Starting phenix.real_space_refine on Tue Aug 26 16:02:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itl_60870/08_2025/9itl_60870_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itl_60870/08_2025/9itl_60870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itl_60870/08_2025/9itl_60870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itl_60870/08_2025/9itl_60870.map" model { file = "/net/cci-nas-00/data/ceres_data/9itl_60870/08_2025/9itl_60870_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itl_60870/08_2025/9itl_60870_neut.cif" } resolution = 3.31 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= 0.017 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 24485 2.51 5 N 6795 2.21 5 O 7302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 38691 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: "S" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 538 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} 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: "W" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 538 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "X" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 767 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 2, 'TRANS': 151} 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: "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: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 123} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 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: 8.56, per 1000 atoms: 0.22 Number of scatterers: 38691 At special positions: 0 Unit cell: (129.27, 140.43, 229.71, 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 7302 8.00 N 6795 7.00 C 24485 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: 3.00 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 238.4 nanoseconds 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9586 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 35 sheets defined 59.3% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.615A pdb=" N ILE A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 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 223 through 226 removed outlier: 3.675A pdb=" N GLU A 226 " --> pdb=" O GLY A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 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 315 removed outlier: 4.207A pdb=" N ARG A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) 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 407 removed outlier: 4.927A pdb=" N LYS A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.731A 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 Processing helix chain 'A' and resid 501 through 519 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.911A 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: 3.661A 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: 6.126A 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 Processing helix chain 'B' and resid 302 through 303 No H-bonds generated for 'chain 'B' and resid 302 through 303' Processing helix chain 'B' and resid 304 through 315 removed outlier: 3.885A pdb=" N ARG B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 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: 3.950A pdb=" N ALA B 384 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 414 removed outlier: 4.065A pdb=" N GLY B 395 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.786A 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: 3.983A 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 157 through 164 removed outlier: 3.576A pdb=" N ASP C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) 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 removed outlier: 3.570A pdb=" N GLN C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 277 through 292 Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.566A pdb=" N ALA C 300 " --> pdb=" O GLY C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 303 No H-bonds generated for 'chain 'C' and resid 302 through 303' Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.682A pdb=" N ARG C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 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: 3.847A pdb=" N ALA C 384 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.799A pdb=" N GLY C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LYS C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 removed outlier: 4.921A pdb=" N GLN C 412 " --> pdb=" O ALA C 409 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 414 " --> pdb=" O ALA C 411 " (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 Processing helix chain 'C' and resid 483 through 493 removed outlier: 4.117A pdb=" N ARG C 487 " --> pdb=" O HIS C 483 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 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 194 through 201 Processing helix chain 'D' and resid 222 through 243 removed outlier: 4.698A pdb=" N GLY D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 243 " --> pdb=" O TYR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 268 Processing helix chain 'D' and resid 281 through 290 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: 4.425A pdb=" N ILE D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 5.621A pdb=" N SER D 393 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 410 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 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 242 removed outlier: 4.858A pdb=" N GLY E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.579A 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 324 removed outlier: 3.626A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) 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 387 removed outlier: 4.248A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE E 383 " --> pdb=" O ASP E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 392 removed outlier: 3.526A pdb=" N GLU E 391 " --> pdb=" O GLY E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 410 Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 458 through 468 Processing helix chain 'F' and resid 20 through 24 removed outlier: 4.129A pdb=" N VAL F 24 " --> pdb=" O GLU F 21 " (cutoff:3.500A) 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: 3.738A pdb=" N ARG F 226 " --> pdb=" O PRO F 222 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR F 239 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE F 240 " --> pdb=" O MET F 236 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 243 " --> pdb=" O TYR F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 268 removed outlier: 3.708A pdb=" N PHE F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 315 through 323 removed outlier: 3.898A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 360 through 380 removed outlier: 4.604A pdb=" N LEU F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 6.046A 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 393 through 410 Processing helix chain 'F' and resid 414 through 418 removed outlier: 3.885A 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 Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.534A pdb=" N VAL F 462 " --> pdb=" O ASP F 458 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 110 removed outlier: 3.580A pdb=" N THR S 106 " --> pdb=" O LYS S 102 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU S 108 " --> pdb=" O ARG S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 154 Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.637A pdb=" N VAL T 53 