Starting phenix.real_space_refine on Tue Aug 26 17:12:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itj_60868/08_2025/9itj_60868.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itj_60868/08_2025/9itj_60868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itj_60868/08_2025/9itj_60868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itj_60868/08_2025/9itj_60868.map" model { file = "/net/cci-nas-00/data/ceres_data/9itj_60868/08_2025/9itj_60868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itj_60868/08_2025/9itj_60868.cif" } resolution = 2.84 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 97 5.16 5 C 24951 2.51 5 N 6955 2.21 5 O 7461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39476 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3749 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 25, 'TRANS': 467} Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3793 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 26, 'TRANS': 471} Chain: "C" Number of atoms: 3948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3948 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 26, 'TRANS': 491} Chain: "D" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3593 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 438} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3593 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 438} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3608 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 440} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2215 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "H" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "I" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "J" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "K" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "O" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "P" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Q" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 509 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "R" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 990 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 123} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "T" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1827 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain breaks: 1 Chain: "U" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1223 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain: "V" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1230 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "X" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 772 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 590 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 3, 'GLN:plan1': 12, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 292 Chain: "Y" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 763 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 1, 'TRANS': 151} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 366 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 12, 'ASN:plan1': 4, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 289 Chain: "Z" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1148 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 734 Unresolved non-hydrogen angles: 960 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 9, 'PHE:plan': 32, 'ASP:plan': 3, 'ASN:plan1': 12, 'ARG:plan': 6, 'GLN:plan1': 3, 'TYR:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 380 Chain: "S" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 923 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 140} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "W" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 923 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 140} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.09, per 1000 atoms: 0.26 Number of scatterers: 39476 At special positions: 0 Unit cell: (133.92, 145.08, 245.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 97 16.00 P 9 15.00 Mg 3 11.99 O 7461 8.00 N 6955 7.00 C 24951 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: 3.74 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9880 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 35 sheets defined 59.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 278 through 292 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 387 through 408 removed outlier: 5.022A pdb=" N LYS A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.841A pdb=" N GLN A 412 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.507A pdb=" N ARG A 487 " --> pdb=" O HIS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 519 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.647A pdb=" N LEU B 110 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.590A pdb=" N GLN B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 246 through 260 removed outlier: 5.914A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.841A pdb=" N ALA B 300 " --> pdb=" O GLY B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.572A pdb=" N GLY B 324 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.836A pdb=" N ALA B 384 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 414 removed outlier: 3.930A pdb=" N GLY B 395 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LYS B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N PHE B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 435 Processing helix chain 'B' and resid 444 through 457 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 482 Processing helix chain 'B' and resid 483 through 493 removed outlier: 4.170A pdb=" N ARG B 487 " --> pdb=" O HIS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'C' and resid 5 through 12 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.505A pdb=" N LEU C 110 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 111 " --> pdb=" O GLN C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 111' Processing helix chain 'C' and resid 157 through 164 Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 208 through 222 Processing helix chain 'C' and resid 238 through 259 Proline residue: C 246 - end of helix removed outlier: 3.529A pdb=" N ILE C 256 " --> pdb=" O MET C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.573A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.560A pdb=" N LEU C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.577A pdb=" N ALA C 384 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.915A pdb=" N GLY C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 removed outlier: 3.810A pdb=" N ALA C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLN C 412 " --> pdb=" O ALA C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 436 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'C' and resid 467 through 482 removed outlier: 4.027A pdb=" N ALA C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 493 removed outlier: 4.119A pdb=" N ARG C 487 " --> pdb=" O HIS C 483 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 519 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 158 through 174 Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 194 through 201 Processing helix chain 'D' and resid 222 through 243 removed outlier: 4.689A pdb=" N GLY D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 243 " --> pdb=" O TYR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.573A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.607A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 379 through 388 removed outlier: 3.554A pdb=" N ILE D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 395 through 410 removed outlier: 3.533A pdb=" N THR D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 444 through 447 removed outlier: 3.949A pdb=" N HIS D 447 " --> pdb=" O GLU D 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 444 through 447' Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'E' and resid 191 through 201 Processing helix chain 'E' and resid 222 through 243 removed outlier: 4.841A pdb=" N GLY E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.647A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 388 removed outlier: 4.343A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE E 383 " --> pdb=" O ASP E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 392 Processing helix chain 'E' and resid 395 through 410 Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 443 removed outlier: 3.986A pdb=" N GLY E 443 " --> pdb=" O ARG E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 158 through 171 Processing helix chain 'F' and resid 193 through 201 Processing helix chain 'F' and resid 222 through 243 removed outlier: 4.755A pdb=" N GLY F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR F 239 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE F 240 " --> pdb=" O MET F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 269 Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 315 through 322 Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 345 through 349 removed outlier: 3.524A pdb=" N SER F 349 " --> pdb=" O PRO F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 380 removed outlier: 4.515A pdb=" N LEU F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR F 377 " --> pdb=" O VAL F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 388 through 392 removed outlier: 3.708A pdb=" N GLU F 391 " --> pdb=" O GLY F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 411 removed outlier: 3.937A pdb=" N SER F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 418 removed outlier: 3.892A pdb=" N GLN F 418 " --> pdb=" O THR F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.616A pdb=" N TYR F 454 " --> pdb=" O SER F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.550A pdb=" N VAL F 462 " --> pdb=" O ASP F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 59 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 64 through 68 removed outlier: 4.163A pdb=" N THR G 68 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 112 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 148 through 166 removed outlier: 4.098A pdb=" N ILE G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 203 removed outlier: 3.579A pdb=" N THR G 202 " --> pdb=" O ASP G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 286 Proline residue: G 222 - end of helix Processing helix chain 'H' and resid 3 through 38 removed outlier: 4.311A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix Processing helix chain 'H' and resid 41 through 70 removed outlier: 3.757A pdb=" N ILE H 51 " --> pdb=" O THR H 47 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE H 55 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU H 57 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 38 removed outlier: 3.944A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Proline residue: I 20 - end of helix removed outlier: 4.060A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 70 removed outlier: 3.748A pdb=" N LEU I 59 " --> pdb=" O PHE I 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 38 removed outlier: 3.637A pdb=" N VAL J 7 " --> pdb=" O GLY J 3 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Proline residue: J 20 - end of helix Processing helix chain 'J' and resid 41 through 72 Processing helix chain 'K' and resid 3 through 38 removed outlier: 4.477A pdb=" N GLY K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Proline residue: K 20 - end of helix Processing helix chain 'K' and resid 41 through 72 removed outlier: 3.621A pdb=" N THR K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE K 55 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 38 removed outlier: 4.326A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) Proline residue: L 20 - end of helix Processing helix chain 'L' and resid 41 through 73 removed outlier: 4.205A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY L 52 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 removed outlier: 4.384A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 41 through 72 removed outlier: 4.809A pdb=" N THR M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU M 59 " --> pdb=" O PHE M 55 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA M 60 " --> pdb=" O THR M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 17 through 38 removed outlier: 3.736A pdb=" N VAL N 22 " --> pdb=" O ILE N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 73 removed outlier: 3.917A pdb=" N TYR N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY N 71 " --> pdb=" O ALA N 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 3.514A pdb=" N VAL O 7 " --> pdb=" O GLY O 3 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Proline residue: O 20 - end of helix Processing helix chain 'O' and resid 41 through 72 removed outlier: 3.835A pdb=" N THR O 47 " --> pdb=" O ASN O 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.622A pdb=" N VAL P 7 " --> pdb=" O GLY P 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 