Starting phenix.real_space_refine on Thu Mar 5 02:15:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qle_4580/03_2026/6qle_4580.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qle_4580/03_2026/6qle_4580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qle_4580/03_2026/6qle_4580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qle_4580/03_2026/6qle_4580.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qle_4580/03_2026/6qle_4580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qle_4580/03_2026/6qle_4580.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 76 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 11655 2.51 5 N 3146 2.21 5 O 3285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s 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: 18162 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 952 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 87 Chain: "I" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2332 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 6 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'UNK:plan-1': 11, 'TYR:plan': 2, 'ARG:plan': 4, 'GLU:plan': 9, 'ASP:plan': 8, 'ASN:plan1': 4, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "I" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 367 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 13, 'ASN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "K" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 774 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "L" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1941 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "N" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2922 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 5 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 76 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1658 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1865 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 92 Chain: "Q" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1584 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'UNK:plan-1': 15, 'ARG:plan': 5, 'GLU:plan': 15, 'ASN:plan1': 4, 'ASP:plan': 6, 'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 155 Chain: "U" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1231 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 2 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 26, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 9, 'GLU:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 90 Chain: "Y" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1541 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 15, 'TYR:plan': 1, 'GLU:plan': 16, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "Z" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 995 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 118 Time building chain proxies: 4.06, per 1000 atoms: 0.22 Number of scatterers: 18162 At special positions: 0 Unit cell: (184.21, 173.31, 131.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 3285 8.00 N 3146 7.00 C 11655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 742.2 milliseconds 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 13 sheets defined 64.2% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'H' and resid 5 through 39 removed outlier: 4.092A pdb=" N HIS H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 73 Processing helix chain 'H' and resid 83 through 94 removed outlier: 4.377A pdb=" N ASN H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 135 Processing helix chain 'I' and resid 323 through 328 removed outlier: 3.672A pdb=" N UNK I 327 " --> pdb=" O UNK I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 339 removed outlier: 4.207A pdb=" N LEU I 339 " --> pdb=" O LEU I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 340 through 350 removed outlier: 4.401A pdb=" N ILE I 346 " --> pdb=" O SER I 342 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER I 349 " --> pdb=" O LEU I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 369 Processing helix chain 'I' and resid 374 through 377 removed outlier: 3.562A pdb=" N GLU I 377 " --> pdb=" O THR I 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 374 through 377' Processing helix chain 'I' and resid 378 through 387 Processing helix chain 'I' and resid 389 through 401 removed outlier: 3.639A pdb=" N CYS I 401 " --> pdb=" O ILE I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 421 Processing helix chain 'I' and resid 422 through 424 No H-bonds generated for 'chain 'I' and resid 422 through 424' Processing helix chain 'I' and resid 431 through 448 removed outlier: 4.108A pdb=" N PHE I 435 " --> pdb=" O GLY I 431 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE I 444 " --> pdb=" O MET I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 473 removed outlier: 3.892A pdb=" N THR I 461 " --> pdb=" O THR I 457 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN I 471 " --> pdb=" O GLN I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 493 Processing helix chain 'I' and resid 506 through 524 Processing helix chain 'I' and resid 538 through 548 Processing helix chain 'I' and resid 550 through 569 Processing helix chain 'I' and resid 576 through 592 Processing helix chain 'I' and resid 607 through 619 removed outlier: 3.937A pdb=" N PHE I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR I 619 " --> pdb=" O LEU I 615 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 653 Processing helix chain 'I' and resid 666 through 675 removed outlier: 3.731A pdb=" N UNK I 670 " --> pdb=" O UNK I 666 " (cutoff:3.500A) Processing helix chain 'I' and resid 693 through 707 removed outlier: 3.898A pdb=" N ARG I 697 " --> pdb=" O ILE I 693 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL I 698 " --> pdb=" O HIS I 694 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR I 707 " --> pdb=" O HIS I 703 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 721 Processing helix chain 'I' and resid 722 through 726 Processing helix chain 'K' and resid 8 through 40 Processing helix chain 'K' and resid 51 through 59 removed outlier: 3.656A pdb=" N LYS K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 128 Processing helix chain 'L' and resid 19 through 28 Processing helix chain 'L' and resid 94 through 108 removed outlier: 3.564A pdb=" N TYR L 107 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 