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA T 69 " --> pdb=" O LEU T 65 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 99 Processing helix chain 'T' and resid 102 through 125 Proline residue: T 108 - end of helix removed outlier: 3.522A pdb=" N PHE T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 189 Processing helix chain 'T' and resid 190 through 214 removed outlier: 3.663A pdb=" N THR T 194 " --> pdb=" O ASP T 190 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE T 200 " --> pdb=" O ALA T 196 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER T 201 " --> pdb=" O ILE T 197 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 240 removed outlier: 3.693A pdb=" N PHE T 236 " --> pdb=" O GLY T 232 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE T 237 " --> pdb=" O ILE T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 240 through 267 removed outlier: 4.213A pdb=" N PHE T 244 " --> pdb=" O LEU T 240 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE T 254 " --> pdb=" O LEU T 250 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU T 267 " --> pdb=" O VAL T 263 " (cutoff:3.500A) Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.571A pdb=" N LEU T 289 " --> pdb=" O PHE T 285 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 139 removed outlier: 6.066A pdb=" N ARG U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) Proline residue: U 32 - end of helix removed outlier: 3.730A pdb=" N LYS U 78 " --> pdb=" O GLN U 74 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU U 85 " --> pdb=" O ALA U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 147 removed outlier: 3.596A pdb=" N ARG U 147 " --> pdb=" O GLU U 143 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 158 removed outlier: 3.751A pdb=" N SER U 156 " --> pdb=" O LEU U 152 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 29 removed outlier: 3.547A pdb=" N PHE V 11 " --> pdb=" O ASN V 7 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 113 removed outlier: 3.548A pdb=" N GLN V 89 " --> pdb=" O GLU V 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 120 removed outlier: 4.031A pdb=" N ARG V 117 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 137 removed outlier: 3.500A pdb=" N VAL V 132 " --> pdb=" O ILE V 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 158 removed outlier: 3.650A pdb=" N SER V 156 " --> pdb=" O LEU V 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA V 158 " --> pdb=" O ALA V 154 " (cutoff:3.500A) Processing helix chain 'W' and resid 98 through 109 Processing helix chain 'W' and resid 142 through 152 Processing helix chain 'X' and resid 7 through 122 Proline residue: X 32 - end of helix removed outlier: 3.850A 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 156 Processing helix chain 'Y' and resid 9 through 148 removed outlier: 3.584A pdb=" N ARG Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Proline residue: Y 32 - end of helix removed outlier: 3.540A pdb=" N ASN Y 35 " --> pdb=" O ARG Y 31 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG Y 62 " --> pdb=" O LEU Y 58 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 158 removed outlier: 3.688A pdb=" N ALA Y 154 " --> pdb=" O ALA Y 151 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA Y 158 " --> pdb=" O GLU Y 155 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 53 Processing helix chain 'Z' and resid 54 through 69 removed outlier: 3.648A pdb=" N ALA Z 69 " --> pdb=" O LEU Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 99 Processing helix chain 'Z' and resid 106 through 125 removed outlier: 3.621A pdb=" N LEU Z 125 " --> pdb=" O ASN Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 214 Processing helix chain 'Z' and resid 233 through 267 Proline residue: Z 243 - end of helix removed outlier: 3.903A pdb=" N LEU Z 267 " --> pdb=" O VAL Z 263 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 Processing helix chain 'G' and resid 5 through 60 Proline residue: G 44 - end of helix removed outlier: 3.754A pdb=" N GLU G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 52 " --> pdb=" O ARG G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 92 through 112 removed outlier: 4.386A pdb=" N ALA G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 148 through 165 removed outlier: 3.970A pdb=" N ILE G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 286 Proline residue: G 222 - end of helix removed outlier: 4.322A pdb=" N ILE G 281 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.658A pdb=" N ILE H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix removed outlier: 3.977A pdb=" N GLY H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 70 removed outlier: 3.779A pdb=" N THR H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE H 55 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU H 57 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE H 68 " --> pdb=" O LEU H 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 38 removed outlier: 3.531A pdb=" N VAL I 7 " --> pdb=" O GLY I 3 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 18 " --> pdb=" O GLY I 14 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Proline residue: I 20 - end of helix removed outlier: 4.110A pdb=" N GLY I 23 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN I 33 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 70 removed outlier: 3.779A pdb=" N THR I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE I 55 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR I 56 " --> pdb=" O GLY I 52 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 17 removed outlier: 3.571A pdb=" N VAL J 7 " --> pdb=" O GLY J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 38 removed outlier: 3.539A pdb=" N GLY J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 72 removed outlier: 3.908A pdb=" N THR J 47 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU J 59 " --> pdb=" O PHE J 55 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 38 removed outlier: 4.453A pdb=" N GLY K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Proline residue: K 20 - end of helix removed outlier: 3.832A pdb=" N GLY K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 72 removed outlier: 3.601A pdb=" N THR K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE K 55 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 38 removed outlier: 3.780A pdb=" N ILE L 18 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) Proline residue: L 20 - end of helix removed outlier: 3.514A pdb=" N VAL L 28 " --> pdb=" O ILE L 24 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 73 removed outlier: 4.559A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 17 removed outlier: 3.556A pdb=" N ALA M 17 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 38 removed outlier: 4.049A pdb=" N GLY M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL M 28 " --> pdb=" O ILE M 24 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN M 33 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 72 removed outlier: 3.637A pdb=" N VAL M 46 " --> pdb=" O GLU M 42 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU M 59 " --> pdb=" O PHE M 55 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA M 60 " --> pdb=" O THR M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 removed outlier: 3.509A pdb=" N VAL N 7 " --> pdb=" O GLY N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 38 removed outlier: 3.711A pdb=" N GLY N 25 " --> pdb=" O GLY N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 72 removed outlier: 3.714A pdb=" N TYR