38 Processing helix chain 'P' and resid 41 through 72 removed outlier: 3.870A pdb=" N PHE P 55 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE P 68 " --> pdb=" O LEU P 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.523A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Proline residue: Q 20 - end of helix Processing helix chain 'Q' and resid 41 through 72 removed outlier: 3.606A pdb=" N VAL Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA Q 60 " --> pdb=" O THR Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 100 removed outlier: 3.998A pdb=" N GLU R 98 " --> pdb=" O GLN R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 128 Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.954A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 99 removed outlier: 3.502A pdb=" N ASN T 82 " --> pdb=" O ARG T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 124 Proline residue: T 108 - end of helix Processing helix chain 'T' and resid 186 through 189 Processing helix chain 'T' and resid 190 through 214 removed outlier: 3.653A pdb=" N THR T 194 " --> pdb=" O ASP T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 266 removed outlier: 3.994A pdb=" N ILE T 233 " --> pdb=" O SER T 229 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE T 234 " --> pdb=" O PHE T 230 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU T 235 " --> pdb=" O VAL T 231 " (cutoff:3.500A) Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 273 through 304 Processing helix chain 'U' and resid 9 through 139 removed outlier: 5.884A pdb=" N ARG U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) Proline residue: U 32 - end of helix Processing helix chain 'U' and resid 140 through 147 Processing helix chain 'U' and resid 148 through 160 removed outlier: 3.663A pdb=" N ILE U 153 " --> pdb=" O HIS U 149 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 29 Processing helix chain 'V' and resid 29 through 113 Processing helix chain 'V' and resid 113 through 120 removed outlier: 4.026A pdb=" N ARG V 117 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 148 through 158 Processing helix chain 'X' and resid 7 through 122 Proline residue: X 32 - end of helix removed outlier: 3.936A pdb=" N SER X 122 " --> pdb=" O ILE X 118 " (cutoff:3.500A) Processing helix chain 'X' and resid 126 through 138 Processing helix chain 'X' and resid 149 through 155 removed outlier: 4.124A pdb=" N ALA X 154 " --> pdb=" O ASP X 150 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 148 Proline residue: Y 32 - end of helix removed outlier: 4.434A pdb=" N ARG Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 158 removed outlier: 3.854A pdb=" N ALA Y 154 " --> pdb=" O ALA Y 151 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU Y 157 " --> pdb=" O ALA Y 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 53 Processing helix chain 'Z' and resid 54 through 66 Processing helix chain 'Z' and resid 78 through 99 Processing helix chain 'Z' and resid 106 through 125 removed outlier: 3.608A pdb=" N LEU Z 125 " --> pdb=" O ASN Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 192 through 214 Processing helix chain 'Z' and resid 233 through 267 Proline residue: Z 243 - end of helix removed outlier: 3.546A pdb=" N LEU Z 267 " --> pdb=" O VAL Z 263 " (cutoff:3.500A) Processing helix chain 'Z' and resid 274 through 304 removed outlier: 3.529A pdb=" N GLY Z 278 " --> pdb=" O LEU Z 274 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 33 removed outlier: 4.505A pdb=" N LEU S 14 " --> pdb=" O LEU S 10 " (cutoff:3.500A) Proline residue: S 31 - end of helix Processing helix chain 'S' and resid 37 through 45 Processing helix chain 'S' and resid 50 through 63 removed outlier: 3.592A pdb=" N ASN S 55 " --> pdb=" O PRO S 51 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET S 60 " --> pdb=" O PHE S 56 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 79 removed outlier: 4.005A pdb=" N ASN S 70 " --> pdb=" O THR S 66 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA S 71 " --> pdb=" O GLY S 67 " (cutoff:3.500A) Proline residue: S 77 - end of helix Processing helix chain 'S' and resid 98 through 110 Processing helix chain 'S' and resid 143 through 154 Processing helix chain 'W' and resid 10 through 30 Processing helix chain 'W' and resid 39 through 45 removed outlier: 4.249A pdb=" N ALA W 43 " --> pdb=" O SER W 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL W 44 " --> pdb=" O GLU W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 64 removed outlier: 4.326A pdb=" N GLU W 63 " --> pdb=" O THR W 59 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 81 Proline residue: W 77 - end of helix removed outlier: 3.583A pdb=" N LEU W 80 " --> pdb=" O LEU W 76 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU W 81 " --> pdb=" O PRO W 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 98 through 109 Processing helix chain 'W' and resid 142 through 152 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.572A pdb=" N ALA A 79 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.572A pdb=" N ALA A 79 " --> pdb=" O LEU A 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 73 current: chain 'F' and resid 30 through 33 removed outlier: 6.639A pdb=" N LYS F 55 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLN F 48 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL F 53 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL F 14 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE F 10 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG F 16 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.947A pdb=" N LYS A 132 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.571A pdb=" N CYS A 200 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL A 231 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR A 202 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA A 233 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA A 204 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 276 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 205 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 275 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL A 333 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 277 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLU A 335 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.701A pdb=" N ALA B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 81 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA B 70 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 83 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLY B 68 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU B 52 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE B 53 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN B 28 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLY B 99 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 13.310A pdb=" N GLN B 26 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 removed outlier: 4.174A pdb=" N LYS B 132 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.587A pdb=" N ALA B 271 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 333 through 335 removed outlier: 6.457A pdb=" N ILE B 174 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AB3, first strand: chain 'C' and resid 27 through 28 removed outlier: 6.528A pdb=" N VAL S 91 " --> pdb=" O HIS S 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.793A pdb=" N SER C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU C 73 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA C 79 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG E 16 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE E 10 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL E 57 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL E 45 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 97 through 101 removed outlier: 6.143A pdb=" N ARG C 100 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 53 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU C 52 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 103 through 106 removed outlier: 4.367A pdb=" N LYS C 132 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.803A pdb=" N CYS C 200 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL C 231 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR C 202 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 333 through 336 removed outlier: 6.693A pdb=" N LEU C 173 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU C 359 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 175 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 261 through 263 Processing sheet with id=AC2, first strand: chain 'D' and resid 44 through 49 removed outlier: 5.572A pdb=" N VAL D 45 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL D 57 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL D 14 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE D 10 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG D 16 " --> pdb=" O GLN D 8 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AC4, first strand: chain 'D' and resid 79 through 81 Processing sheet with id=AC5, first strand: chain 'D' and resid 90 through 91 removed outlier: 6.664A pdb=" N SER D 178 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL D 215 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE D 180 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY D 217 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY D 182 " --> pdb=" O GLY D 217 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE D 177 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N PHE D 250 " --> pdb=" O PHE D 177 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL D 179 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP D 252 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA D 181 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE D 251 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N THR D 149 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS D 148 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE D 329 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA D 150 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 202 through 203 Processing sheet with id=AC7, first strand: chain 'E' and resid 79 through 81 Processing sheet with id=AC8, first strand: chain 'E' and resid 90 through 91 removed outlier: 6.507A pdb=" N PHE E 91 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN E 218 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER E 178 " --> pdb=" O VAL E 213 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL E 215 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE E 180 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY E 217 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLY E 182 " --> pdb=" O GLY E 217 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE E 177 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N MET E 303 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU E 249 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR E 149 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS E 148 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE E 329 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA E 150 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 129 through 130 removed outlier: 4.062A pdb=" N PHE E 143 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 202 through 203 Processing sheet with id=AD2, first strand: chain 'F' and resid 79 through 81 Processing sheet with id=AD3, first strand: chain 'F' and resid 90 through 91 removed outlier: 6.493A pdb=" N ILE F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N MET F 303 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU F 249 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR F 149 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL F 306 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE F 151 " --> pdb=" O VAL F 306 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 128 through 129 removed outlier: 3.831A pdb=" N GLN F 128 " --> pdb=" O ARG F 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 202 through 203 Processing sheet with id=AD6, first strand: chain 'G' and resid 138 through 140 removed outlier: 3.615A pdb=" N GLY G 138 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL G 79 " --> pdb=" O ASP G 117 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU G 81 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE G 121 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL G 83 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N TYR G 172 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA G 80 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE G 174 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU G 82 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N SER G 176 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL G 84 " --> pdb=" O SER G 176 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 208 