127 Processing helix chain 'L' and resid 153 through 157 removed outlier: 3.704A pdb=" N LYS L 156 " --> pdb=" O THR L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 187 removed outlier: 3.566A pdb=" N ASP L 186 " --> pdb=" O HIS L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 197 Processing helix chain 'L' and resid 229 through 240 removed outlier: 3.591A pdb=" N ILE L 240 " --> pdb=" O VAL L 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 25 removed outlier: 3.654A pdb=" N VAL N 20 " --> pdb=" O ASP N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 43 removed outlier: 3.602A pdb=" N LEU N 32 " --> pdb=" O PRO N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 removed outlier: 3.736A pdb=" N LEU N 60 " --> pdb=" O GLU N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 65 Processing helix chain 'N' and resid 67 through 77 removed outlier: 3.971A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 removed outlier: 3.613A pdb=" N LEU N 89 " --> pdb=" O ASN N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 104 removed outlier: 3.836A pdb=" N PHE N 104 " --> pdb=" O PRO N 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 101 through 104' Processing helix chain 'N' and resid 126 through 137 removed outlier: 4.184A pdb=" N GLU N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN N 131 " --> pdb=" O LYS N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 232 removed outlier: 3.771A pdb=" N ARG N 222 " --> pdb=" O ASP N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 259 removed outlier: 3.934A pdb=" N ILE N 254 " --> pdb=" O SER N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 265 removed outlier: 4.339A pdb=" N GLU N 265 " --> pdb=" O ARG N 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 Processing helix chain 'N' and resid 318 through 334 Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 428 through 433 Processing helix chain 'O' and resid 154 through 172 Processing helix chain 'O' and resid 245 through 253 Processing helix chain 'O' and resid 254 through 257 removed outlier: 3.950A pdb=" N LEU O 257 " --> pdb=" O ASN O 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 254 through 257' Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.731A pdb=" N PHE O 267 " --> pdb=" O ASP O 263 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE O 285 " --> pdb=" O ARG O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 340 through 349 removed outlier: 3.709A pdb=" N TRP O 344 " --> pdb=" O ASN O 340 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU O 348 " --> pdb=" O TRP O 344 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU O 349 " --> pdb=" O GLU O 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 359 removed outlier: 3.709A pdb=" N GLU O 356 " --> pdb=" O LEU O 352 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 109 Processing helix chain 'P' and resid 133 through 140 removed outlier: 3.749A pdb=" N THR P 140 " --> pdb=" O LYS P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 159 Processing helix chain 'P' and resid 230 through 234 removed outlier: 3.763A pdb=" N ALA P 233 " --> pdb=" O GLN P 230 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR P 234 " --> pdb=" O LEU P 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 230 through 234' Processing helix chain 'P' and resid 236 through 264 Processing helix chain 'P' and resid 333 through 348 removed outlier: 3.735A pdb=" N TYR P 348 " --> pdb=" O LEU P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 353 through 363 Processing helix chain 'Q' and resid 126 through 137 removed outlier: 3.995A pdb=" N UNK Q 130 " --> pdb=" O UNK Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 161 through 187 Processing helix chain 'Q' and resid 193 through 217 Processing helix chain 'Q' and resid 233 through 291 Processing helix chain 'Q' and resid 323 through 332 Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 358 through 382 removed outlier: 4.239A pdb=" N GLU Q 362 " --> pdb=" O PRO Q 358 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP Q 380 " --> pdb=" O GLN Q 376 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER Q 381 " --> pdb=" O MET Q 377 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 387 Processing helix chain 'U' and resid 132 through 156 Processing helix chain 'U' and resid 167 through 231 removed outlier: 4.981A pdb=" N LEU U 173 " --> pdb=" O LEU U 169 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU U 175 " --> pdb=" O TYR U 171 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN U 200 " --> pdb=" O ASN U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 removed outlier: 3.519A pdb=" N HIS U 237 " --> pdb=" O GLY U 233 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU U 264 " --> pdb=" O THR U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 288 through 299 Processing helix chain 'U' and resid 305 through 321 removed outlier: 3.616A pdb=" N LEU U 320 " --> pdb=" O LEU U 316 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.778A pdb=" N SER Y 7 " --> pdb=" O ASP Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 31 removed outlier: 3.782A pdb=" N LEU Y 30 " --> pdb=" O MET Y 27 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA Y 31 " --> pdb=" O ASP Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 57 through 82 removed outlier: 3.887A pdb=" N SER Y 76 " --> pdb=" O GLU Y 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN Y 77 " --> pdb=" O LEU Y 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 102 removed outlier: 3.755A pdb=" N ARG Y 98 " --> pdb=" O GLY Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 118 Processing helix chain 'Y' and resid 137 through 186 removed outlier: 3.547A pdb=" N GLU Y 186 " --> pdb=" O LYS Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 217 removed outlier: 5.286A pdb=" N ASN Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY Y 199 " --> pdb=" O ALA Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 237 Processing helix chain 'Z' and resid 4 through 14 removed outlier: 3.828A pdb=" N ASN Z 9 " --> pdb=" O GLN Z 5 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER Z 14 " --> pdb=" O TYR Z 10 " (cutoff:3.500A) Processing helix chain 'Z' and resid 15 through 19 removed outlier: 3.951A pdb=" N THR Z 18 " --> pdb=" O LEU Z 15 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU Z 19 " --> pdb=" O LEU Z 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 