N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR N 56 " --> pdb=" O GLY N 52 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU N 59 " --> pdb=" O PHE N 55 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 3.657A pdb=" N ALA O 10 " --> pdb=" O LEU O 6 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Proline residue: O 20 - end of helix removed outlier: 3.831A pdb=" N GLY O 25 " --> pdb=" O GLY O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 73 removed outlier: 3.683A pdb=" N THR O 47 " --> pdb=" O ASN O 43 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 18 through 38 removed outlier: 3.573A pdb=" N VAL P 28 " --> pdb=" O ILE P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 73 removed outlier: 3.721A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE P 55 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR P 56 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA P 58 " --> pdb=" O ALA P 54 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE P 66 " --> pdb=" O PHE P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.515A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Proline residue: Q 20 - end of helix removed outlier: 3.700A pdb=" N GLY Q 23 " --> pdb=" O GLY Q 19 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY Q 25 " --> pdb=" O GLY Q 21 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL Q 28 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN Q 33 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 55 removed outlier: 4.873A pdb=" N THR Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR Q 48 " --> pdb=" O ARG Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 72 removed outlier: 3.592A pdb=" N GLY Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE Q 72 " --> pdb=" O PHE Q 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 92 through 100 Processing helix chain 'R' and resid 107 through 128 removed outlier: 3.575A pdb=" N VAL R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.806A pdb=" N GLY A 30 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ARG A 100 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 52 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 70 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 68 " --> pdb=" O VAL A 54 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 5 through 11 current: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.806A pdb=" N GLY A 30 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ARG A 100 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 52 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 70 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 68 " --> pdb=" O VAL A 54 " (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: 6.641A pdb=" N LYS F 55 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN F 48 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL F 53 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL F 14 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE F 10 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG F 16 " --> pdb=" O GLN F 8 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 5 through 11 current: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 removed outlier: 4.143A pdb=" N LYS A 132 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 5.994A pdb=" N VAL A 199 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL A 274 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 201 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP A 276 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A 203 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 275 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL A 333 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A 277 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A 335 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.095A pdb=" N ILE B 53 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU B 52 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B 70 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE D 7 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS D 18 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL D 57 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D 45 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.586A pdb=" N ALA B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU B 73 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA B 79 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR B 67 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.826A 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: 6.641A pdb=" N CYS B 200 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL B 231 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR B 202 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA B 233 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 204 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 7.043A pdb=" N ALA C 79 " --> pdb=" O LEU C 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 5 through 11 current: chain 'C' and resid 94 through 101 removed outlier: 4.019A pdb=" N SER C 97 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN C 28 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA W 89 " --> pdb=" O THR W 119 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS W 121 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL W 91 " --> pdb=" O HIS W 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 7.043A pdb=" N ALA C 79 " --> pdb=" O LEU C 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 73 current: chain 'E' and resid 31 through 34 removed outlier: 6.377A pdb=" N VAL E 45 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E 57 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE E 10 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG E 16 " --> pdb=" O GLN E 8 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 5 through 11 current: chain 'C' and resid 94 through 101 removed outlier: 4.019A pdb=" N SER C 97 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN C 28 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA W 89 " --> pdb=" O THR W 119 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS W 121 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL W 91 " --> pdb=" O HIS W 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 103 through 106 removed outlier: 4.408A pdb=" N LYS C 132 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.220A pdb=" N CYS C 200 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL C 231 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR C 202 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL C 199 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL C 274 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 201 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 152 through 153 removed outlier: 4.535A pdb=" N ILE C 166 " --> pdb=" O VAL C 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 333 through 336 removed outlier: 7.039A pdb=" N ILE C 174 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR C 336 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY C 176 " --> pdb=" O THR C 336 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU C 173 " --> pdb=" O ILE C 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 261 through 263 Processing sheet with id=AB9, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AC1, first strand: chain 'D' and resid 79 through 81 Processing sheet with id=AC2, first strand: chain 'D' and resid 90 through 91 removed outlier: 3.761A pdb=" N VAL D 183 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N