through 209 removed outlier: 5.906A pdb=" N THR G 208 " --> pdb=" O MET R 41 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE R 43 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR R 80 " --> pdb=" O SER R 63 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLY R 65 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA R 78 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET R 67 " --> pdb=" O ILE R 76 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE R 76 " --> pdb=" O MET R 67 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL R 69 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL R 74 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N HIS R 4 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE R 76 " --> pdb=" O HIS R 4 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU R 6 " --> pdb=" O ILE R 76 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA R 78 " --> pdb=" O GLU R 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL R 8 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR R 80 " --> pdb=" O VAL R 8 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 13 through 15 removed outlier: 6.430A pdb=" N ILE R 7 " --> pdb=" O ILE R 14 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N HIS R 4 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE R 76 " --> pdb=" O HIS R 4 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU R 6 " --> pdb=" O ILE R 76 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA R 78 " --> pdb=" O GLU R 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL R 8 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR R 80 " --> pdb=" O VAL R 8 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL R 74 " --> pdb=" O VAL R 69 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL R 69 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE R 76 " --> pdb=" O MET R 67 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET R 67 " --> pdb=" O ILE R 76 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA R 78 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLY R 65 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR R 80 " --> pdb=" O SER R 63 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU R 48 " --> pdb=" O PRO R 25 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP R 50 " --> pdb=" O SER R 23 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE R 22 " --> pdb=" O ILE R 33 " (cutoff:3.500A) 2578 hydrogen bonds defined for protein. 7509 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: 9.76 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6899 1.32 - 1.44: 9411 1.44 - 1.57: 23520 1.57 - 1.69: 15 1.69 - 1.81: 182 Bond restraints: 40027 Sorted by residual: bond pdb=" N ASP S 123 " pdb=" CA ASP S 123 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.66e+01 bond pdb=" CA ALA F 260 " pdb=" CB ALA F 260 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.58e-02 4.01e+03 1.37e+01 bond pdb=" C PHE F 255 " pdb=" O PHE F 255 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.16e-02 7.43e+03 1.14e+01 bond pdb=" CA SER G 176 " pdb=" CB SER G 176 " ideal model delta sigma weight residual 1.527 1.484 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" C ALA F 260 " pdb=" O ALA F 260 " ideal model delta sigma weight residual 1.237 1.198 0.038 1.16e-02 7.43e+03 1.08e+01 ... (remaining 40022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 52500 1.91 - 3.81: 1647 3.81 - 5.72: 215 5.72 - 7.63: 36 7.63 - 9.54: 7 Bond angle restraints: 54405 Sorted by residual: angle pdb=" N ILE T 233 " pdb=" CA ILE T 233 " pdb=" C ILE T 233 " ideal model delta sigma weight residual 110.72 101.22 9.50 1.01e+00 9.80e-01 8.84e+01 angle pdb=" N ARG D 376 " pdb=" CA ARG D 376 " pdb=" C ARG D 376 " ideal model delta sigma weight residual 113.18 103.79 9.39 1.21e+00 6.83e-01 6.02e+01 angle pdb=" N GLU D 390 " pdb=" CA GLU D 390 " pdb=" C GLU D 390 " ideal model delta sigma weight residual 111.74 102.47 9.27 1.35e+00 5.49e-01 4.72e+01 angle pdb=" N ASP D 379 " pdb=" CA ASP D 379 " pdb=" C ASP D 379 " ideal model delta sigma weight residual 112.87 105.27 7.60 1.20e+00 6.94e-01 4.01e+01 angle pdb=" N LEU T 218 " pdb=" CA LEU T 218 " pdb=" C LEU T 218 " ideal model delta sigma weight residual 111.28 104.39 6.89 1.09e+00 8.42e-01 4.00e+01 ... (remaining 54400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 22344 17.79 - 35.57: 1499 35.57 - 53.36: 260 53.36 - 71.15: 64 71.15 - 88.93: 26 Dihedral angle restraints: 24193 sinusoidal: 8809 harmonic: 15384 Sorted by residual: dihedral pdb=" C ASN F 253 " pdb=" N ASN F 253 " pdb=" CA ASN F 253 " pdb=" CB ASN F 253 " ideal model delta harmonic sigma weight residual -122.60 -135.39 12.79 0 2.50e+00 1.60e-01 2.62e+01 dihedral pdb=" C PHE F 216 " pdb=" N PHE F 216 " pdb=" CA PHE F 216 " pdb=" CB PHE F 216 " ideal model delta harmonic sigma weight residual -122.60 -134.76 12.16 0 2.50e+00 1.60e-01 2.36e+01 dihedral pdb=" CA ARG F 372 " pdb=" C ARG F 372 " pdb=" N VAL F 373 " pdb=" CA VAL F 373 " ideal model delta harmonic sigma weight residual 180.00 157.56 22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 24190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 5975 0.096 - 0.192: 461 0.192 - 0.288: 33 0.288 - 0.384: 4 0.384 - 0.480: 2 Chirality restraints: 6475 Sorted by residual: chirality pdb=" CA PHE F 216 " pdb=" N PHE F 216 " pdb=" C PHE F 216 " pdb=" CB PHE F 216 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CA ASN F 253 " pdb=" N ASN F 253 " pdb=" C ASN F 253 " pdb=" CB ASN F 253 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CA ARG D 376 " pdb=" N ARG D 376 " pdb=" C ARG D 376 " pdb=" CB ARG D 376 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 6472 not shown) Planarity restraints: 7188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 374 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LEU F 374 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU F 374 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN F 375 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 146 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.62e+00 pdb=" NE ARG W 146 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG W 146 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG W 146 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG W 146 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 19 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO Q 20 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO Q 20 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Q 20 " 0.042 5.00e-02 4.00e+02 ... (remaining 7185 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 248 2.55 - 3.14: 33804 3.14 - 3.72: 64466 3.72 - 4.31: 87884 4.31 - 4.90: 146738 Nonbonded interactions: 333140 Sorted by model distance: nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 1.962 2.170 nonbonded pdb=" OG1 THR B 183 " pdb="MG MG B 602 " model vdw 1.975 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.004 2.170 nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.005 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 2.050 2.170 ... (remaining 333135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 519 or resid 601 through 602)) selection = (chain 'C' and (resid 27 through 519 or resid 601 through 602)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 3 through 468) } ncs_group { reference = chain 'H' selection = (chain 'I' and resid 2 through 72) selection = (chain 'J' and resid 2 through 72) selection = (chain 'K' and resid 2 through 72) selection = (chain 'L' and resid 2 through 72) selection = chain 'M' selection = (chain 'N' and resid 2 through 72) selection = (chain 'O' and resid 2 through 72) selection = (chain 'P' and resid 2 through 72) selection = (chain 'Q' and resid 2 through 72) } ncs_group { reference = chain 'S' selection = chain 'W' } ncs_group { reference = (chain 'T' and ((resid 31 through 41 and (name N or name CA or name C or name O \ or name CB )) or resid 42 or (resid 43 through 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 or (resid 46 through 78 and (name N or na \ me CA or name C or name O or name CB )) or resid 79 or (resid 80 through 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 or (resid 121 \ through 123 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 24 or (resid 125 through 127 and (name N or name CA or name C or name O or name \ CB )) or resid 128 or (resid 129 and (name N or name CA or name C or name O or n \ ame CB )) or resid 130 or (resid 131 through 132 and (name N or name CA or name \ C or name O or name CB )) or resid 133 or (resid 134 and (name N or name CA or n \ ame C or name O or name CB )) or resid 135 through 177 or (resid 178 through 208 \ and (name N or name CA or name C or name O or name CB )) or resid 209 or (resid \ 210 through 213 and (name N or name CA or name C or name O or name CB )) or res \ id 214 or (resid 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 or (resid 217 through 225 and (name N or name CA or name C or name O \ or name CB )) or resid 226 or (resid 227 through 231 and (name N or name CA or n \ ame C or name O or name CB )) or resid 232 or (resid 233 through 251 and (name N \ or name CA or name C or name O or name CB )) or resid 252 or (resid 253 through \ 256 and (name N or name CA or name C or name O or name CB )) or resid 257 or (r \ esid 258 through 277 and (name N or name CA or name C or name O or name CB )) or \ resid 278 or (resid 279 through 283 and (name N or name CA or name C or name O \ or name CB )) or resid 284 or (resid 285 through 304 and (name N or name CA or n \ ame C or name O or name CB )))) selection = chain 'Z' } ncs_group { reference = (chain 'U' and ((resid 8 through 140 and (name N or name CA or name C or name O \ or name CB )) or (resid 141 through 147 and (name N or name CA or name C or name \ O or name CB )) or resid 148 or (resid 149 through 158 and (name N or name CA o \ r name C or name O or name CB )))) selection = (chain 'V' and ((resid 8 through 140 and (name N or name CA or name C or name O \ or name CB )) or (resid 141 through 147 and (name N or name CA or name C or name \ O or name CB )) or resid 148 or (resid 149 through 158 and (name N or name CA o \ r name C or name O or name CB )))) selection = (chain 'X' and resid 8 through 158) selection = (chain 'Y' and resid 8 through 158) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 38.680 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 0.076 40027 Z= 0.289 Angle : 0.736 9.537 54405 Z= 0.476 Chirality : 0.053 0.480 6475 Planarity : 0.005 0.125 7188 Dihedral : 12.934 88.933 14313 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.72 % Allowed : 1.73 % Favored : 97.55 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.12), residues: 5361 helix: 1.18 (0.10), residues: 2900 sheet: -0.74 (0.23), residues: 521 loop : -1.05 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 427 TYR 0.030 0.001 TYR E 454 PHE 0.026 0.001 PHE Q 55 TRP 0.013 0.001 TRP A 471 HIS 0.011 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00474 (40027) covalent geometry : angle 0.73555 (54405) hydrogen bonds : bond 0.14377 ( 2568) hydrogen bonds : angle 6.40055 ( 7509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 1032 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 VAL cc_start: 0.8656 (p) cc_final: 0.8323 (m) REVERT: A 362 ASP cc_start: 0.8494 (m-30) cc_final: 0.8236 (m-30) REVERT: A 425 ILE cc_start: 0.7412 (mt) cc_final: 0.7130 (mp) REVERT: A 426 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7740 (pt0) REVERT: B 225 MET cc_start: 0.9005 (tpt) cc_final: 0.8375 (mmt) REVERT: B 390 MET cc_start: 0.8758 (tpp) cc_final: 0.8392 (tpp) REVERT: B 396 LYS cc_start: 0.8762 (tptp) cc_final: 0.8479 (tmtt) REVERT: B 400 GLU cc_start: 0.7751 (tp30) cc_final: 0.7333 (tp30) REVERT: B 437 GLN cc_start: 0.7991 (tt0) cc_final: 0.7732 (tt0) REVERT: C 179 GLN cc_start: 0.8558 (mt0) cc_final: 0.8357 (mt0) REVERT: C 448 GLN cc_start: 0.8675 (mt0) cc_final: 0.8463 (mt0) REVERT: C 480 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7566 (mmt90) REVERT: D 193 LEU cc_start: 0.7351 (mp) cc_final: 0.7118 (mt) REVERT: D 204 GLU cc_start: 0.6693 (pt0) cc_final: 0.6212 (pp20) REVERT: D 432 LYS cc_start: 0.8425 (mptt) cc_final: 0.8224 (mmmm) REVERT: D 439 ARG cc_start: 0.7391 (mtm110) cc_final: 0.7139 (mtp-110) REVERT: E 9 GLU cc_start: 0.7679 (tt0) cc_final: 0.7464 (tt0) REVERT: E 312 ASP cc_start: 0.8461 (m-30) cc_final: 0.8081 (m-30) REVERT: E 332 GLU cc_start: 0.6285 (tm-30) cc_final: 0.5992 (tm-30) REVERT: E 377 TYR cc_start: 0.7997 (t80) cc_final: 0.7761 (t80) REVERT: E 391 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8165 (mp0) REVERT: E 420 PHE cc_start: 0.7632 (m-80) cc_final: 0.7431 (m-80) REVERT: F 364 TYR cc_start: 0.7921 (t80) cc_final: 0.7672 (t80) REVERT: G 6 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6815 (tp30) REVERT: G 119 TYR cc_start: 0.7546 (m-80) cc_final: 0.7259 (m-80) REVERT: G 236 SER cc_start: 0.8972 (t) cc_final: 0.8657 (m) REVERT: H 33 GLN cc_start: 