15 through 19' Processing helix chain 'Z' and resid 37 through 83 Processing helix chain 'Z' and resid 88 through 124 removed outlier: 3.697A pdb=" N ASN Z 124 " --> pdb=" O ALA Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 152 Processing sheet with id=AA1, first strand: chain 'L' and resid 73 through 76 removed outlier: 3.961A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 31 through 33 removed outlier: 3.964A pdb=" N ASP L 32 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG L 59 " --> pdb=" O ASP L 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 38 through 39 Processing sheet with id=AA4, first strand: chain 'L' and resid 130 through 132 Processing sheet with id=AA5, first strand: chain 'N' and resid 141 through 148 removed outlier: 4.265A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 141 through 148 removed outlier: 4.265A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 295 through 298 removed outlier: 3.756A pdb=" N LYS N 295 " --> pdb=" O ILE P 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 397 through 400 removed outlier: 7.027A pdb=" N THR N 388 " --> pdb=" O ILE N 442 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 175 through 180 removed outlier: 3.510A pdb=" N THR O 176 " --> pdb=" O ARG O 205 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU O 180 " --> pdb=" O MET O 201 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N MET O 201 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS O 225 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU O 235 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 186 through 188 removed outlier: 3.502A pdb=" N LYS O 187 " --> pdb=" O PHE O 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 305 through 309 removed outlier: 3.813A pdb=" N LYS O 314 " --> pdb=" O LEU O 330 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS O 320 " --> pdb=" O ILE O 324 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE O 324 " --> pdb=" O LYS O 320 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 168 through 172 removed outlier: 3.526A pdb=" N SER P 168 " --> pdb=" O ASN P 186 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN P 186 " --> pdb=" O SER P 168 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG P 172 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL P 182 " --> pdb=" O ARG P 172 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 270 through 272 removed outlier: 3.538A pdb=" N TYR P 272 " --> pdb=" O ILE P 281 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5704 1.34 - 1.46: 3046 1.46 - 1.58: 9550 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 18425 Sorted by residual: bond pdb=" CG1 ILE O 240 " pdb=" CD1 ILE O 240 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.11e+00 bond pdb=" C VAL L 40 " pdb=" N PRO L 41 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.47e+00 bond pdb=" CA GLY Y 220 " pdb=" C GLY Y 220 " ideal model delta sigma weight residual 1.511 1.530 -0.019 1.25e-02 6.40e+03 2.34e+00 bond pdb=" N GLY Y 220 " pdb=" CA GLY Y 220 " ideal model delta sigma weight residual 1.453 1.473 -0.020 1.43e-02 4.89e+03 2.01e+00 bond pdb=" CB VAL I 545 " pdb=" CG2 VAL I 545 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 ... (remaining 18420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 24684 3.09 - 6.18: 223 6.18 - 9.27: 35 9.27 - 12.36: 3 12.36 - 15.45: 4 Bond angle restraints: 24949 Sorted by residual: angle pdb=" N PRO Y 223 " pdb=" CA PRO Y 223 " pdb=" CB PRO Y 223 " ideal model delta sigma weight residual 103.25 110.23 -6.98 1.05e+00 9.07e-01 4.43e+01 angle pdb=" N PRO H 136 " pdb=" CA PRO H 136 " pdb=" CB PRO H 136 " ideal model delta sigma weight residual 103.00 110.28 -7.28 1.10e+00 8.26e-01 4.38e+01 angle pdb=" N PRO Z 137 " pdb=" CA PRO Z 137 " pdb=" CB PRO Z 137 " ideal model delta sigma weight residual 103.44 110.08 -6.64 1.12e+00 7.97e-01 3.52e+01 angle pdb=" C THR I 574 " pdb=" N ASN I 575 " pdb=" CA ASN I 575 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C GLU L 135 " pdb=" N ASN L 136 " pdb=" CA ASN L 136 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 ... (remaining 24944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 9948 17.59 - 35.19: 1043 35.19 - 52.78: 182 52.78 - 70.37: 28 70.37 - 87.96: 9 Dihedral angle restraints: 11210 sinusoidal: 4090 harmonic: 7120 Sorted by residual: dihedral pdb=" CA VAL L 40 " pdb=" C VAL L 40 " pdb=" N PRO L 41 " pdb=" CA PRO L 41 " ideal model delta harmonic sigma weight residual -180.00 -117.85 -62.15 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" CA MET P 274 " pdb=" C MET P 274 " pdb=" N ASN P 275 " pdb=" CA ASN P 275 " ideal model delta harmonic sigma weight residual -180.00 -144.70 -35.30 0 5.00e+00 4.00e-02 4.99e+01 dihedral pdb=" CA ALA I 638 " pdb=" C ALA I 638 " pdb=" N LEU I 639 " pdb=" CA LEU I 639 " ideal model delta harmonic sigma weight residual 180.00 153.13 26.87 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 11207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2340 0.052 - 0.103: 521 0.103 - 0.155: 139 0.155 - 0.206: 18 0.206 - 0.258: 10 Chirality restraints: 3028 Sorted by residual: chirality pdb=" CB VAL P 224 " pdb=" CA VAL P 224 " pdb=" CG1 VAL P 224 " pdb=" CG2 VAL P 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CG LEU Q 211 " pdb=" CB LEU Q 211 " pdb=" CD1 LEU Q 211 " pdb=" CD2 LEU Q 211 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PRO Y 223 " pdb=" N PRO Y 223 " pdb=" C PRO Y 223 " pdb=" CB PRO Y 223 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3025 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 40 " -0.061 5.00e-02 4.00e+02 9.33e-02 1.39e+01 pdb=" N PRO L 41 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO L 41 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO L 41 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 40 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C VAL L 40 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL L 40 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO L 41 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 437 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C VAL I 437 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL I 437 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS I 438 " -0.014 2.00e-02 2.50e+03 ... (remaining 3119 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4935 2.81 - 3.33: 16351 3.33 - 3.85: 29096 3.85 - 