MET D 303 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D 249 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N THR D 149 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS D 148 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE D 329 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA D 150 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 129 through 130 removed outlier: 4.360A pdb=" N PHE D 143 " --> pdb=" O PHE D 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 202 through 203 Processing sheet with id=AC5, first strand: chain 'E' and resid 79 through 82 removed outlier: 3.732A pdb=" N GLU E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 90 through 91 removed outlier: 6.620A pdb=" N SER E 178 " --> pdb=" O VAL E 213 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL E 215 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N PHE E 180 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY E 217 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY E 182 " --> pdb=" O GLY E 217 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE E 177 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N MET E 303 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU E 249 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR E 149 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS E 148 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE E 329 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA E 150 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 129 through 130 removed outlier: 4.034A pdb=" N PHE E 143 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 202 through 203 Processing sheet with id=AC9, first strand: chain 'F' and resid 79 through 81 Processing sheet with id=AD1, first strand: chain 'F' and resid 89 through 90 removed outlier: 6.627A pdb=" N ARG F 89 " --> pdb=" O MET F 214 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N VAL F 213 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER F 178 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N MET F 303 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU F 249 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR F 149 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL F 306 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE F 151 " --> pdb=" O VAL F 306 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 128 through 129 removed outlier: 4.124A pdb=" N GLN F 128 " --> pdb=" O ARG F 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 202 through 203 Processing sheet with id=AD4, first strand: chain 'S' and resid 118 through 121 removed outlier: 6.542A pdb=" N ALA S 89 " --> pdb=" O THR S 119 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N HIS S 121 " --> pdb=" O ALA S 89 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL S 91 " --> pdb=" O HIS S 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 138 through 140 removed outlier: 4.302A pdb=" N GLY G 138 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER G 78 " --> pdb=" O GLU G 170 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N TYR G 172 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA G 80 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE G 174 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU G 82 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N SER G 176 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N VAL G 84 " --> pdb=" O SER G 176 " (cutoff:3.500A) removed outlier: 11.163A pdb=" N PHE G 178 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 13 through 15 Processing sheet with id=AD7, first strand: chain 'R' and resid 13 through 15 removed outlier: 6.438A pdb=" N HIS R 4 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE R 76 " --> pdb=" O HIS R 4 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU R 6 " --> pdb=" O ILE R 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 31 through 33 removed outlier: 4.159A pdb=" N MET R 21 " --> pdb=" O ILE R 52 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE R 51 " --> pdb=" O THR R 58 " (cutoff:3.500A) 2463 hydrogen bonds defined for protein. 7158 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: 7.00 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 6723 1.27 - 1.41: 8802 1.41 - 1.54: 23477 1.54 - 1.68: 58 1.68 - 1.82: 182 Bond restraints: 39242 Sorted by residual: bond pdb=" C PHE H 72 " pdb=" O PHE H 72 " ideal model delta sigma weight residual 1.231 1.134 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" N LEU R 70 " pdb=" CA LEU R 70 " ideal model delta sigma weight residual 1.453 1.485 -0.032 8.30e-03 1.45e+04 1.51e+01 bond pdb=" N PHE A 499 " pdb=" CA PHE A 499 " ideal model delta sigma weight residual 1.463 1.486 -0.023 6.90e-03 2.10e+04 1.09e+01 bond pdb=" N VAL R 81 " pdb=" CA VAL R 81 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.09e+01 bond pdb=" N VAL F 183 " pdb=" CA VAL F 183 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 8.92e+00 ... (remaining 39237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 52305 2.04 - 4.07: 878 4.07 - 6.11: 105 6.11 - 8.14: 22 8.14 - 10.18: 4 Bond angle restraints: 53314 Sorted by residual: angle pdb=" CA PHE M 72 " pdb=" CB PHE M 72 " pdb=" CG PHE M 72 " ideal model delta sigma weight residual 113.80 118.78 -4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" C ASP A 276 " pdb=" CA ASP A 276 " pdb=" CB ASP A 276 " ideal model delta sigma weight residual 115.79 110.25 5.54 1.19e+00 7.06e-01 2.17e+01 angle pdb=" CA PHE M 72 " pdb=" C PHE M 72 " pdb=" O PHE M 72 " ideal model delta sigma weight residual 120.80 112.99 7.81 1.70e+00 3.46e-01 2.11e+01 angle pdb=" N VAL R 128 " pdb=" CA VAL R 128 " pdb=" C VAL R 128 " ideal model delta sigma weight residual 112.17 107.98 4.19 9.50e-01 1.11e+00 1.95e+01 angle pdb=" C PHE C 499 " pdb=" CA PHE C 499 " pdb=" CB PHE C 499 " ideal model delta sigma weight residual 112.76 105.52 7.24 1.86e+00 2.89e-01 1.52e+01 ... (remaining 53309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 21871 17.86 - 35.72: 1531 35.72 - 53.58: 245 53.58 - 71.44: 62 71.44 - 89.30: 25 Dihedral angle restraints: 23734 sinusoidal: 8801 harmonic: 14933 Sorted by residual: dihedral pdb=" CA VAL E 275 " pdb=" C VAL E 275 " pdb=" N GLY E 276 " pdb=" CA GLY E 276 " ideal model delta harmonic sigma weight residual -180.00 -153.65 -26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LYS T 101 " pdb=" C LYS T 101 " pdb=" N TYR T 102 " pdb=" CA TYR T 102 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA SER E 273 " pdb=" C SER E 273 " pdb=" N GLN E 274 " pdb=" CA GLN E 274 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 23731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4808 0.047 - 0.094: 1158 0.094 - 0.142: 318 0.142 - 0.189: 35 0.189 - 0.236: 9 Chirality restraints: 6328 Sorted by residual: chirality pdb=" CB ILE L 18 " pdb=" CA ILE L 18 " pdb=" CG1 ILE L 18 " pdb=" CG2 ILE L 18 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA LEU G 192 " pdb=" N LEU G 192 " pdb=" C LEU G 192 " pdb=" CB LEU G 192 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE G 199 " pdb=" N ILE G 199 " pdb=" C ILE G 199 " pdb=" CB ILE G 199 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 6325 not shown) Planarity restraints: 7029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY L 19 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO L 20 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO L 20 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 20 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 374 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C