0.8577 (mt0) cc_final: 0.8228 (tp40) REVERT: J 53 ILE cc_start: 0.6994 (mt) cc_final: 0.6617 (mt) REVERT: K 50 PHE cc_start: 0.8013 (m-10) cc_final: 0.7765 (m-80) REVERT: M 62 PHE cc_start: 0.8616 (m-80) cc_final: 0.8303 (m-10) REVERT: N 2 GLU cc_start: 0.6371 (tp30) cc_final: 0.5292 (mt-10) REVERT: O 53 ILE cc_start: 0.8499 (mp) cc_final: 0.8025 (mp) REVERT: R 50 ASP cc_start: 0.8028 (m-30) cc_final: 0.6785 (m-30) REVERT: R 51 ILE cc_start: 0.7178 (mp) cc_final: 0.6951 (mp) REVERT: R 53 LYS cc_start: 0.9148 (tptp) cc_final: 0.8576 (tptp) REVERT: R 54 ASN cc_start: 0.8574 (m110) cc_final: 0.8362 (m-40) REVERT: R 120 ARG cc_start: 0.7935 (mtp-110) cc_final: 0.7706 (mtm-85) REVERT: T 129 VAL cc_start: 0.7819 (t) cc_final: 0.7379 (t) REVERT: T 208 TRP cc_start: 0.8282 (m100) cc_final: 0.7834 (m100) REVERT: T 255 PHE cc_start: 0.8322 (t80) cc_final: 0.7983 (t80) REVERT: T 280 GLU cc_start: 0.8515 (tp30) cc_final: 0.8230 (tp30) REVERT: T 289 LEU cc_start: 0.8984 (tp) cc_final: 0.8725 (tm) REVERT: U 65 TYR cc_start: 0.8533 (t80) cc_final: 0.8220 (t80) REVERT: U 112 GLN cc_start: 0.8566 (tt0) cc_final: 0.8041 (tm-30) REVERT: V 53 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8296 (mttt) REVERT: V 64 ASP cc_start: 0.8792 (m-30) cc_final: 0.8056 (m-30) REVERT: W 107 ARG cc_start: 0.8021 (ttp-110) cc_final: 0.7657 (ptm-80) outliers start: 27 outliers final: 15 residues processed: 1052 average time/residue: 0.6950 time to fit residues: 902.7551 Evaluate side-chains 648 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 633 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 28 ASN B 309 HIS C 26 GLN C 309 HIS ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 HIS E 29 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN G 190 GLN G 267 ASN H 33 GLN K 33 GLN O 33 GLN P 33 GLN T 223 ASN U 74 GLN S 151 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.079008 restraints weight = 70789.457| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.50 r_work: 0.2909 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 40027 Z= 0.245 Angle : 0.700 10.515 54405 Z= 0.370 Chirality : 0.049 0.255 6475 Planarity : 0.006 0.070 7188 Dihedral : 6.391 85.402 5945 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.92 % Allowed : 14.96 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.12), residues: 5361 helix: 1.43 (0.10), residues: 2907 sheet: -0.69 (0.23), residues: 530 loop : -1.01 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 103 TYR 0.030 0.002 TYR P 48 PHE 0.024 0.002 PHE T 61 TRP 0.012 0.002 TRP T 122 HIS 0.007 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00586 (40027) covalent geometry : angle 0.70028 (54405) hydrogen bonds : bond 0.05088 ( 2568) hydrogen bonds : angle 4.82465 ( 7509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 687 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.9342 (mt) cc_final: 0.9126 (mp) REVERT: A 87 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: A 106 VAL cc_start: 0.9150 (p) cc_final: 0.8802 (m) REVERT: A 177 ASP cc_start: 0.8589 (t0) cc_final: 0.8381 (t0) REVERT: A 362 ASP cc_start: 0.9048 (m-30) cc_final: 0.8809 (m-30) REVERT: A 380 ARG cc_start: 0.8539 (mpp80) cc_final: 0.8336 (mpp80) REVERT: A 513 LYS cc_start: 0.8572 (mmmt) cc_final: 0.8230 (mttm) REVERT: B 225 MET cc_start: 0.9493 (tpt) cc_final: 0.8974 (mmt) REVERT: B 390 MET cc_start: 0.9197 (tpp) cc_final: 0.8962 (tpp) REVERT: B 396 LYS cc_start: 0.8730 (tptp) cc_final: 0.8388 (tmtt) REVERT: B 400 GLU cc_start: 0.8323 (tp30) cc_final: 0.7790 (tp30) REVERT: B 403 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8346 (tp40) REVERT: B 407 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7913 (mp) REVERT: B 480 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8005 (mtp180) REVERT: C 161 ASP cc_start: 0.9045 (t0) cc_final: 0.8785 (m-30) REVERT: C 448 GLN cc_start: 0.8817 (mt0) cc_final: 0.8576 (mt0) REVERT: C 480 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.7962 (mtt90) REVERT: D 59 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8380 (mmm) REVERT: D 204 GLU cc_start: 0.7615 (pt0) cc_final: 0.6905 (pp20) REVERT: D 307 TYR cc_start: 0.8740 (t80) cc_final: 0.8475 (t80) REVERT: E 9 GLU cc_start: 0.8747 (tt0) cc_final: 0.8468 (tt0) REVERT: E 197 MET cc_start: 0.8680 (mmt) cc_final: 0.8344 (mpp) REVERT: E 221 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: E 332 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7154 (tm-30) REVERT: E 372 ARG cc_start: 0.9032 (ttp80) cc_final: 0.8739 (ttp80) REVERT: E 390 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8822 (mp0) REVERT: E 391 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8288 (mp0) REVERT: E 401 GLN cc_start: 0.8362 (tt0) cc_final: 0.7932 (mt0) REVERT: E 420 PHE cc_start: 0.7791 (m-80) cc_final: 0.7501 (m-80) REVERT: E 455 MET cc_start: 0.7982 (mmm) cc_final: 0.7753 (tpp) REVERT: F 185 GLU cc_start: 0.8385 (tp30) cc_final: 0.8123 (tp30) REVERT: F 287 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: F 350 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8580 (p) REVERT: F 364 TYR cc_start: 0.8735 (t80) cc_final: 0.8499 (t80) REVERT: G 6 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7204 (tm-30) REVERT: G 71 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6869 (tm-30) REVERT: G 209 TYR cc_start: 0.8536 (m-10) cc_final: 0.8218 (m-10) REVERT: G 236 SER cc_start: 0.9225 (t) cc_final: 0.8990 (p) REVERT: H 33 GLN cc_start: 0.8478 (mt0) cc_final: 0.8226 (mt0) REVERT: H 57 GLU cc_start: 0.7365 (mp0) cc_final: 0.6966 (mp0) REVERT: H 61 ILE cc_start: 0.8018 (mm) cc_final: 0.7805 (pp) REVERT: H 70 ILE cc_start: 0.6803 (mm) cc_final: 0.6337 (tt) REVERT: I 5 ASN cc_start: 0.7552 (p0) cc_final: 0.7306 (t0) REVERT: I 24 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8351 (pt) REVERT: I 33 GLN cc_start: 0.7513 (mm110) cc_final: 0.7185 (mm-40) REVERT: L 32 VAL cc_start: 0.8396 (t) cc_final: 0.8191 (p) REVERT: L 57 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8184 (mm-30) REVERT: M 35 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6786 (tp) REVERT: M 44 ARG cc_start: 0.6477 (ptp-110) cc_final: 0.5810 (ptm160) REVERT: O 61 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7530 (pp) REVERT: P 4 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.7031 (tp) REVERT: P 41 ILE cc_start: 0.8101 (pt) cc_final: 0.7878 (pp) REVERT: P 42 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7787 (pp20) REVERT: Q 44 ARG cc_start: 0.7024 (ptp90) cc_final: 0.6785 (pmm150) REVERT: Q 72 PHE cc_start: 0.8278 (m-80) cc_final: 0.8068 (m-80) REVERT: R 118 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8042 (mtmt) REVERT: R 120 ARG cc_start: 0.8299 (mtp-110) cc_final: 0.7963 (mtm-85) REVERT: T 33 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7644 (tp30) REVERT: T 89 GLU cc_start: 0.8721 (pt0) cc_final: 0.8271 (pt0) REVERT: T 96 ARG cc_start: 0.9276 (ptp90) cc_final: 0.8698 (ptp90) REVERT: T 102 TYR cc_start: 0.8761 (m-80) cc_final: 0.8273 (m-80) REVERT: T 122 TRP cc_start: 0.7404 (m100) cc_final: 0.7008 (m100) REVERT: T 195 PHE cc_start: 0.8971 (m-80) cc_final: 0.8703 (m-80) REVERT: T 255 PHE cc_start: 0.8889 (t80) cc_final: 0.8477 (t80) REVERT: U 15 LEU cc_start: 0.9129 (tm) cc_final: 0.8904 (pp) REVERT: U 65 TYR cc_start: 0.8058 (t80) cc_final: 0.7771 (t80) REVERT: U 112 GLN cc_start: 0.8641 (tt0) cc_final: 0.8011 (tm-30) REVERT: V 53 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8358 (mttt) REVERT: V 64 ASP cc_start: 0.8916 (m-30) cc_final: 0.8236 (m-30) outliers start: 147 outliers final: 41 residues processed: 763 average time/residue: 0.6700 time to fit residues: 635.9939 Evaluate side-chains 631 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 578 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain O residue 38 ASN Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 127 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 168 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 390 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 428 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 215 optimal weight: 0.0060 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 170 GLN A 458 ASN B 26 GLN B 28 ASN C 309 HIS ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 GLN R 54 ASN U 74 GLN S 151 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.132674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080507 restraints weight = 70574.265| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.53 r_work: 0.2935 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 40027 Z= 0.150 Angle : 0.625 13.028 54405 Z= 0.321 Chirality : 0.045 0.269 6475 Planarity : 0.005 0.073 7188 Dihedral : 6.109 81.511 5931 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.57 % Allowed : 17.60 % Favored : 78.82 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.12), residues: 5361 helix: 1.58 (0.10), residues: 2932 sheet: -0.72 (0.23), residues: 517 loop : -0.90 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 37 TYR 0.020 0.001 TYR T 207 PHE 0.020 0.001 PHE F 255 TRP 0.006 0.001 TRP T 208 HIS 0.005 0.001 HIS B 483 Details of bonding type rmsd covalent geometry : bond 0.00343 (40027) covalent geometry : angle 0.62483 (54405) hydrogen bonds : bond 0.04565 ( 2568) hydrogen bonds : angle 4.58258 ( 7509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 645 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: A 106 VAL cc_start: 0.9060 (p) cc_final: 0.8707 (m) REVERT: A 177 ASP cc_start: 0.8585 (t0) cc_final: 0.8364 (t0) REVERT: A 208 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7301 (ptm-80) REVERT: A 237 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: A 380 ARG cc_start: 0.8548 (mpp80) cc_final: 0.8303 (mpp80) REVERT: A 513 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8377 (mttm) REVERT: B 86 ASP cc_start: 0.8903 (p0) cc_final: 0.8416 (p0) REVERT: B 225 MET cc_start: 0.9548 (tpt) cc_final: 0.9119 (mmt) REVERT: B 396 LYS cc_start: 0.8709 (tptp) cc_final: 0.8435 (tmtt) REVERT: B 400 GLU cc_start: 0.8342 (tp30) cc_final: 0.7831 (tp30) REVERT: B 480 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8141 (mtp180) REVERT: C 480 ARG cc_start: 0.8692 (ttm-80) cc_final: 0.8034 (mtt90) REVERT: D 59 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8266 (mmm) REVERT: D 204 GLU cc_start: 0.7689 (pt0) cc_final: 0.6995 (pp20) REVERT: D 303 MET cc_start: 0.9577 (tmm) cc_final: 0.7421 (tmm) REVERT: D 419 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8752 (pp30) REVERT: E 9 GLU cc_start: 0.8674 (tt0) cc_final: 0.8439 (tt0) REVERT: E 169 ASN cc_start: 0.8969 (m-40) cc_final: 0.8748 (m110) REVERT: E 185 GLU cc_start: 0.8529 (tp30) cc_final: 0.8161 (tp30) REVERT: E 197 MET cc_start: 0.8693 (mmt) cc_final: 0.8374 (mpp) REVERT: E 221 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: E 332 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7253 (tm-30) REVERT: E 390 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8828 (mp0) REVERT: E 391 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8234 (mp0) REVERT: E 401 GLN cc_start: 0.8391 (tt0) cc_final: 0.8058 (mt0) REVERT: E 455 MET cc_start: 0.7914 (mmm) cc_final: 0.7703 (tpp) REVERT: F 203 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.6996 (p0) REVERT: F 206 THR cc_start: 0.7551 (OUTLIER) cc_final: 0.6452 (t) REVERT: F 283 THR cc_start: 0.8945 (m) cc_final: 0.8614 (p) REVERT: F 287 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: F 350 THR cc_start: 0.8946 (p) cc_final: 0.8652 (p) REVERT: F 364 TYR cc_start: 0.8797 (t80) cc_final: 0.8591 (t80) REVERT: G 71 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7161 (tm-30) REVERT: G 77 LYS cc_start: 0.8975 (ptpp) cc_final: 0.8666 (pmtt) REVERT: G 236 SER cc_start: 0.9259 (t) cc_final: 0.9039 (p) REVERT: H 15 LEU cc_start: 0.7404 (mm) cc_final: 0.7180 (tp) REVERT: H 33 GLN cc_start: 0.8532 (mt0) cc_final: 0.7901 (mm110) REVERT: H 57 GLU cc_start: 0.7358 (mp0) cc_final: 0.6954 (mp0) REVERT: H 61 ILE cc_start: 0.7990 (mm) cc_final: 0.7729 (pp) REVERT: I 33 GLN cc_start: 0.7412 (mm110) cc_final: 0.7068 (mm-40) REVERT: I 44 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7315 (ttt90) REVERT: I 50 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: L 57 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8340 (mm-30) REVERT: M 35 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.6862 (tp) REVERT: M 66 ILE cc_start: 0.3982 (mm) cc_final: 0.3710 (mp) REVERT: N 9 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.7075 (p) REVERT: P 4 LEU cc_start: 0.7250 (mt) cc_final: 0.7010 (tp) REVERT: Q 53 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7679 (mp) REVERT: Q 72 PHE cc_start: 0.8318 (m-80) cc_final: 0.8063 (m-80) REVERT: R 51 ILE cc_start: 0.7773 (mt) cc_final: 0.7310 (mt) REVERT: R 60 PHE cc_start: 0.5594 (m-80) cc_final: 0.5252 (m-80) REVERT: R 118 LYS cc_start: 0.8332 (mtpt) cc_final: 0.8059 (mtmt) REVERT: R 120 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.8048 (mtm-85) REVERT: T 33 