4.38: 30891 4.38 - 4.90: 55881 Nonbonded interactions: 137154 Sorted by model distance: nonbonded pdb=" O ILE I 383 " pdb=" OG SER I 387 " model vdw 2.282 3.040 nonbonded pdb=" O ILE K 70 " pdb=" OG SER K 73 " model vdw 2.300 3.040 nonbonded pdb=" O LEU I 535 " pdb=" OH TYR I 560 " model vdw 2.304 3.040 nonbonded pdb=" O SER O 214 " pdb=" OG SER O 214 " model vdw 2.311 3.040 nonbonded pdb=" O SER O 153 " pdb=" OG SER O 153 " model vdw 2.319 3.040 ... (remaining 137149 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.620 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.005 0.069 18425 Z= 0.220 Angle : 0.840 15.451 24949 Z= 0.454 Chirality : 0.050 0.258 3028 Planarity : 0.006 0.093 3122 Dihedral : 14.608 87.965 6534 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 0.27 % Allowed : 7.68 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -3.18 (0.14), residues: 2278 helix: -1.42 (0.11), residues: 1370 sheet: -2.46 (0.34), residues: 214 loop : -3.11 (0.19), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 375 TYR 0.027 0.002 TYR Z 43 PHE 0.026 0.002 PHE I 610 TRP 0.014 0.002 TRP L 102 HIS 0.006 0.001 HIS I 694 Details of bonding type rmsd covalent geometry : bond 0.00459 (18425) covalent geometry : angle 0.83978 (24949) hydrogen bonds : bond 0.14345 ( 1185) hydrogen bonds : angle 6.06798 ( 3528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 493 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 LEU cc_start: 0.8161 (tp) cc_final: 0.7869 (mt) REVERT: H 24 ARG cc_start: 0.6014 (mtp-110) cc_final: 0.5625 (mtm180) REVERT: I 405 TYR cc_start: 0.8752 (m-80) cc_final: 0.8510 (m-80) REVERT: I 438 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7994 (mmtm) REVERT: I 590 ASN cc_start: 0.7613 (t0) cc_final: 0.7315 (t0) REVERT: I 611 PHE cc_start: 0.7081 (m-80) cc_final: 0.6860 (m-80) REVERT: I 697 ARG cc_start: 0.4641 (ptp-170) cc_final: 0.4086 (mmt180) REVERT: K 99 ASP cc_start: 0.7862 (m-30) cc_final: 0.7609 (m-30) REVERT: K 104 LEU cc_start: 0.7341 (tp) cc_final: 0.6814 (tp) REVERT: K 124 GLN cc_start: 0.5331 (tm-30) cc_final: 0.4800 (mm-40) REVERT: L 107 TYR cc_start: 0.6893 (m-80) cc_final: 0.6392 (m-80) REVERT: L 217 MET cc_start: 0.7229 (mtt) cc_final: 0.6997 (mtm) REVERT: N 21 PHE cc_start: 0.7064 (t80) cc_final: 0.6701 (t80) REVERT: N 392 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8134 (tm-30) REVERT: O 184 ILE cc_start: 0.8246 (mp) cc_final: 0.8004 (mp) REVERT: O 280 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7864 (mtmt) REVERT: O 292 LYS cc_start: 0.8021 (mttp) cc_final: 0.7446 (tppt) REVERT: O 313 ILE cc_start: 0.8264 (mp) cc_final: 0.7974 (mt) REVERT: O 341 LYS cc_start: 0.5903 (mttt) cc_final: 0.5656 (mmtm) REVERT: P 173 ASP cc_start: 0.7331 (m-30) cc_final: 0.7084 (m-30) REVERT: P 254 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8333 (ttpp) REVERT: Q 266 GLN cc_start: 0.8324 (tp40) cc_final: 0.8073 (mm-40) REVERT: U 182 SER cc_start: 0.8586 (t) cc_final: 0.8350 (p) REVERT: U 185 MET cc_start: 0.8147 (mmm) cc_final: 0.7944 (tpp) REVERT: U 200 ASN cc_start: 0.7350 (m-40) cc_final: 0.7086 (t0) REVERT: U 241 ASN cc_start: 0.8147 (m-40) cc_final: 0.7928 (m-40) REVERT: Y 15 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7808 (tp30) REVERT: Y 69 ASN cc_start: 0.8479 (m-40) cc_final: 0.8192 (t0) REVERT: Z 62 LYS cc_start: 0.8914 (tttt) cc_final: 0.8205 (mtmt) REVERT: Z 71 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7827 (ttp80) REVERT: Z 80 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8509 (tp-100) outliers start: 5 outliers final: 1 residues processed: 498 average time/residue: 0.1650 time to fit residues: 116.6965 Evaluate side-chains 321 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 215 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 HIS H 49 GLN I 376 GLN I 467 GLN I 490 GLN I 521 GLN I 595 ASN ** I 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 ASN K 122 GLN L 36 GLN L 118 GLN L 213 HIS L 238 GLN N 141 HIS N 165 ASN N 213 HIS O 238 HIS O 274 GLN O 322 ASN P 135 GLN P 297 GLN Q 245 GLN U 219 GLN U 228 GLN Y 170 GLN Y 198 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.165166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143639 restraints weight = 26467.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.138097 restraints weight = 32870.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.135646 restraints weight = 35184.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136612 restraints weight = 29195.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.136909 restraints weight = 20325.535| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18425 Z= 0.124 Angle : 0.581 9.252 24949 Z= 0.301 Chirality : 0.039 0.233 3028 Planarity : 0.004 0.085 3122 Dihedral : 4.678 46.252 2543 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.76 % Allowed : 15.20 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.81 (0.17), residues: 2278 helix: 0.74 (0.13), residues: 1400 sheet: -2.10 (0.33), residues: 225 loop : -2.74 (0.21), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 225 TYR 0.030 0.001 TYR Z 43 PHE 0.049 0.002 PHE I 546 TRP 0.009 0.001 TRP L 102 HIS 0.003 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00259 (18425) covalent geometry : angle 0.58103 (24949) hydrogen bonds : bond 0.04263 ( 1185) hydrogen bonds : angle 4.16385 ( 3528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 354 time to evaluate : 0.608 Fit side-chains REVERT: I 489 MET cc_start: 0.7688 (mmp) cc_final: 0.7180 (mmp) REVERT: I 497 LYS cc_start: 0.7356 (mttt) cc_final: 0.7113 (tptm) REVERT: I 569 MET cc_start: 0.5762 (ptm) cc_final: 0.5470 (ptp) REVERT: I 590 ASN cc_start: 0.7379 (t0) cc_final: 0.7146 (t0) REVERT: I 697 ARG cc_start: 0.4583 (ptp-170) cc_final: 0.3954 (mmt90) REVERT: K 97 SER cc_start: 0.8776 (t) cc_final: 0.8483 (m) REVERT: L 12 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7520 (tttp) REVERT: L 238 GLN cc_start: 0.8181 (tp40) cc_final: 0.7976 (tp-100) REVERT: N 97 MET cc_start: 0.7567 (ttm) cc_final: 0.7343 (ttm) REVERT: N 392 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7511 (tm-30) REVERT: O 280 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8118 (mtmt) REVERT: O 292 LYS cc_start: 0.8128 (mttp) cc_final: 0.7754 (tppt) REVERT: O 313 ILE cc_start: 0.8420 (mp) cc_final: 0.8133 (mt) REVERT: P 248 ASP cc_start: 0.7562 (t0) cc_final: 0.7359 (t0) REVERT: Q 266 GLN cc_start: 0.8473 (tp40) cc_final: 0.8233 (mm-40) REVERT: U 255 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7531 (mtt180) REVERT: Y 198 ASN cc_start: 0.6994 (t0) cc_final: 0.6612 (t0) REVERT: Z 62 LYS cc_start: 0.8228 (tttt) cc_final: 0.8014 (mtmt) outliers start: 32 outliers final: 12 residues processed: 373 average time/residue: 0.1398 time to fit residues: 76.7674 Evaluate side-chains 307 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 294 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain U residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 62 optimal weight: 0.9980 chunk 180 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 156 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN H 50 GLN L 78 ASN L 185 ASN O 274 GLN P 135 GLN P 297 GLN ** U 237 HIS ** 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 = 0.3988 r_free = 0.3988 target = 0.163373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136450 restraints weight = 27009.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135118 restraints weight = 35072.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136337 restraints weight = 32060.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.136528 restraints weight = 22037.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.136603 restraints weight = 21489.767| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18425 Z= 0.135 Angle : 0.563 8.659 24949 Z= 0.292 Chirality : 0.040 0.292 3028 Planarity : 0.004 0.079 3122 Dihedral : 4.452 45.930 2543 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.25 % Allowed : 18.50 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.18), residues: 2278 helix: 1.54 (0.14), residues: 1406 sheet: -1.80 (0.34), residues: 225 loop : -2.56 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 229 TYR 0.028 0.002 TYR Z 43 PHE 0.019 0.001 PHE Q 325 TRP 0.010 0.001 TRP L 102 HIS 0.003 0.001 HIS N 149 Details of bonding type rmsd covalent geometry : bond 0.00302 (18425) covalent geometry : angle 0.56338 (24949) hydrogen bonds : bond 0.03998 ( 1185) hydrogen bonds : angle 3.89125 ( 3528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 489 MET cc_start: 0.7832 (mmp) cc_final: 0.7113 (mmt) REVERT: I 569 MET cc_start: 0.5819 (ptm) cc_final: 0.5511 (ptp) REVERT: I 590 ASN cc_start: 0.7400 (t0) cc_final: 0.7197 (t0) REVERT: L 238 GLN cc_start: 0.8259 (tp40) cc_final: 0.7968 (tp-100) REVERT: N 255 MET cc_start: 0.8948 (mmm) cc_final: 0.8711 (mmm) REVERT: O 280 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8108 (mtmt) REVERT: O 292 LYS cc_start: 0.8261 (mttp) cc_final: 0.7745 (tppt) REVERT: Q 266 GLN cc_start: 0.8451 (tp40) cc_final: 0.8190 (mm-40) REVERT: Y 198 ASN cc_start: 0.7087 (t0) cc_final: 0.6762 (t0) REVERT: Z 4 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7290 (tm-30) outliers start: 41 outliers final: 21 residues processed: 342 average time/residue: 0.1445 time to fit residues: 72.9904 Evaluate side-chains 303 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 282 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 297 GLN Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 89 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 153 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 0.3980 chunk 162 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN H 50 GLN L 28 ASN L 238 GLN N 435 ASN P 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135398 restraints weight = 26789.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135184 restraints weight = 42102.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134222 restraints weight = 29969.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.133779 restraints weight = 26246.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134255 restraints weight = 23569.528| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18425 Z= 0.178 Angle : 0.587 8.594 24949 Z= 0.304 Chirality : 0.041 0.251 3028 Planarity : 0.004 0.075 3122 Dihedral : 4.465 45.162 2543 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.69 % Allowed : 19.54 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.48 (0.18), residues: 2278 helix: 1.85 (0.14), residues: 1406 sheet: -1.63 (0.34), residues: 228 loop : -2.50 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 74 TYR 0.021 0.002 TYR Z 43 PHE 0.023 0.002 PHE I 604 TRP 0.012 0.001 TRP I 362 HIS 0.004 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00419 (18425) covalent geometry : angle 0.58675 (24949) hydrogen bonds : bond 0.04113 ( 1185) hydrogen bonds : angle 3.86058 ( 3528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 297 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: I 345 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7234 (tt) REVERT: I 440 MET cc_start: 0.8886 (mmm) cc_final: 0.8472 (mmm) REVERT: I 489 MET cc_start: 0.7913 (mmp) cc_final: 0.7237 (mmt) REVERT: I 542 MET cc_start: 0.5900 (tpp) cc_final: 0.5185 (tpp) REVERT: I 546 PHE cc_start: 0.6701 (m-80) cc_final: 0.5937 (m-80) REVERT: I 569 MET cc_start: 0.5961 (ptm) cc_final: 0.5692 (ptp) REVERT: I 590 ASN cc_start: 0.7485 (t0) cc_final: 0.7245 (t0) REVERT: L 12 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7623 (tttp) REVERT: L 238 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8110 (tp-100) REVERT: O 280 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8311 (mtmt) REVERT: Q 266 GLN cc_start: 0.8453 (tp40) cc_final: 0.8167 (mm-40) REVERT: Q 335 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7167 (mpp) REVERT: Y 183 GLU cc_start: 0.6914 (tt0) cc_final: 0.6664 (tt0) REVERT: Y 198 ASN cc_start: 0.7166 (t0) cc_final: 0.6797 (t0) outliers start: 49 outliers final: 26 residues processed: 329 average time/residue: 0.1419 time to fit residues: 69.0678 Evaluate side-chains 301 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 49 optimal weight: 0.9980 chunk 216 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 182 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN H 50 GLN K 77 ASN L 24 ASN N 133 GLN P 135 GLN P 297 GLN Z 8 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.161061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.137504 restraints weight = 26847.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131985 restraints weight = 40132.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.131133 restraints weight = 33149.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.131466 restraints weight = 29368.