LEU F 374 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU F 374 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN F 375 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY I 19 " -0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO I 20 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO I 20 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 20 " -0.033 5.00e-02 4.00e+02 ... (remaining 7026 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 344 2.55 - 3.14: 33399 3.14 - 3.73: 65428 3.73 - 4.31: 86357 4.31 - 4.90: 141200 Nonbonded interactions: 326728 Sorted by model distance: nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 1.965 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2B ATP B 602 " model vdw 1.974 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ATP C 602 " model vdw 2.008 2.170 nonbonded pdb="MG MG A 601 " pdb=" O3G ATP A 602 " model vdw 2.075 2.170 nonbonded pdb="MG MG A 601 " pdb=" O2B ATP A 602 " model vdw 2.120 2.170 ... (remaining 326723 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: 0.010 Normalize map: mean=0, sd=1: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.470 Find NCS groups from input model: 0.840 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 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 : 0.003 0.097 39242 Z= 0.199 Angle : 0.626 10.178 53314 Z= 0.367 Chirality : 0.045 0.236 6328 Planarity : 0.004 0.072 7029 Dihedral : 12.957 89.301 14148 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 0.27 % Allowed : 0.40 % Favored : 99.33 % 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: 5204 helix: 1.53 (0.10), residues: 2759 sheet: -0.42 (0.24), residues: 533 loop : -0.57 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 391 TYR 0.033 0.001 TYR T 277 PHE 0.024 0.001 PHE C 499 TRP 0.010 0.002 TRP T 208 HIS 0.002 0.001 HIS T 31 Details of bonding type rmsd covalent geometry : bond 0.00332 (39242) covalent geometry : angle 0.62616 (53314) hydrogen bonds : bond 0.21487 ( 2439) hydrogen bonds : angle 6.99002 ( 7158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 915 time to evaluate : 1.225 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.8703 (tpt) cc_final: 0.8498 (tpt) REVERT: A 358 TYR cc_start: 0.7121 (m-80) cc_final: 0.6562 (m-80) REVERT: B 76 ASP cc_start: 0.8654 (t70) cc_final: 0.8407 (t0) REVERT: B 380 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7158 (mmm-85) REVERT: B 406 ASP cc_start: 0.8566 (m-30) cc_final: 0.8193 (m-30) REVERT: B 413 PHE cc_start: 0.4161 (m-10) cc_final: 0.3943 (m-10) REVERT: C 188 ASP cc_start: 0.8640 (t70) cc_final: 0.8321 (t0) REVERT: C 413 PHE cc_start: 0.4717 (m-80) cc_final: 0.4514 (m-80) REVERT: C 417 LEU cc_start: 0.6866 (mt) cc_final: 0.6504 (mt) REVERT: C 430 ARG cc_start: 0.7580 (mtt-85) cc_final: 0.7306 (mtt-85) REVERT: C 433 GLU cc_start: 0.8350 (tp30) cc_final: 0.6933 (tm-30) REVERT: C 480 ARG cc_start: 0.8886 (ttm-80) cc_final: 0.8564 (mtm-85) REVERT: D 138 ASP cc_start: 0.7565 (m-30) cc_final: 0.7158 (m-30) REVERT: D 210 ASP cc_start: 0.8748 (t0) cc_final: 0.8151 (m-30) REVERT: D 311 ASP cc_start: 0.8401 (m-30) cc_final: 0.7902 (p0) REVERT: D 332 GLU cc_start: 0.7802 (tp30) cc_final: 0.7376 (tp30) REVERT: D 418 GLN cc_start: 0.8677 (tt0) cc_final: 0.8303 (tt0) REVERT: D 420 PHE cc_start: 0.8377 (m-80) cc_final: 0.7868 (m-80) REVERT: D 455 MET cc_start: 0.7686 (mmp) cc_final: 0.7127 (mmm) REVERT: E 47 GLN cc_start: 0.8484 (mt0) cc_final: 0.8098 (mt0) REVERT: E 197 MET cc_start: 0.8307 (mmp) cc_final: 0.7821 (mtp) REVERT: E 392 LEU cc_start: 0.8460 (mt) cc_final: 0.8208 (mt) REVERT: F 22 ASP cc_start: 0.8442 (m-30) cc_final: 0.7459 (t0) REVERT: F 193 LEU cc_start: 0.7577 (mp) cc_final: 0.7294 (mt) REVERT: F 197 MET cc_start: 0.8102 (mpp) cc_final: 0.7777 (mpp) REVERT: F 252 ASP cc_start: 0.7909 (t70) cc_final: 0.7529 (t70) REVERT: F 280 THR cc_start: 0.8639 (p) cc_final: 0.8391 (p) REVERT: S 119 THR cc_start: 0.9264 (t) cc_final: 0.8972 (t) REVERT: T 85 GLU cc_start: 0.6817 (pp20) cc_final: 0.5588 (tt0) REVERT: T 92 TYR cc_start: 0.8267 (t80) cc_final: 0.7815 (t80) REVERT: T 122 TRP cc_start: 0.8604 (m100) cc_final: 0.7772 (m100) REVERT: T 251 PHE cc_start: 0.7782 (t80) cc_final: 0.7146 (t80) REVERT: T 255 PHE cc_start: 0.8289 (t80) cc_final: 0.7709 (t80) REVERT: T 260 LEU cc_start: 0.8641 (tt) cc_final: 0.8074 (mt) REVERT: U 30 TYR cc_start: 0.5385 (t80) cc_final: 0.4680 (t80) REVERT: U 50 ASP cc_start: 0.8721 (m-30) cc_final: 0.8094 (m-30) REVERT: U 64 ASP cc_start: 0.9082 (m-30) cc_final: 0.8811 (m-30) REVERT: V 120 MET cc_start: 0.5619 (ppp) cc_final: 0.5232 (ptp) REVERT: W 97 LEU cc_start: 0.8967 (tp) cc_final: 0.8515 (tp) REVERT: W 109 LEU cc_start: 0.9538 (tp) cc_final: 0.9303 (pp) REVERT: W 136 ASP cc_start: 0.8509 (p0) cc_final: 0.8289 (p0) REVERT: W 151 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8480 (tm-30) REVERT: G 5 ARG cc_start: 0.8438 (ttp80) cc_final: 0.8065 (ptm-80) REVERT: G 24 MET cc_start: 0.6627 (mmm) cc_final: 0.6272 (mmm) REVERT: G 105 PHE cc_start: 0.7701 (t80) cc_final: 0.6960 (t80) REVERT: G 175 TYR cc_start: 0.6236 (p90) cc_final: 0.5839 (p90) REVERT: G 228 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7454 (mp10) REVERT: G 257 ASP cc_start: 0.8776 (m-30) cc_final: 0.8490 (m-30) REVERT: H 24 ILE cc_start: 0.6627 (mt) cc_final: 0.6408 (pt) REVERT: H 66 ILE cc_start: 0.6662 (mm) cc_final: 0.6455 (mm) REVERT: I 29 SER cc_start: 0.8948 (t) cc_final: 0.8514 (m) REVERT: I 51 ILE cc_start: 0.7704 (mt) cc_final: 0.7364 (mt) REVERT: J 15 LEU cc_start: 0.8353 (tp) cc_final: 0.7936 (tp) REVERT: J 46 VAL cc_start: 0.7531 (t) cc_final: 0.7021 (t) REVERT: J 50 PHE cc_start: 0.7533 (m-10) cc_final: 0.6733 (m-80) REVERT: L 27 ILE cc_start: 0.8073 (mm) cc_final: 0.7578 (mm) REVERT: M 15 LEU cc_start: 0.8913 (tp) cc_final: 0.8451 (tp) REVERT: M 48 TYR cc_start: 0.7868 (m-80) cc_final: 0.7655 (m-80) REVERT: N 43 ASN cc_start: 0.8275 (p0) cc_final: 0.7973 (p0) REVERT: N 66 ILE cc_start: 0.7643 (mm) cc_final: 0.7345 (mm) REVERT: O 50 PHE cc_start: 0.8417 (m-80) cc_final: 0.8078 (m-80) REVERT: O 59 LEU cc_start: 0.8552 (mt) cc_final: 0.8225 (mp) REVERT: O 62 PHE cc_start: 0.8109 (t80) cc_final: 0.7765 (t80) REVERT: R 8 VAL cc_start: 0.7900 (t) cc_final: 0.7685 (p) REVERT: R 37 HIS cc_start: 0.5582 (t-90) cc_final: 0.5167 (t-90) REVERT: R 51 ILE cc_start: 0.7494 (mp) cc_final: 0.7264 (mp) REVERT: R 100 GLU cc_start: 0.8862 (tp30) cc_final: 0.8596 (tm-30) REVERT: R 104 ARG cc_start: 0.8468 (tmm160) cc_final: 0.8204 (tmm-80) REVERT: R 107 GLN cc_start: 0.6316 (pm20) cc_final: 0.5901 (mp-120) outliers start: 10 outliers final: 3 residues processed: 922 average time/residue: 0.2177 time to fit residues: 325.9223 Evaluate side-chains 553 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 550 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain G residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 40.0000 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 265 optimal weight: 6.9990 chunk 497 optimal weight: 0.0980 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 120 GLN ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 195 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 HIS E 456 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 121 HIS ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 GLN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 ASN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.114362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.080266 restraints weight = 106171.899| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.80 