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7607 (tp30) REVERT: T 89 GLU cc_start: 0.8762 (pt0) cc_final: 0.8353 (pt0) REVERT: T 102 TYR cc_start: 0.8704 (m-80) cc_final: 0.8390 (m-80) REVERT: T 122 TRP cc_start: 0.7585 (m100) cc_final: 0.7172 (m100) REVERT: T 195 PHE cc_start: 0.8974 (m-80) cc_final: 0.8715 (m-80) REVERT: T 255 PHE cc_start: 0.8889 (t80) cc_final: 0.8419 (t80) REVERT: T 277 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: T 296 TYR cc_start: 0.8609 (t80) cc_final: 0.8400 (t80) REVERT: U 12 ILE cc_start: 0.8016 (pt) cc_final: 0.7757 (pp) REVERT: U 15 LEU cc_start: 0.9103 (tm) cc_final: 0.8890 (pp) REVERT: U 65 TYR cc_start: 0.8096 (t80) cc_final: 0.7885 (t80) REVERT: U 74 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7933 (pp30) REVERT: U 112 GLN cc_start: 0.8670 (tt0) cc_final: 0.8039 (tm-30) REVERT: U 130 ASP cc_start: 0.9079 (t0) cc_final: 0.8722 (m-30) REVERT: V 53 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8481 (mtmm) REVERT: V 64 ASP cc_start: 0.8955 (m-30) cc_final: 0.8271 (m-30) REVERT: V 130 ASP cc_start: 0.9043 (m-30) cc_final: 0.8808 (m-30) REVERT: S 107 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.7857 (ptt90) outliers start: 134 outliers final: 36 residues processed: 723 average time/residue: 0.6491 time to fit residues: 591.5643 Evaluate side-chains 643 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 590 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 277 TYR Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 127 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 475 optimal weight: 30.0000 chunk 519 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 293 optimal weight: 9.9990 chunk 357 optimal weight: 7.9990 chunk 511 optimal weight: 40.0000 chunk 144 optimal weight: 0.6980 chunk 275 optimal weight: 0.6980 chunk 378 optimal weight: 30.0000 chunk 174 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN C 309 HIS ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN E 128 GLN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS G 190 GLN O 33 GLN U 97 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.128824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.077400 restraints weight = 70773.208| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.86 r_work: 0.2811 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 40027 Z= 0.275 Angle : 0.691 12.401 54405 Z= 0.360 Chirality : 0.048 0.264 6475 Planarity : 0.005 0.077 7188 Dihedral : 6.159 88.282 5926 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.32 % Allowed : 18.99 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.12), residues: 5361 helix: 1.46 (0.09), residues: 2953 sheet: -0.75 (0.23), residues: 554 loop : -0.94 (0.15), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 44 TYR 0.027 0.002 TYR O 48 PHE 0.023 0.002 PHE F 255 TRP 0.006 0.001 TRP T 208 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00657 (40027) covalent geometry : angle 0.69055 (54405) hydrogen bonds : bond 0.04717 ( 2568) hydrogen bonds : angle 4.60238 ( 7509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 611 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8195 (pm20) REVERT: A 177 ASP cc_start: 0.8610 (t0) cc_final: 0.8375 (t0) REVERT: A 237 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: A 513 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8391 (mmtm) REVERT: B 47 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8228 (pp30) REVERT: B 91 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8599 (tt0) REVERT: C 480 ARG cc_start: 0.8877 (ttm-80) cc_final: 0.8641 (ttm-80) REVERT: D 59 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8393 (mmm) REVERT: D 61 SER cc_start: 0.8859 (m) cc_final: 0.8516 (t) REVERT: D 196 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7448 (mm-30) REVERT: D 204 GLU cc_start: 0.7846 (pt0) cc_final: 0.7141 (pp20) REVERT: D 369 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: D 419 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8841 (pp30) REVERT: E 9 GLU cc_start: 0.8923 (tt0) cc_final: 0.8645 (tt0) REVERT: E 197 MET cc_start: 0.8765 (mmt) cc_final: 0.8423 (mpp) REVERT: E 221 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: E 259 GLN cc_start: 0.8345 (tt0) cc_final: 0.8067 (tt0) REVERT: E 390 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8860 (mp0) REVERT: E 391 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8293 (mp0) REVERT: E 401 GLN cc_start: 0.8404 (tt0) cc_final: 0.8094 (mt0) REVERT: E 432 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8350 (mptp) REVERT: F 126 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8761 (tm-30) REVERT: F 287 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8444 (mt-10) REVERT: F 335 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8636 (mm) REVERT: F 350 THR cc_start: 0.9069 (p) cc_final: 0.8867 (p) REVERT: G 6 GLU cc_start: 0.8130 (tp30) cc_final: 0.7775 (tp30) REVERT: G 71 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7005 (pm20) REVERT: G 77 LYS cc_start: 0.8984 (ptpp) cc_final: 0.8679 (pmtt) REVERT: H 33 GLN cc_start: 0.8603 (mt0) cc_final: 0.8335 (mt0) REVERT: H 57 GLU cc_start: 0.7408 (mp0) cc_final: 0.7138 (mp0) REVERT: H 61 ILE cc_start: 0.7939 (mm) cc_final: 0.7433 (pp) REVERT: H 64 LEU cc_start: 0.6220 (mp) cc_final: 0.5994 (mt) REVERT: H 70 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6160 (pp) REVERT: I 33 GLN cc_start: 0.7405 (mm110) cc_final: 0.7136 (mm110) REVERT: I 50 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: K 42 GLU cc_start: 0.7588 (pp20) cc_final: 0.7324 (pp20) REVERT: K 43 ASN cc_start: 0.8877 (p0) cc_final: 0.7896 (m-40) REVERT: L 33 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8242 (mm110) REVERT: L 70 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6623 (tt) REVERT: M 35 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.6968 (tp) REVERT: M 66 ILE cc_start: 0.4050 (mm) cc_final: 0.3796 (mp) REVERT: N 9 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7090 (p) REVERT: Q 72 PHE cc_start: 0.8279 (m-80) cc_final: 0.8039 (m-80) REVERT: R 51 ILE cc_start: 0.7917 (mt) cc_final: 0.7688 (mp) REVERT: R 53 LYS cc_start: 0.8604 (tptp) cc_final: 0.7776 (ptpp) REVERT: R 118 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8030 (mtmt) REVERT: R 120 ARG cc_start: 0.8553 (mtp-110) cc_final: 0.8250 (mtm-85) REVERT: T 33 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7565 (tp30) REVERT: T 89 GLU cc_start: 0.8855 (pt0) cc_final: 0.8522 (pt0) REVERT: T 102 TYR cc_start: 0.8748 (m-80) cc_final: 0.8337 (m-80) REVERT: T 122 TRP cc_start: 0.7845 (m100) cc_final: 0.7505 (m100) REVERT: T 206 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8697 (mm-30) REVERT: T 251 PHE cc_start: 0.8662 (t80) cc_final: 0.8020 (t80) REVERT: T 255 PHE cc_start: 0.8925 (t80) cc_final: 0.8449 (t80) REVERT: T 277 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: U 12 ILE cc_start: 0.8038 (pt) cc_final: 0.7785 (pp) REVERT: U 15 LEU cc_start: 0.9071 (tm) cc_final: 0.8863 (pp) REVERT: U 65 TYR cc_start: 0.8043 (t80) cc_final: 0.7824 (t80) REVERT: U 112 GLN cc_start: 0.8618 (tt0) cc_final: 0.7961 (tm-30) REVERT: U 121 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8534 (mm) REVERT: U 130 ASP cc_start: 0.9109 (t0) cc_final: 0.8760 (m-30) REVERT: V 53 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8490 (mtmm) REVERT: V 64 ASP cc_start: 0.8899 (m-30) cc_final: 0.8170 (m-30) REVERT: V 130 ASP cc_start: 0.9082 (m-30) cc_final: 0.8845 (m-30) REVERT: S 107 ARG cc_start: 0.8532 (ttp-110) cc_final: 0.8269 (ttp-110) REVERT: S 152 ARG cc_start: 0.8515 (tpm170) cc_final: 0.8190 (tmm160) REVERT: W 146 ARG cc_start: 0.8197 (ptp-110) cc_final: 0.7994 (mtm110) outliers start: 162 outliers final: 63 residues processed: 714 average time/residue: 0.6753 time to fit residues: 601.2960 Evaluate side-chains 643 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 561 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 419 GLN Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 399 THR Chi-restraints excluded: chain E residue 432 LYS Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 335 ILE Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 277 TYR Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain U residue 88 LYS Chi-restraints excluded: chain U residue 121 LEU Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain V residue 149 HIS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain W residue 105 ILE Chi-restraints excluded: chain W residue 127 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 437 optimal weight: 10.0000 chunk 523 optimal weight: 40.0000 chunk 131 optimal weight: 0.0770 chunk 341 optimal weight: 8.9990 chunk 203 optimal weight: 0.5980 chunk 183 optimal weight: 0.0470 chunk 242 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN ** H 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 GLN P 33 GLN ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 287 GLN U 74 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.132049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080619 restraints weight = 69388.745| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.73 r_work: 0.2888 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 40027 Z= 0.138 Angle : 0.620 12.432 54405 Z= 0.319 Chirality : 0.045 0.372 6475 Planarity : 0.005 0.072 7188 Dihedral : 5.943 83.170 5926 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.52 % Allowed : 21.42 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.12), residues: 5361 helix: 1.66 (0.10), residues: 2928 sheet: -0.79 (0.22), residues: 574 loop : -0.87 (0.15), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 44 TYR 0.021 0.001 TYR T 207 PHE 0.022 0.001 PHE U 23 TRP 0.005 0.001 TRP T 208 HIS 0.005 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00316 (40027) covalent geometry : angle 0.61993 (54405) hydrogen bonds : bond 0.04282 ( 2568) hydrogen bonds : angle 4.42858 ( 7509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 610 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: A 177 ASP cc_start: 0.8569 (t0) cc_final: 0.8325 (t0) REVERT: A 237 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: A 380 ARG cc_start: 0.8814 (mpp80) cc_final: 0.8338 (mtt-85) REVERT: A 459 TYR cc_start: 0.8309 (m-80) cc_final: 0.7914 (m-10) REVERT: A 513 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8592 (mmtm) REVERT: B 47 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8218 (pp30) REVERT: B 86 ASP cc_start: 0.8903 (p0) cc_final: 0.8401 (p0) REVERT: C 480 ARG cc_start: 0.8915 (ttm-80) cc_final: 0.8706 (ttm-80) REVERT: D 369 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: E 9 GLU cc_start: 0.8830 (tt0) cc_final: 0.8554 (tt0) REVERT: E 192 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: E 197 MET cc_start: 0.8743 (mmt) cc_final: 0.8457 (mpp) REVERT: E 221 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: E 259 GLN cc_start: 0.8360 (tt0) cc_final: 0.8082 (tt0) REVERT: E 390 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8868 (mp0) REVERT: E 391 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8208 (mp0) REVERT: E 401 GLN cc_start: 0.8398 (tt0) cc_final: 0.8138 (mt0) REVERT: E 432 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8415 (mptp) REVERT: F 126 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8719 (tm-30) REVERT: F 197 MET cc_start: 0.8772 (mmm) cc_final: 0.7849 (mtm) REVERT: F 203 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7141 (p0) REVERT: F 234 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8934 (mm) REVERT: F 287 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8359 (mt-10) REVERT: F 297 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8480 (ttp-170) REVERT: G 6 GLU cc_start: 0.8012 (tp30) cc_final: 0.7644 (tp30) REVERT: G 71 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7162 (pm20) REVERT: G 77 LYS cc_start: 0.9031 (ptpp) cc_final: 0.8751 (pmtt) REVERT: G 112 MET cc_start: 0.8959 (mmp) cc_final: 0.8377 (mtt) REVERT: G 168 TYR cc_start: 0.7649 (m-80) cc_final: 0.6585 (m-80) REVERT: G 172 TYR cc_start: 0.8376 (m-80) cc_final: 0.8155 (m-80) REVERT: G 184 GLN cc_start: 0.8669 (mp-120) cc_final: 0.8430 (mp10) REVERT: G 214 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7210 (pp20) REVERT: H 33 GLN cc_start: 0.8558 (mt0) cc_final: 0.8311 (mt0) REVERT: H 48 TYR cc_start: 0.8296 (m-80) cc_final: 0.8087 (m-80) REVERT: H 57 GLU cc_start: 0.7406 (mp0) cc_final: 0.7088 (mp0) REVERT: H 61 ILE cc_start: 0.8017 (mm) cc_final: 0.7784 (pp) REVERT: I 33 GLN cc_start: 0.7556 (mm110) cc_final: 0.7342 (mm110) REVERT: I 42 GLU cc_start: 0.8142 (tt0) cc_final: 0.7937 (tm-30) REVERT: I 50 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: K 42 GLU cc_start: 0.7514 (pp20) cc_final: 0.7270 (pp20) REVERT: K 43 ASN cc_start: 0.8880 (p0) cc_final: 0.7914 (m-40) REVERT: L 33 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8266 (mm110) REVERT: L 70 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6676 (tt) REVERT: M 66 ILE cc_start: 0.3986 (mm) cc_final: 