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131794 restraints weight = 22803.452| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18425 Z= 0.133 Angle : 0.554 8.253 24949 Z= 0.287 Chirality : 0.040 0.422 3028 Planarity : 0.004 0.073 3122 Dihedral : 4.293 43.238 2543 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.63 % Allowed : 20.09 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 0.84 (0.18), residues: 2278 helix: 2.12 (0.14), residues: 1411 sheet: -1.40 (0.35), residues: 228 loop : -2.39 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 74 TYR 0.019 0.001 TYR Y 193 PHE 0.017 0.001 PHE Q 325 TRP 0.012 0.001 TRP I 424 HIS 0.005 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00299 (18425) covalent geometry : angle 0.55407 (24949) hydrogen bonds : bond 0.03868 ( 1185) hydrogen bonds : angle 3.72558 ( 3528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 298 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 345 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7260 (tt) REVERT: I 489 MET cc_start: 0.8143 (mmp) cc_final: 0.7347 (mmt) REVERT: I 569 MET cc_start: 0.6236 (ptm) cc_final: 0.5936 (ptp) REVERT: I 590 ASN cc_start: 0.7567 (t0) cc_final: 0.7294 (t0) REVERT: L 233 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8380 (mp) REVERT: N 383 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6930 (mt-10) REVERT: O 280 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8134 (mtmt) REVERT: P 126 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7800 (mm-30) REVERT: Q 335 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7146 (mpp) REVERT: Y 15 GLU cc_start: 0.7639 (tp30) cc_final: 0.7233 (tp30) REVERT: Y 183 GLU cc_start: 0.7046 (tt0) cc_final: 0.6792 (tt0) outliers start: 48 outliers final: 28 residues processed: 333 average time/residue: 0.1339 time to fit residues: 66.1782 Evaluate side-chains 304 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 297 GLN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 0.0170 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN H 50 GLN ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN ** L 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 133 GLN ** N 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 GLN Z 8 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.161025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138183 restraints weight = 26647.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134533 restraints weight = 36953.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132295 restraints weight = 32973.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132907 restraints weight = 28496.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132591 restraints weight = 21364.506| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18425 Z= 0.132 Angle : 0.559 9.477 24949 Z= 0.288 Chirality : 0.040 0.219 3028 Planarity : 0.004 0.072 3122 Dihedral : 4.221 42.019 2543 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.96 % Allowed : 20.42 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.02 (0.19), residues: 2278 helix: 2.24 (0.14), residues: 1412 sheet: -1.27 (0.35), residues: 228 loop : -2.31 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 74 TYR 0.019 0.001 TYR Y 193 PHE 0.058 0.001 PHE I 546 TRP 0.016 0.001 TRP I 424 HIS 0.012 0.001 HIS Z 8 Details of bonding type rmsd covalent geometry : bond 0.00298 (18425) covalent geometry : angle 0.55942 (24949) hydrogen bonds : bond 0.03793 ( 1185) hydrogen bonds : angle 3.68601 ( 3528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 287 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 9 TRP cc_start: 0.5584 (m-10) cc_final: 0.5317 (m-10) REVERT: H 13 GLN cc_start: 0.6508 (mp10) cc_final: 0.6276 (mm-40) REVERT: H 125 MET cc_start: 0.7193 (tpp) cc_final: 0.6735 (tpp) REVERT: I 345 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7214 (tt) REVERT: I 440 MET cc_start: 0.8905 (mmm) cc_final: 0.8494 (mmm) REVERT: I 489 MET cc_start: 0.8033 (mmp) cc_final: 0.7307 (mmt) REVERT: I 569 MET cc_start: 0.6231 (ptm) cc_final: 0.5953 (ptp) REVERT: I 590 ASN cc_start: 0.7491 (t0) cc_final: 0.7273 (t0) REVERT: K 96 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7167 (tm-30) REVERT: L 233 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8327 (mp) REVERT: N 383 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6964 (mt-10) REVERT: O 280 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8123 (mtmt) REVERT: O 301 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8629 (mp) REVERT: P 126 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7819 (mm-30) REVERT: Q 335 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7043 (mpp) REVERT: U 253 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7203 (m-40) REVERT: U 299 MET cc_start: 0.8743 (tpp) cc_final: 0.8502 (mmt) REVERT: Y 153 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8177 (mtmm) REVERT: Y 183 GLU cc_start: 0.7042 (tt0) cc_final: 0.6794 (tt0) outliers start: 54 outliers final: 31 residues processed: 325 average time/residue: 0.1368 time to fit residues: 66.5442 Evaluate side-chains 313 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 276 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain I residue 593 TYR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain Q residue 354 LEU Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain U residue 263 LEU Chi-restraints excluded: chain Y residue 153 LYS Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 114 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 24 optimal weight: 0.0370 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 HIS Z 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.161204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140229 restraints weight = 26820.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.136942 restraints weight = 33965.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134964 restraints weight = 29720.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135617 restraints weight = 27871.