r_work: 0.3121 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 39242 Z= 0.256 Angle : 0.695 12.631 53314 Z= 0.365 Chirality : 0.049 0.296 6328 Planarity : 0.005 0.061 7029 Dihedral : 6.322 87.885 5767 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.70 % Allowed : 9.90 % Favored : 87.40 % 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: 0.63 (0.12), residues: 5204 helix: 1.33 (0.10), residues: 2845 sheet: -0.38 (0.24), residues: 526 loop : -0.71 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 114 TYR 0.023 0.002 TYR E 454 PHE 0.029 0.002 PHE T 119 TRP 0.008 0.001 TRP T 122 HIS 0.005 0.001 HIS B 483 Details of bonding type rmsd covalent geometry : bond 0.00586 (39242) covalent geometry : angle 0.69531 (53314) hydrogen bonds : bond 0.05245 ( 2439) hydrogen bonds : angle 4.99184 ( 7158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 555 time to evaluate : 1.420 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: A 52 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: A 257 MET cc_start: 0.8632 (mmm) cc_final: 0.8164 (mtm) REVERT: B 76 ASP cc_start: 0.8683 (t70) cc_final: 0.8460 (t0) REVERT: B 85 ASP cc_start: 0.8207 (m-30) cc_final: 0.7474 (p0) REVERT: B 198 MET cc_start: 0.9166 (tpp) cc_final: 0.8729 (ttm) REVERT: C 413 PHE cc_start: 0.5557 (m-80) cc_final: 0.5313 (m-80) REVERT: C 417 LEU cc_start: 0.8194 (mt) cc_final: 0.7712 (mt) REVERT: D 210 ASP cc_start: 0.8971 (t0) cc_final: 0.8670 (m-30) REVERT: D 454 TYR cc_start: 0.8445 (t80) cc_final: 0.8096 (t80) REVERT: E 165 GLU cc_start: 0.8697 (tp30) cc_final: 0.8397 (tp30) REVERT: E 191 ASN cc_start: 0.7263 (OUTLIER) cc_final: 0.7044 (t0) REVERT: E 197 MET cc_start: 0.8625 (mmp) cc_final: 0.8175 (mtp) REVERT: F 22 ASP cc_start: 0.8275 (m-30) cc_final: 0.7988 (p0) REVERT: F 307 TYR cc_start: 0.8758 (t80) cc_final: 0.8327 (t80) REVERT: S 152 ARG cc_start: 0.3782 (tmt170) cc_final: 0.3145 (ptt90) REVERT: T 122 TRP cc_start: 0.8474 (m100) cc_final: 0.7736 (m100) REVERT: T 251 PHE cc_start: 0.8031 (t80) cc_final: 0.7777 (t80) REVERT: T 260 LEU cc_start: 0.8716 (tt) cc_final: 0.8172 (mt) REVERT: T 264 MET cc_start: 0.8786 (ppp) cc_final: 0.8578 (ppp) REVERT: U 30 TYR cc_start: 0.5554 (t80) cc_final: 0.4816 (t80) REVERT: V 120 MET cc_start: 0.5950 (ppp) cc_final: 0.5514 (ptp) REVERT: V 130 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6578 (t0) REVERT: W 109 LEU cc_start: 0.9575 (tp) cc_final: 0.9169 (pp) REVERT: W 151 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8801 (tm-30) REVERT: G 5 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8209 (ptm-80) REVERT: G 105 PHE cc_start: 0.7332 (t80) cc_final: 0.6858 (t80) REVERT: G 117 ASP cc_start: 0.7660 (t0) cc_final: 0.7065 (t0) REVERT: H 18 ILE cc_start: 0.9024 (tp) cc_final: 0.8524 (tp) REVERT: I 29 SER cc_start: 0.8884 (t) cc_final: 0.8509 (m) REVERT: I 44 ARG cc_start: 0.7130 (tpp-160) cc_final: 0.6925 (tpp-160) REVERT: I 49 MET cc_start: 0.7881 (tmm) cc_final: 0.7616 (tmm) REVERT: J 45 VAL cc_start: 0.8993 (m) cc_final: 0.8747 (m) REVERT: J 50 PHE cc_start: 0.7500 (m-10) cc_final: 0.7050 (m-80) REVERT: M 15 LEU cc_start: 0.8488 (tp) cc_final: 0.8186 (tp) REVERT: M 46 VAL cc_start: 0.7775 (t) cc_final: 0.7542 (p) REVERT: M 48 TYR cc_start: 0.8210 (m-80) cc_final: 0.7879 (m-80) REVERT: M 57 GLU cc_start: 0.8904 (pt0) cc_final: 0.8346 (tp30) REVERT: N 15 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8604 (tp) REVERT: N 64 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7323 (tp) REVERT: O 18 ILE cc_start: 0.8300 (pt) cc_final: 0.7931 (pt) REVERT: O 33 GLN cc_start: 0.8973 (mm110) cc_final: 0.8689 (mm-40) REVERT: O 37 ARG cc_start: 0.8952 (mmt90) cc_final: 0.8304 (mpt-90) REVERT: O 50 PHE cc_start: 0.8492 (m-80) cc_final: 0.8249 (m-80) REVERT: R 36 ARG cc_start: 0.7702 (ttt-90) cc_final: 0.6943 (ttt180) REVERT: R 37 HIS cc_start: 0.6244 (t-90) cc_final: 0.5844 (t-90) REVERT: R 107 GLN cc_start: 0.6558 (pm20) cc_final: 0.6144 (mp-120) outliers start: 101 outliers final: 64 residues processed: 615 average time/residue: 0.1997 time to fit residues: 206.7311 Evaluate side-chains 542 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 473 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 135 CYS Chi-restraints excluded: chain T residue 197 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 297 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 318 optimal weight: 5.9990 chunk 332 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 271 optimal weight: 0.9980 chunk 424 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 471 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 309 HIS D 8 GLN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 GLN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 ASN N 33 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.115019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.081176 restraints weight = 105281.236| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.74 r_work: 0.3158 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39242 Z= 0.157 Angle : 0.608 11.752 53314 Z= 0.316 Chirality : 0.046 0.515 6328 Planarity : 0.004 0.058 7029 Dihedral : 6.213 89.441 5766 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Rotamer: Outliers : 2.75 % Allowed : 12.30 % Favored : 84.95 % 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: 0.71 (0.12), residues: 5204 helix: 1.42 (0.10), residues: 2843 sheet: -0.45 (0.23), residues: 543 loop : -0.67 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 86 TYR 0.018 0.001 TYR T 296 PHE 0.019 0.001 PHE J 62 TRP 0.007 0.001 TRP A 471 HIS 0.006 0.001 HIS B 483 Details of bonding type rmsd covalent geometry : bond 0.00352 (39242) covalent geometry : angle 0.60796 (53314) hydrogen bonds : bond 0.04667 ( 2439) hydrogen bonds : angle 4.72521 ( 7158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 527 time to evaluate : 1.739 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 52 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: A 257 MET cc_start: 0.8549 (mmm) cc_final: 0.8288 (mtm) REVERT: B 54 VAL cc_start: 0.8315 (t) cc_final: 0.8102 (m) REVERT: B 55 GLU cc_start: 0.8399 (tt0) cc_final: 0.8076 (tt0) REVERT: B 76 ASP cc_start: 0.8640 (t70) cc_final: 0.8389 (t0) REVERT: B 85 ASP cc_start: 0.8122 (m-30) cc_final: 0.7600 (p0) REVERT: B 198 MET cc_start: 0.9174 (tpp) cc_final: 0.8225 (ttm) REVERT: B 493 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8404 (p0) REVERT: C 413 PHE cc_start: 0.5649 (m-80) cc_final: 0.5393 (m-80) REVERT: C 417 LEU cc_start: 0.8121 (mt) cc_final: 0.7646 (mt) REVERT: D 210 ASP cc_start: 0.8905 (t0) cc_final: 0.8642 (m-30) REVERT: D 303 MET cc_start: 0.9261 (tmm) cc_final: 0.9037 (tmm) REVERT: D 454 TYR cc_start: 0.8503 (t80) cc_final: 0.8214 (t80) REVERT: E 21 GLU cc_start: 0.8056 (pm20) cc_final: 0.7709 (pm20) REVERT: E 165 GLU cc_start: 0.8651 (tp30) cc_final: 0.8427 (tp30) REVERT: E 187 SER cc_start: 0.8578 (m) cc_final: 0.7872 (t) REVERT: E 197 MET cc_start: 0.8581 (mmp) cc_final: 0.8185 (mtp) REVERT: E 386 ILE cc_start: 0.8643 (mm) cc_final: 0.8316 (pt) REVERT: F 9 GLU cc_start: 0.8341 (mp0) cc_final: 0.8019 (mm-30) REVERT: F 22 ASP cc_start: 0.8298 (m-30) cc_final: 0.8029 (p0) REVERT: F 59 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8084 (mtt) REVERT: F 307 TYR cc_start: 0.8728 (t80) cc_final: 0.8198 (t80) REVERT: S 152 ARG cc_start: 0.3747 (tmt170) cc_final: 0.3117 (ptt90) REVERT: T 122 TRP cc_start: 0.8532 (m100) cc_final: 0.7863 (m100) REVERT: T 251 PHE cc_start: 0.7916 (t80) cc_final: 0.7655 (t80) REVERT: T 260 LEU cc_start: 0.8739 (tt) cc_final: 0.8187 (mt) REVERT: U 64 ASP cc_start: 0.9168 (m-30) cc_final: 0.8929 (m-30) REVERT: V 120 MET cc_start: 0.5957 (ppp) cc_final: 0.5562 (ptp) REVERT: V 130 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6561 (t0) REVERT: W 109 LEU cc_start: 0.9590 (tp) cc_final: 0.9222 (pp) REVERT: W 140 ASP cc_start: 0.8118 (t70) cc_final: 0.7916 (t0) REVERT: G 26 MET cc_start: 0.8243 (ppp) cc_final: 0.8017 (ppp) REVERT: G 105 PHE cc_start: 0.6995 (t80) cc_final: 0.6772 (t80) REVERT: G 117 ASP cc_start: 0.7796 (t0) cc_final: 0.7239 (t0) REVERT: I 29 SER cc_start: 0.8871 (t) cc_final: 0.8536 (m) REVERT: I 49 MET cc_start: 0.7633 (tmm) cc_final: 0.7311 (tmm) REVERT: J 46 VAL cc_start: 0.8085 (t) cc_final: 0.7488 (t) REVERT: J 50 PHE cc_start: 0.7505 (m-10) cc_final: 0.6825 (m-80) REVERT: K 48 TYR cc_start: 0.7394 (m-80) cc_final: 0.7164 (m-80) REVERT: M 46 VAL cc_start: 0.7794 (t) cc_final: 0.7565 (p) REVERT: M 48 TYR cc_start: 0.8220 (m-80) cc_final: 0.7913 (m-80) REVERT: M 57 GLU cc_start: 0.8880 (pt0) cc_final: 0.8292 (tp30) REVERT: N 49 MET cc_start: 0.8215 (ppp) cc_final: 0.7891 (ppp) REVERT: N 57 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: N 64 LEU cc_start: 0.7335 (mm) cc_final: 0.6782 (tp) REVERT: N 66 ILE cc_start: 0.6737 (mm) cc_final: 0.6474 (mm) REVERT: O 33 GLN cc_start: 0.8967 (mm110) cc_final: 0.8741 (mm-40) REVERT: O 37 ARG cc_start: 0.8888 (mmt90) cc_final: 0.8411 (mpt-90) REVERT: O 46 VAL cc_start: 0.8626 (t) cc_final: 0.7948 (m) REVERT: O 48 TYR cc_start: 0.7916 (m-80) cc_final: 0.7557 (m-80) REVERT: O 49 MET cc_start: 0.8662 (ptm) cc_final: 0.7930 (ppp) REVERT: O 59 LEU cc_start: 0.8291 (mt) cc_final: 0.7920 (mp) REVERT: P 33 GLN cc_start: 0.8387 (mm110) cc_final: 0.8122 (mm-40) REVERT: Q 44 ARG cc_start: 0.4257 (tpt170) cc_final: 0.4003 (tpm170) REVERT: R 21 MET cc_start: 0.4827 (tmm) cc_final: 0.4595 (tpp) REVERT: R 37 HIS cc_start: 0.6241 (t-90) cc_final: 0.5857 (t-90) REVERT: R 100 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8752 (tm-30) REVERT: R 119 LEU cc_start: 0.8965 (mt) cc_final: 0.8664 (pp) outliers start: 103 outliers final: 68 residues processed: 586 average time/residue: 0.2261 time to fit residues: 226.2892 Evaluate side-chains 559 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 486 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 493 ASN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 197 ILE Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 ASP Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 126 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 373 optimal weight: 8.9990 chunk 290 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 358 optimal weight: 50.0000 chunk 292 optimal weight: 8.9990 chunk 354 optimal weight: 20.0000 chunk 312 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN D 418 GLN E 324 HIS E 401 GLN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 GLN G 228 GLN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 ASN ** R 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.109763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073254 restraints weight = 105728.355| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.34 r_work: 0.3015 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 39242 Z= 0.349 Angle : 0.753 13.650 53314 Z= 0.394 Chirality : 0.050 0.394 6328 Planarity : 0.005 0.062 7029 Dihedral : 6.436 89.935 5766 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 3.95 % Allowed : 13.80 % Favored : 82.25 % 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: 0.32 (0.12), residues: 5204 helix: 1.13 (0.10), residues: 2842 sheet: -0.76 (0.23), residues: 541 loop : -0.87 (0.15), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 311 TYR 0.025 0.003 TYR C 344 PHE 0.029 0.002 PHE K 62 TRP 0.012 0.002 TRP A 471 HIS 0.005 0.002 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00810 (39242) covalent geometry : angle 0.75315 (53314) hydrogen bonds : bond 0.04893 ( 2439) hydrogen bonds : angle 4.89311 ( 7158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 495 time to evaluate : 1.354 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: B 76 ASP cc_start: 0.8725 (t70) cc_final: 0.8427 (t0) REVERT: B 85 ASP cc_start: 0.8237 (m-30) cc_final: 0.7641 (p0) REVERT: B 198 MET cc_start: 0.9180 (tpp) cc_final: 0.8933 (ttt) REVERT: C 143 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8927 (t) REVERT: C 417 LEU cc_start: 0.8353 (mt) cc_final: 0.7834 (mt) REVERT: C 430 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7871 (mtt-85) REVERT: D 418 GLN cc_start: 0.8890 (tt0) cc_final: 0.8093 (tt0) REVERT: D 454 TYR cc_start: 0.8592 (t80) cc_final: 0.8228 (t80) REVERT: E 187 SER cc_start: 0.8719 (m) cc_final: 0.8225 (t) REVERT: E 193 LEU cc_start: 0.8810 (mp) cc_final: 0.8571 (mt) REVERT: E 197 MET cc_start: 0.8876 (mmp) cc_final: 0.8369 (mtp) REVERT: E 303 MET cc_start: 0.9116 (tpp) cc_final: 0.8781 (ttp) REVERT: E 386 ILE cc_start: 0.8755 (mm) cc_final: 0.8346 (pt) REVERT: E 455 MET cc_start: 0.8641 (tpp) cc_final: 0.8423 (tpp) REVERT: E 459 PHE cc_start: 0.7793 (t80) cc_final: 0.7581 (t80) REVERT: F 9 GLU cc_start: 0.8510 (mp0) cc_final: 0.8120 (mm-30) REVERT: F 59 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8060 (mtt) REVERT: F 307 TYR cc_start: 0.8957 (t80) cc_final: 0.8707 (t80) REVERT: F 332 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8670 (mm-30) REVERT: S 110 GLN cc_start: 0.8974 (pp30) cc_final: 0.8764 (pm20) REVERT: S 151 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8552 (mm-40) REVERT: S 152 ARG cc_start: 0.3980 (tmt170) cc_final: 0.3409 (ptt90) REVERT: T 85 GLU cc_start: 0.6623 (pp20) cc_final: 0.6101 (mm-30) REVERT: T 122 TRP cc_start: 0.8541 (m100) cc_final: 0.7912 (m100) REVERT: T 194 THR cc_start: 0.8402 (p) cc_final: 0.8146 (p) REVERT: T 251 PHE cc_start: 0.8034 (t80) cc_final: 0.7571 (t80) REVERT: V 120 MET cc_start: 0.6383 (ppp) cc_final: 0.6140 (ptp) REVERT: V 130 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6682 (t0) REVERT: W 151 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8650 (tm-30) REVERT: G 26 MET cc_start: 0.8444 (ppp) cc_final: 0.8069 (tmm) REVERT: G 105 PHE cc_start: 0.7281 (t80) cc_final: 0.7018 (t80) REVERT: G 117 ASP cc_start: 0.8132 (t0) cc_final: 0.7454 (t0) REVERT: G 172 TYR cc_start: 0.9259 (m-10) cc_final: 0.8872 (m-10) REVERT: G 277 GLU cc_start: 0.8476 (tp30) cc_final: 0.7958 (tp30) REVERT: K 48 TYR cc_start: 0.7315 (m-80) cc_final: 0.7046 (m-80) REVERT: M 48 TYR cc_start: 0.8439 (m-80) cc_final: 0.8009 (m-80) REVERT: M 57 GLU cc_start: 0.8881 (pt0) cc_final: 0.8213 (tp30) REVERT: N 48 TYR cc_start: 0.8354 (m-80) cc_final: 0.7898 (m-80) REVERT: N 49 MET cc_start: 0.8270 (ppp) cc_final: 0.7811 (ppp) REVERT: N 64 LEU cc_start: 0.7348 (mm) cc_final: 0.7134 (tp) REVERT: N 66 ILE cc_start: 0.7072 (mm) cc_final: 0.6830 (tp) REVERT: O 33 GLN cc_start: 0.8978 (mm110) cc_final: 0.8612 (mm-40) REVERT: O 37 ARG cc_start: 0.8914 (mmt90) cc_final: 0.8349 (mpt-90) REVERT: O 46 VAL cc_start: 0.8600 (t) cc_final: 0.8071 (m) REVERT: O 48 TYR cc_start: 0.8001 (m-80) cc_final: 0.7529 (m-80) REVERT: O 49 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.7902 (ppp) REVERT: P 46 VAL cc_start: 0.8680 (t) cc_final: 0.8042 (p) REVERT: P 49 MET cc_start: 0.7799 (ptt) cc_final: 0.7248 (ptt) REVERT: Q 44 ARG cc_start: 0.4626 (tpt170) cc_final: 0.4369 (tpt170) REVERT: Q 48 TYR cc_start: 0.5429 (m-80) cc_final: 0.5177 (m-80) REVERT: R 36 ARG cc_start: 0.7599 (ttt-90) cc_final: 0.6963 (ttt180) REVERT: R 37 HIS cc_start: 0.6857 (t-90) cc_final: 0.6371 (t-90) REVERT: R 41 MET cc_start: 0.8725 (ppp) cc_final: 0.8476 (ppp) REVERT: R 100 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8700 (tm-30) outliers start: 148 outliers final: 97 residues processed: 592 average time/residue: 0.1838 time to fit residues: 186.4842 Evaluate side-chains 561 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 460 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 113 TYR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 135 CYS Chi-restraints excluded: chain T residue 197 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 125 THR 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 G residue 70 LEU Chi-restraints excluded: chain G residue 175 TYR Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 453 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 309 optimal weight: 0.0980 chunk 505 optimal weight: 0.0670 chunk 371 optimal weight: 6.9990 chunk 400 optimal weight: 8.