0.3728 (mp) REVERT: N 9 THR cc_start: 0.7213 (OUTLIER) cc_final: 0.6968 (p) REVERT: N 61 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8279 (pp) REVERT: Q 57 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7291 (mt-10) REVERT: Q 72 PHE cc_start: 0.8253 (m-80) cc_final: 0.7997 (m-80) REVERT: R 42 THR cc_start: 0.8972 (p) cc_final: 0.8648 (t) REVERT: R 53 LYS cc_start: 0.8527 (tptp) cc_final: 0.8014 (ptpp) REVERT: R 111 ASP cc_start: 0.8282 (m-30) cc_final: 0.8057 (m-30) REVERT: R 118 LYS cc_start: 0.8411 (mtpt) cc_final: 0.8027 (mtmt) REVERT: R 120 ARG cc_start: 0.8516 (mtp-110) cc_final: 0.8225 (mtm-85) REVERT: T 33 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7590 (tp30) REVERT: T 89 GLU cc_start: 0.8824 (pt0) cc_final: 0.8463 (pt0) REVERT: T 102 TYR cc_start: 0.8730 (m-80) cc_final: 0.8313 (m-80) REVERT: T 122 TRP cc_start: 0.7883 (m100) cc_final: 0.7397 (m100) REVERT: T 251 PHE cc_start: 0.8663 (t80) cc_final: 0.8024 (t80) REVERT: T 255 PHE cc_start: 0.8912 (t80) cc_final: 0.8460 (t80) REVERT: T 277 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: T 296 TYR cc_start: 0.8568 (t80) cc_final: 0.8344 (t80) REVERT: U 12 ILE cc_start: 0.8055 (pt) cc_final: 0.7787 (pp) REVERT: U 15 LEU cc_start: 0.9077 (tm) cc_final: 0.8867 (pp) REVERT: U 74 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8371 (pp30) REVERT: U 112 GLN cc_start: 0.8648 (tt0) cc_final: 0.8068 (tm-30) REVERT: U 130 ASP cc_start: 0.9117 (t0) cc_final: 0.8777 (m-30) REVERT: U 150 ASP cc_start: 0.8692 (m-30) cc_final: 0.8463 (m-30) REVERT: V 64 ASP cc_start: 0.8920 (m-30) cc_final: 0.8173 (m-30) REVERT: V 130 ASP cc_start: 0.9121 (m-30) cc_final: 0.8868 (m-30) REVERT: S 104 ARG cc_start: 0.9143 (mtp85) cc_final: 0.8751 (ttm110) REVERT: W 107 ARG cc_start: 0.8732 (tmm160) cc_final: 0.8393 (ptm-80) REVERT: W 108 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8593 (tm-30) REVERT: W 112 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.5889 (ptp90) REVERT: W 146 ARG cc_start: 0.8145 (ptp-110) cc_final: 0.7652 (mtm110) outliers start: 132 outliers final: 55 residues processed: 692 average time/residue: 0.5786 time to fit residues: 503.1909 Evaluate side-chains 643 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 570 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 432 LYS Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain Q residue 50 PHE Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 96 ARG Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 277 TYR Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain V residue 149 HIS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 105 ILE Chi-restraints excluded: chain W residue 112 ARG Chi-restraints excluded: chain W residue 127 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 186 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 350 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 322 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 47 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 GLN O 33 GLN P 33 GLN U 74 GLN ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.129995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.077439 restraints weight = 70343.679| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.57 r_work: 0.2854 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 40027 Z= 0.195 Angle : 0.646 12.160 54405 Z= 0.332 Chirality : 0.046 0.383 6475 Planarity : 0.005 0.073 7188 Dihedral : 5.919 85.764 5925 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.95 % Allowed : 21.71 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.12), residues: 5361 helix: 1.68 (0.10), residues: 2939 sheet: -0.67 (0.22), residues: 575 loop : -0.86 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 107 TYR 0.024 0.001 TYR E 364 PHE 0.020 0.001 PHE F 255 TRP 0.007 0.001 TRP T 208 HIS 0.010 0.001 HIS U 149 Details of bonding type rmsd covalent geometry : bond 0.00464 (40027) covalent geometry : angle 0.64620 (54405) hydrogen bonds : bond 0.04345 ( 2568) hydrogen bonds : angle 4.39828 ( 7509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 591 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8666 (pp30) cc_final: 0.8434 (pp30) REVERT: A 64 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: A 177 ASP cc_start: 0.8606 (t0) cc_final: 0.8342 (t0) REVERT: A 237 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: A 380 ARG cc_start: 0.8859 (mpp80) cc_final: 0.8369 (mtm-85) REVERT: A 403 GLN cc_start: 0.8812 (mt0) cc_final: 0.8378 (mt0) REVERT: A 459 TYR cc_start: 0.8189 (m-80) cc_final: 0.7925 (m-10) REVERT: A 513 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8616 (mmtm) REVERT: B 47 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8316 (pp30) REVERT: C 480 ARG cc_start: 0.8928 (ttm-80) cc_final: 0.8701 (ttm-80) REVERT: D 61 SER cc_start: 0.8969 (m) cc_final: 0.8643 (t) REVERT: D 369 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8339 (mp0) REVERT: E 9 GLU cc_start: 0.8823 (tt0) cc_final: 0.8557 (tt0) REVERT: E 197 MET cc_start: 0.8772 (mmt) cc_final: 0.8494 (mpp) REVERT: E 221 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: E 259 GLN cc_start: 0.8315 (tt0) cc_final: 0.8039 (tt0) REVERT: E 390 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8874 (mp0) REVERT: E 391 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8201 (mp0) REVERT: E 401 GLN cc_start: 0.8406 (tt0) cc_final: 0.8160 (mt0) REVERT: E 432 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8451 (mptp) REVERT: F 126 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8734 (tm-30) REVERT: F 197 MET cc_start: 0.8800 (mmm) cc_final: 0.7888 (mtm) REVERT: F 203 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7199 (p0) REVERT: F 234 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8890 (mm) REVERT: F 287 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8431 (mt-10) REVERT: F 297 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8485 (ttp-170) REVERT: G 6 GLU cc_start: 0.7999 (tp30) cc_final: 0.7611 (tp30) REVERT: G 71 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7313 (pm20) REVERT: G 77 LYS cc_start: 0.9026 (ptpp) cc_final: 0.8756 (pmtt) REVERT: G 112 MET cc_start: 0.8971 (mmp) cc_final: 0.8394 (mtt) REVERT: G 213 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8409 (mt-10) REVERT: G 214 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7248 (tm-30) REVERT: H 33 GLN cc_start: 0.8611 (mt0) cc_final: 0.8351 (mt0) REVERT: H 37 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8394 (ttm110) REVERT: I 33 GLN cc_start: 0.7534 (mm110) cc_final: 0.7325 (mm110) REVERT: I 50 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: K 42 GLU cc_start: 0.7551 (pp20) cc_final: 0.7304 (pp20) REVERT: K 43 ASN cc_start: 0.8872 (p0) cc_final: 0.7944 (m-40) REVERT: L 33 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8300 (mm110) REVERT: L 68 PHE cc_start: 0.7578 (m-80) cc_final: 0.6873 (m-80) REVERT: L 70 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6757 (tt) REVERT: M 62 PHE cc_start: 0.8548 (m-10) cc_final: 0.7734 (t80) REVERT: M 66 ILE cc_start: 0.4035 (mm) cc_final: 0.3689 (mp) REVERT: N 9 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.6802 (p) REVERT: N 61 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8298 (pp) REVERT: P 44 ARG cc_start: 0.7501 (ppp80) cc_final: 0.7181 (ppp80) REVERT: Q 72 PHE cc_start: 0.8297 (m-80) cc_final: 0.8047 (m-80) REVERT: R 42 THR cc_start: 0.9016 (p) cc_final: 0.8637 (t) REVERT: R 53 LYS cc_start: 0.8541 (tptp) cc_final: 0.8112 (ptpp) REVERT: R 111 ASP cc_start: 0.8299 (m-30) cc_final: 0.8098 (m-30) REVERT: R 120 ARG cc_start: 0.8550 (mtp-110) cc_final: 0.8264 (mtm-85) REVERT: T 33 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7554 (tp30) REVERT: T 89 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: T 102 TYR cc_start: 0.8753 (m-80) cc_final: 0.8273 (m-80) REVERT: T 122 TRP cc_start: 0.8040 (m100) cc_final: 0.7658 (m100) REVERT: T 190 ASP cc_start: 0.7268 (m-30) cc_final: 0.7031 (m-30) REVERT: T 206 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8329 (mp0) REVERT: T 251 PHE cc_start: 0.8818 (t80) cc_final: 0.8297 (t80) REVERT: T 255 PHE cc_start: 0.8933 (t80) cc_final: 0.8474 (t80) REVERT: T 277 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: T 296 TYR cc_start: 0.8597 (t80) cc_final: 0.8356 (t80) REVERT: U 12 ILE cc_start: 0.8082 (pt) cc_final: 0.7789 (pp) REVERT: U 15 LEU cc_start: 0.9101 (tm) cc_final: 0.8873 (pp) REVERT: U 74 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8402 (pp30) REVERT: U 112 GLN cc_start: 0.8646 (tt0) cc_final: 0.7995 (tm-30) REVERT: U 130 ASP cc_start: 0.9107 (t0) cc_final: 0.8753 (m-30) REVERT: V 64 ASP cc_start: 0.8850 (m-30) cc_final: 0.8358 (m-30) REVERT: V 130 ASP cc_start: 0.9096 (m-30) cc_final: 0.8836 (m-30) REVERT: S 104 ARG cc_start: 0.9138 (mtp85) cc_final: 0.8767 (ttm110) REVERT: S 107 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8377 (ttp-110) REVERT: S 152 ARG cc_start: 0.8451 (tpm170) cc_final: 0.8156 (tmm160) REVERT: W 107 ARG cc_start: 0.8667 (tmm160) cc_final: 0.8342 (ptm-80) REVERT: W 108 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8612 (tm-30) REVERT: W 112 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.5941 (ptp90) REVERT: W 146 ARG cc_start: 0.8150 (ptp-110) cc_final: 0.7681 (mtm110) outliers start: 148 outliers final: 70 residues processed: 685 average time/residue: 0.5966 time to fit residues: 512.4735 Evaluate side-chains 658 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 569 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain E residue 432 LYS Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 96 ARG Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 277 TYR Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain U residue 78 LYS Chi-restraints excluded: chain U residue 88 LYS Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain V residue 149 HIS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 105 ILE Chi-restraints excluded: chain W residue 112 ARG Chi-restraints excluded: chain W residue 127 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 398 optimal weight: 0.0980 chunk 334 optimal weight: 5.9990 chunk 515 optimal weight: 7.9990 chunk 461 optimal weight: 20.0000 chunk 7 optimal weight: 0.0770 chunk 364 optimal weight: 6.9990 chunk 384 optimal weight: 4.9990 chunk 407 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 408 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN O 33 GLN U 74 GLN ** U 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.079012 restraints weight = 70122.535| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.55 r_work: 0.2885 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 40027 Z= 0.145 Angle : 0.640 12.694 54405 Z= 0.326 Chirality : 0.046 0.435 6475 Planarity : 0.005 0.070 7188 Dihedral : 5.850 84.266 5925 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.33 % Allowed : 22.97 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.12), residues: 5361 helix: 1.69 (0.10), residues: 2947 sheet: -0.66 (0.22), residues: 568 loop : -0.87 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 37 TYR 0.027 0.001 TYR E 364 PHE 0.023 0.001 PHE U 23 TRP 0.005 0.001 TRP T 208 HIS 0.004 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00340 (40027) covalent geometry : angle 0.63993 (54405) hydrogen bonds : bond 0.04168 ( 2568) hydrogen bonds : angle 4.34800 ( 7509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 605 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8600 (pp30) cc_final: 0.8311 (pp30) REVERT: A 64 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: A 177 ASP cc_start: 0.8553 (t0) cc_final: 0.8279 (t0) REVERT: A 237 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: A 380 ARG cc_start: 0.8818 (mpp80) cc_final: 0.8343 (mtt-85) REVERT: A 513 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8572 (mmtm) REVERT: B 86 ASP cc_start: 0.8834 (p0) cc_final: 0.8299 (p0) REVERT: C 480 ARG cc_start: 0.8892 (ttm-80) cc_final: 0.8680 (ttm-80) REVERT: D 369 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: E 9 GLU cc_start: 0.8766 (tt0) cc_final: 0.8483 (tt0) REVERT: E 197 MET cc_start: 0.8744 (mmt) cc_final: 0.8487 (mpp) REVERT: E 221 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: E 259 GLN cc_start: 0.8213 (tt0) cc_final: 0.7940 (tt0) REVERT: E 390 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8879 (mp0) REVERT: E 391 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8155 (mp0) REVERT: E 401 GLN cc_start: 0.8385 (tt0) cc_final: 0.8133 (mt0) REVERT: F 15 ILE cc_start: 0.8971 (mt) cc_final: 0.8754 (pp) REVERT: F 126 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8665 (tm-30) REVERT: F 197 MET cc_start: 0.8705 (mmm) cc_final: 0.7787 (mtm) REVERT: F 234 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8779 (mm) REVERT: F 285 MET cc_start: 0.8457 (mmt) cc_final: 0.8179 (tpt) REVERT: F 287 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: F 297 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8423 (ttp-170) REVERT: G 6 