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134993 restraints weight = 22179.713| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18425 Z= 0.130 Angle : 0.563 10.236 24949 Z= 0.288 Chirality : 0.039 0.208 3028 Planarity : 0.004 0.075 3122 Dihedral : 4.158 40.786 2543 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.36 % Allowed : 21.19 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.17 (0.19), residues: 2278 helix: 2.34 (0.14), residues: 1417 sheet: -1.15 (0.35), residues: 228 loop : -2.27 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 74 TYR 0.018 0.001 TYR Y 193 PHE 0.052 0.001 PHE I 546 TRP 0.018 0.001 TRP I 424 HIS 0.015 0.001 HIS Z 8 Details of bonding type rmsd covalent geometry : bond 0.00295 (18425) covalent geometry : angle 0.56262 (24949) hydrogen bonds : bond 0.03768 ( 1185) hydrogen bonds : angle 3.64370 ( 3528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 294 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: I 345 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7329 (tt) REVERT: I 542 MET cc_start: 0.5613 (tpp) cc_final: 0.5055 (tpp) REVERT: I 546 PHE cc_start: 0.6685 (m-80) cc_final: 0.6288 (m-80) REVERT: I 569 MET cc_start: 0.6229 (ptm) cc_final: 0.6012 (ptp) REVERT: I 590 ASN cc_start: 0.7495 (t0) cc_final: 0.7262 (t0) REVERT: K 103 MET cc_start: 0.8608 (tmm) cc_final: 0.8337 (tmm) REVERT: L 233 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8315 (mp) REVERT: N 383 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7205 (mt-10) REVERT: O 280 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8142 (mtmt) REVERT: O 301 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8624 (mp) REVERT: P 126 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7840 (mm-30) REVERT: U 253 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.7107 (m-40) REVERT: Y 15 GLU cc_start: 0.7537 (tp30) cc_final: 0.7069 (tp30) REVERT: Y 183 GLU cc_start: 0.7037 (tt0) cc_final: 0.6799 (tt0) outliers start: 43 outliers final: 28 residues processed: 324 average time/residue: 0.1396 time to fit residues: 67.6984 Evaluate side-chains 308 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 276 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain I residue 571 TYR Chi-restraints excluded: chain I residue 593 TYR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain U residue 263 LEU Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN Z 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.160291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138337 restraints weight = 26847.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134393 restraints weight = 32757.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132130 restraints weight = 25809.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131300 restraints weight = 27759.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131153 restraints weight = 21576.838| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18425 Z= 0.151 Angle : 0.584 9.656 24949 Z= 0.299 Chirality : 0.040 0.212 3028 Planarity : 0.004 0.067 3122 Dihedral : 4.174 40.267 2543 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.80 % Allowed : 21.62 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.21 (0.19), residues: 2278 helix: 2.37 (0.14), residues: 1421 sheet: -1.09 (0.36), residues: 228 loop : -2.29 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 74 TYR 0.023 0.001 TYR Y 91 PHE 0.040 0.001 PHE I 546 TRP 0.021 0.001 TRP I 424 HIS 0.019 0.001 HIS Z 8 Details of bonding type rmsd covalent geometry : bond 0.00355 (18425) covalent geometry : angle 0.58403 (24949) hydrogen bonds : bond 0.03849 ( 1185) hydrogen bonds : angle 3.68081 ( 3528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 345 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7279 (tt) REVERT: I 542 MET cc_start: 0.5714 (tpp) cc_final: 0.5076 (tpp) REVERT: I 546 PHE cc_start: 0.6875 (m-80) cc_final: 0.6385 (m-80) REVERT: I 590 ASN cc_start: 0.7484 (t0) cc_final: 0.7237 (t0) REVERT: L 233 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8331 (mp) REVERT: O 280 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8115 (mtmt) REVERT: O 301 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8659 (mp) REVERT: P 126 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7893 (mm-30) REVERT: Q 335 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6986 (mpp) REVERT: U 253 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7279 (m-40) REVERT: Y 123 MET cc_start: 0.7318 (mmm) cc_final: 0.6803 (mmp) REVERT: Y 183 GLU cc_start: 0.7118 (tt0) cc_final: 0.6889 (tt0) REVERT: Y 198 ASN cc_start: 0.6941 (t0) cc_final: 0.6620 (t0) outliers start: 51 outliers final: 35 residues processed: 327 average time/residue: 0.1374 time to fit residues: 67.3370 Evaluate side-chains 321 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain I residue 571 TYR Chi-restraints excluded: chain I residue 593 TYR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 348 TYR Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain Q residue 281 THR Chi-restraints excluded: chain Q residue 335 MET Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain U residue 263 LEU Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 113 optimal weight: 0.4980 chunk 186 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 200 optimal weight: 0.0070 chunk 138 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 467 GLN ** N 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.161845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135170 restraints weight = 26575.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131307 restraints weight = 40775.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128577 restraints weight = 29584.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129364 restraints weight = 28647.