 (23262) covalent geometry : angle 0.63481 (31600) SS BOND : bond 0.00223 ( 1) SS BOND : angle 0.77833 ( 2) hydrogen bonds : bond 0.02950 ( 886) hydrogen bonds : angle 4.05434 ( 2470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8210.85 seconds wall clock time: 140 minutes 16.04 seconds (8416.04 seconds total)