GLU cc_start: 0.7871 (tp30) cc_final: 0.7537 (tp30) REVERT: G 71 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7288 (pm20) REVERT: G 77 LYS cc_start: 0.9051 (ptpp) cc_final: 0.8758 (pmtt) REVERT: G 213 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8426 (mt-10) REVERT: G 214 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7235 (tm-30) REVERT: G 231 GLN cc_start: 0.8622 (mt0) cc_final: 0.8401 (mm110) REVERT: H 33 GLN cc_start: 0.8569 (mt0) cc_final: 0.8316 (mt0) REVERT: H 48 TYR cc_start: 0.7925 (m-80) cc_final: 0.7516 (t80) REVERT: I 24 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8336 (pt) REVERT: J 48 TYR cc_start: 0.8088 (m-80) cc_final: 0.7648 (m-80) REVERT: K 43 ASN cc_start: 0.8860 (p0) cc_final: 0.7942 (m-40) REVERT: K 50 PHE cc_start: 0.8269 (m-80) cc_final: 0.7940 (m-80) REVERT: L 33 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8062 (mm-40) REVERT: L 49 MET cc_start: 0.7717 (ptm) cc_final: 0.7463 (ppp) REVERT: L 70 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6685 (tt) REVERT: M 62 PHE cc_start: 0.8471 (m-80) cc_final: 0.7721 (t80) REVERT: M 66 ILE cc_start: 0.3959 (mm) cc_final: 0.3595 (mp) REVERT: N 9 THR cc_start: 0.7000 (OUTLIER) cc_final: 0.6699 (p) REVERT: N 61 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8287 (pp) REVERT: Q 72 PHE cc_start: 0.8297 (m-80) cc_final: 0.8071 (m-80) REVERT: R 42 THR cc_start: 0.8971 (p) cc_final: 0.8605 (t) REVERT: R 53 LYS cc_start: 0.8549 (tptp) cc_final: 0.8084 (ptpp) REVERT: R 111 ASP cc_start: 0.8377 (m-30) cc_final: 0.8131 (m-30) REVERT: R 120 ARG cc_start: 0.8544 (mtp-110) cc_final: 0.8242 (mtm-85) REVERT: T 33 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7537 (tp30) REVERT: T 89 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: T 102 TYR cc_start: 0.8760 (m-80) cc_final: 0.8251 (m-80) REVERT: T 122 TRP cc_start: 0.7965 (m100) cc_final: 0.7569 (m100) REVERT: T 190 ASP cc_start: 0.7308 (m-30) cc_final: 0.7086 (m-30) REVERT: T 251 PHE cc_start: 0.8822 (t80) cc_final: 0.8316 (t80) REVERT: T 255 PHE cc_start: 0.8918 (t80) cc_final: 0.8478 (t80) REVERT: T 277 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: T 296 TYR cc_start: 0.8608 (t80) cc_final: 0.8344 (t80) REVERT: U 12 ILE cc_start: 0.8107 (pt) cc_final: 0.7816 (pp) REVERT: U 15 LEU cc_start: 0.9084 (tm) cc_final: 0.8854 (pp) REVERT: U 50 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7727 (t70) REVERT: U 74 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8369 (pp30) REVERT: U 112 GLN cc_start: 0.8637 (tt0) cc_final: 0.8050 (tm-30) REVERT: U 130 ASP cc_start: 0.9098 (t0) cc_final: 0.8765 (m-30) REVERT: V 64 ASP cc_start: 0.8835 (m-30) cc_final: 0.8450 (m-30) REVERT: V 130 ASP cc_start: 0.9079 (m-30) cc_final: 0.8819 (m-30) REVERT: S 104 ARG cc_start: 0.9131 (mtp85) cc_final: 0.8754 (ttm110) REVERT: S 107 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.8348 (ttp-110) REVERT: W 107 ARG cc_start: 0.8714 (tmm160) cc_final: 0.8398 (ptm-80) REVERT: W 108 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8612 (tm-30) REVERT: W 112 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.5955 (ptp90) REVERT: W 146 ARG cc_start: 0.8185 (ptp-110) cc_final: 0.7725 (mtm110) outliers start: 125 outliers final: 64 residues processed: 680 average time/residue: 0.5762 time to fit residues: 491.7356 Evaluate side-chains 659 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 578 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 376 ARG Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 96 ARG Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 277 TYR Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain U residue 50 ASP Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain U residue 88 LYS Chi-restraints excluded: chain U residue 121 LEU Chi-restraints excluded: chain U residue 126 SER Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain V residue 149 HIS Chi-restraints excluded: chain W residue 105 ILE Chi-restraints excluded: chain W residue 112 ARG Chi-restraints excluded: chain W residue 127 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 393 optimal weight: 0.0970 chunk 209 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 chunk 366 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 294 optimal weight: 10.0000 chunk 176 optimal weight: 0.0980 chunk 263 optimal weight: 0.9980 chunk 307 optimal weight: 0.0050 chunk 117 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 GLN U 74 GLN ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.132563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.080344 restraints weight = 70101.082| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.56 r_work: 0.2911 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 40027 Z= 0.135 Angle : 0.644 12.144 54405 Z= 0.328 Chirality : 0.045 0.468 6475 Planarity : 0.005 0.069 7188 Dihedral : 5.766 85.527 5925 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.88 % Allowed : 23.74 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.12), residues: 5361 helix: 1.73 (0.10), residues: 2922 sheet: -0.62 (0.23), residues: 563 loop : -0.82 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 44 TYR 0.028 0.001 TYR O 48 PHE 0.018 0.001 PHE F 255 TRP 0.004 0.001 TRP T 208 HIS 0.004 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00312 (40027) covalent geometry : angle 0.64359 (54405) hydrogen bonds : bond 0.04069 ( 2568) hydrogen bonds : angle 4.32645 ( 7509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 615 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8605 (pp30) cc_final: 0.8290 (pp30) REVERT: A 64 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: A 177 ASP cc_start: 0.8547 (t0) cc_final: 0.8269 (t0) REVERT: A 237 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: A 380 ARG cc_start: 0.8812 (mpp80) cc_final: 0.8034 (mtm-85) REVERT: A 513 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8575 (mmtm) REVERT: B 86 ASP cc_start: 0.8828 (p0) cc_final: 0.8282 (p0) REVERT: B 225 MET cc_start: 0.9521 (tpt) cc_final: 0.9272 (tpt) REVERT: B 289 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8820 (p) REVERT: C 480 ARG cc_start: 0.8897 (ttm-80) cc_final: 0.8694 (ttm-80) REVERT: C 489 LEU cc_start: 0.8418 (tp) cc_final: 0.7949 (tp) REVERT: D 369 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: D 397 LYS cc_start: 0.7842 (pmtt) cc_final: 0.7577 (pttm) REVERT: E 9 GLU cc_start: 0.8703 (tt0) cc_final: 0.8400 (tt0) REVERT: E 197 MET cc_start: 0.8683 (mmt) cc_final: 0.8352 (mtt) REVERT: E 221 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: E 259 GLN cc_start: 0.8195 (tt0) cc_final: 0.7906 (tt0) REVERT: E 390 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8831 (mp0) REVERT: E 391 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8118 (mp0) REVERT: E 396 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7944 (t0) REVERT: E 401 GLN cc_start: 0.8364 (tt0) cc_final: 0.8149 (mt0) REVERT: F 15 ILE cc_start: 0.9000 (mt) cc_final: 0.8768 (pp) REVERT: F 126 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8643 (tm-30) REVERT: F 197 MET cc_start: 0.8670 (mmm) cc_final: 0.7741 (mtm) REVERT: F 234 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8714 (mm) REVERT: F 285 MET cc_start: 0.8308 (mmt) cc_final: 0.8090 (tpt) REVERT: F 287 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: F 297 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8373 (ttp-170) REVERT: G 6 GLU cc_start: 0.7851 (tp30) cc_final: 0.7508 (tp30) REVERT: G 49 MET cc_start: 0.8765 (ttm) cc_final: 0.8530 (mtt) REVERT: G 71 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7252 (pm20) REVERT: G 77 LYS cc_start: 0.9026 (ptpp) cc_final: 0.8743 (pmtt) REVERT: G 112 MET cc_start: 0.8819 (mmp) cc_final: 0.8359 (mtt) REVERT: G 209 TYR cc_start: 0.8644 (m-80) cc_final: 0.8259 (m-80) REVERT: G 213 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8267 (mm-30) REVERT: G 214 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7289 (pp20) REVERT: H 33 GLN cc_start: 0.8534 (mt0) cc_final: 0.8305 (mt0) REVERT: H 37 ARG cc_start: 0.8668 (ttm110) cc_final: 0.8389 (ttm110) REVERT: I 24 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8230 (pp) REVERT: I 37 ARG cc_start: 0.7947 (ptp-110) cc_final: 0.7650 (mtm110) REVERT: J 48 TYR cc_start: 0.8022 (m-80) cc_final: 0.7652 (m-80) REVERT: K 43 ASN cc_start: 0.8824 (p0) cc_final: 0.8282 (m-40) REVERT: K 50 PHE cc_start: 0.8275 (m-80) cc_final: 0.7976 (m-80) REVERT: L 33 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8182 (mm-40) REVERT: L 68 PHE cc_start: 0.7527 (m-80) cc_final: 0.6845 (m-80) REVERT: L 70 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6690 (tt) REVERT: M 62 PHE cc_start: 0.8436 (m-80) cc_final: 0.7776 (t80) REVERT: M 66 ILE cc_start: 0.4054 (mm) cc_final: 0.3700 (mp) REVERT: N 9 THR cc_start: 0.6946 (OUTLIER) cc_final: 0.6673 (p) REVERT: N 61 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8263 (pp) REVERT: O 44 ARG cc_start: 0.7783 (mtp180) cc_final: 0.7171 (ttm170) REVERT: O 48 TYR cc_start: 0.6523 (m-80) cc_final: 0.6028 (m-80) REVERT: Q 72 PHE cc_start: 0.8323 (m-80) cc_final: 0.8077 (m-80) REVERT: R 42 THR cc_start: 0.8982 (p) cc_final: 0.8606 (t) REVERT: R 53 LYS cc_start: 0.8593 (tptp) cc_final: 0.8113 (ptpp) REVERT: R 111 ASP cc_start: 0.8360 (m-30) cc_final: 0.8112 (m-30) REVERT: R 120 ARG cc_start: 0.8554 (mtp-110) cc_final: 0.8249 (mtm-85) REVERT: T 33 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7541 (tp30) REVERT: T 89 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: T 102 TYR cc_start: 0.8765 (m-80) cc_final: 0.8282 (m-80) REVERT: T 119 PHE cc_start: 0.7762 (m-80) cc_final: 0.7033 (m-80) REVERT: T 122 TRP cc_start: 0.8029 (m100) cc_final: 0.7577 (m100) REVERT: T 206 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8487 (mm-30) REVERT: T 251 PHE cc_start: 0.8887 (t80) cc_final: 0.8465 (t80) REVERT: T 255 PHE cc_start: 0.8874 (t80) cc_final: 0.8458 (t80) REVERT: T 289 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8917 (mp) REVERT: U 12 ILE cc_start: 0.8110 (pt) cc_final: 0.7808 (pp) REVERT: U 15 LEU cc_start: 0.9044 (tm) cc_final: 0.8806 (pp) REVERT: U 74 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8290 (pp30) REVERT: U 112 GLN cc_start: 0.8634 (tt0) cc_final: 0.8047 (tm-30) REVERT: U 130 ASP cc_start: 0.9112 (t0) cc_final: 0.8777 (m-30) REVERT: V 64 ASP cc_start: 0.8841 (m-30) cc_final: 0.8444 (m-30) REVERT: S 104 ARG cc_start: 0.9124 (mtp85) cc_final: 0.8776 (ttm110) REVERT: S 107 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.8321 (ttp-110) REVERT: S 152 ARG cc_start: 0.8442 (tpm170) cc_final: 0.8134 (tmm160) REVERT: W 104 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8447 (ptp-110) REVERT: W 146 ARG cc_start: 0.8136 (ptp-110) cc_final: 0.7655 (pmm-80) outliers start: 108 outliers final: 54 residues processed: 677 average time/residue: 0.5839 time to fit residues: 497.3686 Evaluate side-chains 648 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 577 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain Q residue 50 PHE Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain U residue 50 ASP Chi-restraints excluded: chain U residue 74 GLN Chi-restraints excluded: chain U residue 121 LEU Chi-restraints excluded: chain U residue 126 SER Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain W residue 105 ILE Chi-restraints excluded: chain W residue 127 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 290 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 chunk 399 optimal weight: 1.9990 chunk 410 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 443 optimal weight: 1.9990 chunk 465 optimal weight: 40.0000 chunk 488 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN G 231 GLN K 33 GLN O 33 GLN U 74 GLN ** U 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.129752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078649 restraints weight = 70321.150| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.88 r_work: 0.2819 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 40027 Z= 0.224 Angle : 0.698 12.778 54405 Z= 0.358 Chirality : 0.048 0.456 6475 Planarity : 0.005 0.067 7188 Dihedral : 5.857 87.474 5925 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.88 % Allowed : 24.38 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.12), residues: 5361 helix: 1.65 (0.10), residues: 2931 sheet: -0.64 (0.23), residues: 563 loop : -0.89 (0.15), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 44 TYR 0.035 0.002 TYR P 48 PHE 0.024 0.001 PHE U 23 TRP 0.005 0.001 TRP T 122 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00538 (40027) covalent geometry : angle 0.69790 (54405) hydrogen bonds : bond 0.04335 ( 2568) hydrogen bonds : angle 4.42679 ( 7509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 586 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8688 (pp30) cc_final: 0.8359 (pp30) REVERT: A 64 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: A 177 ASP cc_start: 0.8604 (t0) cc_final: 0.8353 (t0) REVERT: A 237 