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130100 restraints weight = 22727.321| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 18425 Z= 0.126 Angle : 0.577 9.643 24949 Z= 0.295 Chirality : 0.039 0.202 3028 Planarity : 0.004 0.065 3122 Dihedral : 4.085 38.591 2543 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.25 % Allowed : 22.23 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.34 (0.19), residues: 2278 helix: 2.46 (0.14), residues: 1419 sheet: -0.95 (0.36), residues: 228 loop : -2.22 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 74 TYR 0.018 0.001 TYR Y 193 PHE 0.038 0.001 PHE I 546 TRP 0.025 0.001 TRP I 424 HIS 0.016 0.001 HIS Z 8 Details of bonding type rmsd covalent geometry : bond 0.00288 (18425) covalent geometry : angle 0.57748 (24949) hydrogen bonds : bond 0.03727 ( 1185) hydrogen bonds : angle 3.63698 ( 3528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 300 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 345 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7379 (tt) REVERT: I 489 MET cc_start: 0.7895 (mmp) cc_final: 0.7418 (mmp) REVERT: I 542 MET cc_start: 0.6271 (tpp) cc_final: 0.5515 (tpp) REVERT: I 546 PHE cc_start: 0.6973 (m-80) cc_final: 0.6451 (m-80) REVERT: I 590 ASN cc_start: 0.7545 (t0) cc_final: 0.7266 (t0) REVERT: K 103 MET cc_start: 0.8552 (tmm) cc_final: 0.8261 (tmm) REVERT: K 125 MET cc_start: 0.6514 (tpt) cc_final: 0.6153 (tpt) REVERT: L 233 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8218 (mp) REVERT: O 280 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8113 (mtmt) REVERT: O 301 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8623 (mp) REVERT: P 126 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7871 (mm-30) REVERT: U 253 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7192 (m-40) REVERT: U 299 MET cc_start: 0.8740 (mmt) cc_final: 0.8498 (tpp) REVERT: Y 15 GLU cc_start: 0.7637 (tp30) cc_final: 0.7136 (tp30) REVERT: Y 183 GLU cc_start: 0.7211 (tt0) cc_final: 0.6994 (tt0) REVERT: Y 198 ASN cc_start: 0.7083 (t0) cc_final: 0.6792 (t0) outliers start: 41 outliers final: 32 residues processed: 328 average time/residue: 0.1424 time to fit residues: 69.5025 Evaluate side-chains 319 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain I residue 571 TYR Chi-restraints excluded: chain I residue 593 TYR Chi-restraints excluded: chain I residue 610 PHE Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 385 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 301 LEU Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 274 MET Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 131 optimal weight: 0.0770 chunk 96 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 193 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 196 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.162426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139902 restraints weight = 26602.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136572 restraints weight = 33365.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134398 restraints weight = 27707.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135266 restraints weight = 26831.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134731 restraints weight = 20402.347| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18425 Z= 0.125 Angle : 0.587 10.128 24949 Z= 0.300 Chirality : 0.040 0.232 3028 Planarity : 0.004 0.064 3122 Dihedral : 4.025 37.313 2543 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.09 % Allowed : 22.89 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.44 (0.19), residues: 2278 helix: 2.52 (0.14), residues: 1417 sheet: -0.83 (0.36), residues: 228 loop : -2.18 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 74 TYR 0.020 0.001 TYR Y 91 PHE 0.037 0.001 PHE I 546 TRP 0.029 0.001 TRP I 424 HIS 0.007 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00285 (18425) covalent geometry : angle 0.58698 (24949) hydrogen bonds : bond 0.03677 ( 1185) hydrogen bonds : angle 3.60760 ( 3528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 345 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7352 (tt) REVERT: I 542 MET cc_start: 0.5743 (tpp) cc_final: 0.5369 (tpp) REVERT: I 546 PHE cc_start: 0.6681 (m-80) cc_final: 0.6201 (m-80) REVERT: K 125 MET cc_start: 0.6314 (tpt) cc_final: 0.5963 (tpt) REVERT: L 233 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8209 (mp) REVERT: O 280 LYS cc_start: 0.8533 (ttpt) cc_final: 0.8102 (mtmt) REVERT: P 126 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7884 (mm-30) REVERT: U 253 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.6917 (m-40) REVERT: U 299 MET cc_start: 0.8566 (mmt) cc_final: 0.8330 (tpp) REVERT: Y 123 MET cc_start: 0.6501 (mmp) cc_final: 0.6082 (mmp) REVERT: Y 198 ASN cc_start: 0.6680 (t0) cc_final: 0.6442 (t0) outliers start: 38 outliers final: 27 residues processed: 323 average time/residue: 0.1421 time to fit residues: 68.0167 Evaluate side-chains 312 residues out of total 2193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 561 LEU Chi-restraints excluded: chain I residue 571 TYR Chi-restraints excluded: chain I residue 593 TYR Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 393 ILE Chi-restraints excluded: chain N residue 399 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 310 VAL Chi-restraints excluded: chain O residue 313 ILE Chi-restraints excluded: chain O residue 319 VAL Chi-restraints excluded: chain O residue 323 GLU Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 276 ASN Chi-restraints excluded: chain P residue 348 TYR Chi-restraints excluded: chain P residue 361 CYS Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 253 ASN Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 103 GLN Chi-restraints excluded: chain Z residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 229 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 GLN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 GLN ** U 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.160100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130915 restraints weight = 26807.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130812 restraints weight = 35532.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131639 restraints weight = 31170.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131725 restraints weight = 21356.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131797 restraints weight = 21207.954| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18425 Z= 0.174 Angle : 0.630 9.531 24949 Z= 0.323 Chirality : 0.041 0.230 3028 Planarity : 0.004 0.067 3122 Dihedral : 4.176 37.475 2543 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.09 % Allowed : 23.38 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 1.33 (0.19), residues: 2278 helix: 2.46 (0.14), residues: 1412 sheet: -0.75 (0.36), residues: 235 loop : -2.29 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 74 TYR 0.028 0.002 TYR Y 91 PHE 0.034 0.002 PHE I 546 TRP 0.041 0.002 TRP I 424 HIS 0.008 0.001 HIS H 57 Details of bonding type rmsd covalent geometry : bond 0.00415 (18425) covalent geometry : angle 0.62970 (24949) hydrogen bonds : bond 0.03912 ( 1185) hydrogen bonds : angle 3.71839 ( 3528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3053.22 seconds wall clock time: 53 minutes 52.72 seconds (3232.72 seconds total)