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8035 (mm-30) REVERT: A 380 ARG cc_start: 0.8897 (mpp80) cc_final: 0.8472 (mtm-85) REVERT: A 459 TYR cc_start: 0.8439 (m-10) cc_final: 0.7993 (m-10) REVERT: B 25 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7948 (mmm-85) REVERT: C 480 ARG cc_start: 0.8936 (ttm-80) cc_final: 0.8729 (ttm-80) REVERT: D 61 SER cc_start: 0.9001 (m) cc_final: 0.8730 (t) REVERT: D 357 ASN cc_start: 0.9394 (m110) cc_final: 0.9177 (m110) REVERT: D 369 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: E 9 GLU cc_start: 0.8832 (tt0) cc_final: 0.8599 (tt0) REVERT: E 197 MET cc_start: 0.8780 (mmt) cc_final: 0.8516 (mpp) REVERT: E 221 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: E 259 GLN cc_start: 0.8319 (tt0) cc_final: 0.8040 (tt0) REVERT: E 390 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8965 (mp0) REVERT: E 391 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8253 (mp0) REVERT: E 401 GLN cc_start: 0.8601 (tt0) cc_final: 0.8325 (mt0) REVERT: E 404 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8061 (mtp85) REVERT: F 126 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8773 (tm-30) REVERT: F 197 MET cc_start: 0.8794 (mmm) cc_final: 0.7900 (mtm) REVERT: F 234 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8918 (mm) REVERT: F 297 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8522 (ttp-170) REVERT: G 6 GLU cc_start: 0.8008 (tp30) cc_final: 0.7634 (tp30) REVERT: G 71 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7357 (pm20) REVERT: G 77 LYS cc_start: 0.9066 (ptpp) cc_final: 0.8767 (pmtt) REVERT: G 112 MET cc_start: 0.8920 (mmp) cc_final: 0.8445 (mtt) REVERT: G 209 TYR cc_start: 0.8692 (m-80) cc_final: 0.8309 (m-80) REVERT: G 213 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: G 214 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7446 (pp20) REVERT: H 33 GLN cc_start: 0.8552 (mt0) cc_final: 0.8327 (mt0) REVERT: I 24 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8237 (pp) REVERT: J 48 TYR cc_start: 0.8045 (m-80) cc_final: 0.7774 (m-80) REVERT: K 43 ASN cc_start: 0.8804 (p0) cc_final: 0.8258 (m-40) REVERT: K 50 PHE cc_start: 0.8295 (m-80) cc_final: 0.8049 (m-80) REVERT: L 33 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8253 (mm-40) REVERT: L 70 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6718 (tt) REVERT: M 62 PHE cc_start: 0.8421 (m-80) cc_final: 0.7784 (t80) REVERT: M 66 ILE cc_start: 0.3961 (mm) cc_final: 0.3642 (mp) REVERT: N 9 THR cc_start: 0.6879 (OUTLIER) cc_final: 0.6606 (t) REVERT: P 2 GLU cc_start: 0.5999 (mt-10) cc_final: 0.5390 (tt0) REVERT: P 35 ILE cc_start: 0.8351 (pp) cc_final: 0.7785 (mp) REVERT: Q 72 PHE cc_start: 0.8263 (m-80) cc_final: 0.8051 (m-80) REVERT: R 42 THR cc_start: 0.9054 (p) cc_final: 0.8654 (t) REVERT: R 53 LYS cc_start: 0.8670 (tptp) cc_final: 0.8191 (ptpp) REVERT: R 111 ASP cc_start: 0.8451 (m-30) cc_final: 0.8249 (m-30) REVERT: R 120 ARG cc_start: 0.8619 (mtp-110) cc_final: 0.8300 (mtm-85) REVERT: T 33 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7523 (tp30) REVERT: T 89 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: T 102 TYR cc_start: 0.8762 (m-80) cc_final: 0.8241 (m-80) REVERT: T 122 TRP cc_start: 0.8181 (m100) cc_final: 0.7845 (m100) REVERT: T 206 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8460 (mm-30) REVERT: T 208 TRP cc_start: 0.8147 (m100) cc_final: 0.7576 (m100) REVERT: T 255 PHE cc_start: 0.8949 (t80) cc_final: 0.8554 (t80) REVERT: T 289 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8880 (mp) REVERT: T 296 TYR cc_start: 0.8510 (t80) cc_final: 0.8205 (t80) REVERT: U 12 ILE cc_start: 0.8112 (pt) cc_final: 0.7804 (pp) REVERT: U 15 LEU cc_start: 0.9040 (tm) cc_final: 0.8798 (pp) REVERT: U 21 LEU cc_start: 0.8612 (tp) cc_final: 0.8205 (mp) REVERT: U 130 ASP cc_start: 0.9123 (t0) cc_final: 0.8788 (m-30) REVERT: V 64 ASP cc_start: 0.8859 (m-30) cc_final: 0.8429 (m-30) REVERT: S 104 ARG cc_start: 0.9114 (mtp85) cc_final: 0.8878 (ttm110) REVERT: S 107 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8308 (ttp-110) REVERT: W 104 ARG cc_start: 0.8791 (ttp80) cc_final: 0.8432 (ptp-110) REVERT: W 146 ARG cc_start: 0.8182 (ptp-110) cc_final: 0.7953 (mtm110) outliers start: 108 outliers final: 60 residues processed: 653 average time/residue: 0.5744 time to fit residues: 471.2171 Evaluate side-chains 633 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 561 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 96 ARG Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain U residue 50 ASP Chi-restraints excluded: chain U residue 126 SER Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain V residue 149 HIS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain W residue 105 ILE Chi-restraints excluded: chain W residue 127 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 235 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 326 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 280 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN O 33 GLN U 112 GLN ** U 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.131683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079411 restraints weight = 69771.268| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.56 r_work: 0.2893 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 40027 Z= 0.149 Angle : 0.693 24.097 54405 Z= 0.350 Chirality : 0.047 0.474 6475 Planarity : 0.005 0.084 7188 Dihedral : 5.787 86.615 5925 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.08 % Allowed : 25.45 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.12), residues: 5361 helix: 1.72 (0.10), residues: 2919 sheet: -0.67 (0.23), residues: 564 loop : -0.85 (0.15), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 78 TYR 0.029 0.001 TYR H 48 PHE 0.029 0.001 PHE R 60 TRP 0.004 0.001 TRP T 208 HIS 0.005 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00350 (40027) covalent geometry : angle 0.69284 (54405) hydrogen bonds : bond 0.04143 ( 2568) hydrogen bonds : angle 4.39490 ( 7509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 591 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8653 (pp30) cc_final: 0.8331 (pp30) REVERT: A 64 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: A 177 ASP cc_start: 0.8599 (t0) cc_final: 0.8340 (t0) REVERT: A 237 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.7979 (mm-30) REVERT: A 380 ARG cc_start: 0.8860 (mpp80) cc_final: 0.8416 (mtm-85) REVERT: B 25 ARG cc_start: 0.8373 (tpp80) cc_final: 0.8003 (mmm-85) REVERT: B 86 ASP cc_start: 0.8822 (p0) cc_final: 0.8274 (p0) REVERT: C 5 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7638 (m) REVERT: C 480 ARG cc_start: 0.8939 (ttm-80) cc_final: 0.8722 (ttm-80) REVERT: D 369 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: D 397 LYS cc_start: 0.8014 (pmtt) cc_final: 0.7754 (pttm) REVERT: E 9 GLU cc_start: 0.8795 (tt0) cc_final: 0.8521 (tt0) REVERT: E 197 MET cc_start: 0.8753 (mmt) cc_final: 0.8423 (mtt) REVERT: E 221 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: E 259 GLN cc_start: 0.8298 (tt0) cc_final: 0.8030 (tt0) REVERT: E 390 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8922 (mp0) REVERT: E 391 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8182 (mp0) REVERT: E 401 GLN cc_start: 0.8547 (tt0) cc_final: 0.8305 (mt0) REVERT: F 15 ILE cc_start: 0.9038 (mt) cc_final: 0.8834 (pp) REVERT: F 126 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8724 (tm-30) REVERT: F 197 MET cc_start: 0.8711 (mmm) cc_final: 0.7787 (mtm) REVERT: F 234 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8866 (mm) REVERT: F 297 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8399 (ttp-170) REVERT: G 6 GLU cc_start: 0.7931 (tp30) cc_final: 0.7564 (tp30) REVERT: G 71 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7318 (pm20) REVERT: G 77 LYS cc_start: 0.9050 (ptpp) cc_final: 0.8768 (pmtt) REVERT: G 209 TYR cc_start: 0.8602 (m-80) cc_final: 0.8327 (m-80) REVERT: G 213 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8208 (mm-30) REVERT: G 214 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7437 (pp20) REVERT: H 33 GLN cc_start: 0.8541 (mt0) cc_final: 0.8300 (mt0) REVERT: H 48 TYR cc_start: 0.6000 (OUTLIER) cc_final: 0.5783 (t80) REVERT: I 24 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8185 (pt) REVERT: J 41 ILE cc_start: 0.7673 (tp) cc_final: 0.7403 (tp) REVERT: K 43 ASN cc_start: 0.8827 (p0) cc_final: 0.8279 (m-40) REVERT: K 50 PHE cc_start: 0.8333 (m-80) cc_final: 0.8080 (m-80) REVERT: L 33 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8236 (mm-40) REVERT: L 68 PHE cc_start: 0.7581 (m-80) cc_final: 0.6846 (m-80) REVERT: L 70 ILE cc_start: 0.7145 (tp) cc_final: 0.6772 (tt) REVERT: M 62 PHE cc_start: 0.8417 (m-80) cc_final: 0.7784 (t80) REVERT: M 66 ILE cc_start: 0.4028 (mm) cc_final: 0.3778 (mp) REVERT: P 2 GLU cc_start: 0.6180 (mt-10) cc_final: 0.5613 (tt0) REVERT: Q 72 PHE cc_start: 0.8286 (m-80) cc_final: 0.8065 (m-80) REVERT: R 19 VAL cc_start: 0.7584 (t) cc_final: 0.7371 (p) REVERT: R 42 THR cc_start: 0.9042 (p) cc_final: 0.8708 (t) REVERT: R 53 LYS cc_start: 0.8670 (tptp) cc_final: 0.8078 (ptpp) REVERT: R 111 ASP cc_start: 0.8437 (m-30) cc_final: 0.8174 (m-30) REVERT: R 120 ARG cc_start: 0.8593 (mtp-110) cc_final: 0.8269 (mtm-85) REVERT: T 33 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7557 (tp30) REVERT: T 84 MET cc_start: 0.8773 (mmm) cc_final: 0.8524 (tpt) REVERT: T 89 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8452 (pt0) REVERT: T 102 TYR cc_start: 0.8752 (m-80) cc_final: 0.8231 (m-80) REVERT: T 119 PHE cc_start: 0.7845 (m-80) cc_final: 0.7106 (m-80) REVERT: T 122 TRP cc_start: 0.8254 (m100) cc_final: 0.7913 (m100) REVERT: T 190 ASP cc_start: 0.7765 (m-30) cc_final: 0.7300 (p0) REVERT: T 206 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8467 (mm-30) REVERT: T 208 TRP cc_start: 0.8211 (m100) cc_final: 0.7603 (m100) REVERT: T 251 PHE cc_start: 0.8984 (t80) cc_final: 0.8579 (t80) REVERT: T 255 PHE cc_start: 0.8956 (t80) cc_final: 0.8506 (t80) REVERT: T 289 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8825 (mp) REVERT: U 12 ILE cc_start: 0.8120 (pt) cc_final: 0.7826 (pp) REVERT: U 15 LEU cc_start: 0.9020 (tm) cc_final: 0.8779 (pp) REVERT: U 21 LEU cc_start: 0.8620 (tp) cc_final: 0.8197 (mp) REVERT: U 50 ASP cc_start: 0.8152 (t70) cc_final: 0.7805 (t70) REVERT: V 64 ASP cc_start: 0.8881 (m-30) cc_final: 0.8458 (m-30) REVERT: S 104 ARG cc_start: 0.9122 (mtp85) cc_final: 0.8835 (ttm110) REVERT: S 107 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8279 (ttp-110) REVERT: W 107 ARG cc_start: 0.8763 (tmm160) cc_final: 0.8390 (ptm-80) REVERT: W 146 ARG cc_start: 0.8137 (ptp-110) cc_final: 0.7643 (mtm110) outliers start: 78 outliers final: 51 residues processed: 636 average time/residue: 0.5942 time to fit residues: 474.3305 Evaluate side-chains 624 residues out of total 4298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 561 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 382 ASP Chi-restraints excluded: chain G residue 91 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain H residue 48 TYR Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain T residue 38 VAL Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 96 ARG Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain U residue 121 LEU Chi-restraints excluded: chain U residue 126 SER Chi-restraints excluded: chain U residue 137 SER Chi-restraints excluded: chain V residue 149 HIS Chi-restraints excluded: chain W residue 105 ILE Chi-restraints excluded: chain W residue 127 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 532 random chunks: chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 0.0070 chunk 381 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 477 optimal weight: 50.0000 chunk 236 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 chunk 416 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN K 33 GLN O 33 GLN ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.130434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077890 restraints weight = 70065.467| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.56 r_work: 0.2872 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 40027 Z= 0.186 Angle : 0.711 15.404 54405 Z= 0.361 Chirality : 0.048 0.335 6475 Planarity : 0.005 0.071 7188 Dihedral : 5.795 89.579 5925 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.11 % Allowed : 25.69 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.12), residues: 5361 helix: 1.70 (0.10), residues: 2913 sheet: -0.67 (0.23), residues: 571 loop : -0.87 (0.15), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG S 152 TYR 0.032 0.002 TYR H 48 PHE 0.022 0.001 PHE R 60 TRP 0.005 0.001 TRP T 122 HIS 0.006 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00447 (40027) covalent geometry : angle 0.71053 (54405) hydrogen bonds : bond 0.04249 ( 2568) hydrogen bonds : angle 4.41922 ( 7509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19714.41 seconds wall clock time: 334 minutes 24.75 seconds (20064.75 seconds total)