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 17 ASN ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 GLN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 ASN ** R 107 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 = 0.3972 r_free = 0.3972 target = 0.113094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076097 restraints weight = 103744.815| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.42 r_work: 0.3113 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 39242 Z= 0.148 Angle : 0.613 12.809 53314 Z= 0.317 Chirality : 0.046 0.376 6328 Planarity : 0.004 0.061 7029 Dihedral : 6.300 89.933 5766 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 3.20 % Allowed : 15.61 % Favored : 81.18 % 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: 0.58 (0.12), residues: 5204 helix: 1.35 (0.10), residues: 2863 sheet: -0.73 (0.23), residues: 545 loop : -0.74 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 256 TYR 0.018 0.001 TYR M 48 PHE 0.032 0.001 PHE O 62 TRP 0.006 0.001 TRP A 471 HIS 0.006 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00334 (39242) covalent geometry : angle 0.61281 (53314) hydrogen bonds : bond 0.04293 ( 2439) hydrogen bonds : angle 4.57839 ( 7158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 525 time to evaluate : 1.423 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: A 95 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7833 (p) REVERT: B 76 ASP cc_start: 0.8541 (t70) cc_final: 0.8206 (t0) REVERT: B 85 ASP cc_start: 0.7950 (m-30) cc_final: 0.7570 (p0) REVERT: B 198 MET cc_start: 0.9117 (tpp) cc_final: 0.8874 (ttt) REVERT: B 308 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8629 (tp) REVERT: C 417 LEU cc_start: 0.8275 (mt) cc_final: 0.7771 (mt) REVERT: D 454 TYR cc_start: 0.8505 (t80) cc_final: 0.8296 (t80) REVERT: E 187 SER cc_start: 0.8665 (m) cc_final: 0.8053 (t) REVERT: E 191 ASN cc_start: 0.7078 (t0) cc_final: 0.6795 (t0) REVERT: E 193 LEU cc_start: 0.8617 (mp) cc_final: 0.8366 (mt) REVERT: E 197 MET cc_start: 0.8764 (mmp) cc_final: 0.8329 (mtp) REVERT: E 386 ILE cc_start: 0.8863 (mm) cc_final: 0.8535 (pt) REVERT: F 307 TYR cc_start: 0.8784 (t80) cc_final: 0.8439 (t80) REVERT: F 322 PHE cc_start: 0.8825 (m-80) cc_final: 0.8597 (m-80) REVERT: S 152 ARG cc_start: 0.4135 (tmt170) cc_final: 0.3691 (ptt180) REVERT: T 85 GLU cc_start: 0.6464 (pp20) cc_final: 0.6091 (mm-30) REVERT: T 122 TRP cc_start: 0.8531 (m100) cc_final: 0.7920 (m100) REVERT: T 194 THR cc_start: 0.8320 (p) cc_final: 0.8035 (p) REVERT: T 251 PHE cc_start: 0.7882 (t80) cc_final: 0.7404 (t80) REVERT: T 260 LEU cc_start: 0.8887 (tt) cc_final: 0.8188 (mt) REVERT: V 120 MET cc_start: 0.6503 (ppp) cc_final: 0.6246 (ptp) REVERT: V 130 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6687 (t0) REVERT: W 109 LEU cc_start: 0.9642 (tp) cc_final: 0.9358 (pp) REVERT: W 151 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8459 (tm-30) REVERT: G 24 MET cc_start: 0.8650 (mmm) cc_final: 0.8168 (mmm) REVERT: G 26 MET cc_start: 0.8378 (ppp) cc_final: 0.7979 (tmm) REVERT: G 105 PHE cc_start: 0.7185 (t80) cc_final: 0.6829 (t80) REVERT: G 117 ASP cc_start: 0.8184 (t0) cc_final: 0.7511 (t0) REVERT: G 172 TYR cc_start: 0.9141 (m-10) cc_final: 0.8794 (m-10) REVERT: G 277 GLU cc_start: 0.8347 (tp30) cc_final: 0.7900 (tp30) REVERT: I 29 SER cc_start: 0.8922 (t) cc_final: 0.8605 (m) REVERT: I 50 PHE cc_start: 0.8751 (m-80) cc_final: 0.8531 (m-80) REVERT: I 70 ILE cc_start: 0.6786 (mm) cc_final: 0.6257 (tt) REVERT: J 62 PHE cc_start: 0.8117 (m-10) cc_final: 0.7884 (m-10) REVERT: M 48 TYR cc_start: 0.8422 (m-80) cc_final: 0.8049 (m-80) REVERT: M 57 GLU cc_start: 0.8794 (pt0) cc_final: 0.8225 (tp30) REVERT: N 48 TYR cc_start: 0.8380 (m-80) cc_final: 0.7958 (m-80) REVERT: N 49 MET cc_start: 0.8358 (ppp) cc_final: 0.8151 (ppp) REVERT: N 57 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: N 66 ILE cc_start: 0.7152 (mm) cc_final: 0.6930 (tp) REVERT: O 33 GLN cc_start: 0.9007 (mm110) cc_final: 0.8655 (mm-40) REVERT: O 37 ARG cc_start: 0.8876 (mmt90) cc_final: 0.8321 (mmp80) REVERT: O 46 VAL cc_start: 0.8668 (t) cc_final: 0.8110 (m) REVERT: O 48 TYR cc_start: 0.7998 (m-80) cc_final: 0.7481 (m-80) REVERT: O 49 MET cc_start: 0.8643 (ptm) cc_final: 0.7841 (ppp) REVERT: O 59 LEU cc_start: 0.8543 (mt) cc_final: 0.8232 (mp) REVERT: P 49 MET cc_start: 0.7475 (ptt) cc_final: 0.6984 (ptt) REVERT: P 68 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7420 (m-80) REVERT: Q 44 ARG cc_start: 0.4394 (tpt170) cc_final: 0.4108 (tpt170) REVERT: R 21 MET cc_start: 0.5194 (tmm) cc_final: 0.4789 (tpp) REVERT: R 36 ARG cc_start: 0.7611 (ttt-90) cc_final: 0.7039 (ttt180) REVERT: R 37 HIS cc_start: 0.6610 (t-90) cc_final: 0.6091 (t-90) REVERT: R 41 MET cc_start: 0.8814 (ppp) cc_final: 0.8454 (ppp) REVERT: R 100 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8605 (tm-30) REVERT: R 126 LEU cc_start: 0.9467 (mm) cc_final: 0.9215 (mp) outliers start: 120 outliers final: 73 residues processed: 604 average time/residue: 0.2078 time to fit residues: 215.1977 Evaluate side-chains 546 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 468 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 42 VAL 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 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 135 CYS Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 403 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 324 optimal weight: 6.9990 chunk 18 optimal weight: 0.1980 chunk 311 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 392 optimal weight: 50.0000 chunk 198 optimal weight: 0.3980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN F 195 HIS ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 137 GLN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 ASN P 43 ASN R 107 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.112387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075760 restraints weight = 104543.758| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.14 r_work: 0.3100 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 39242 Z= 0.178 Angle : 0.624 11.459 53314 Z= 0.323 Chirality : 0.046 0.367 6328 Planarity : 0.004 0.061 7029 Dihedral : 6.221 89.227 5766 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 3.31 % Allowed : 16.57 % Favored : 80.12 % 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: 0.61 (0.12), residues: 5204 helix: 1.40 (0.10), residues: 2862 sheet: -0.75 (0.22), residues: 545 loop : -0.75 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 40 TYR 0.020 0.001 TYR E 454 PHE 0.031 0.001 PHE I 62 TRP 0.006 0.001 TRP A 471 HIS 0.006 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00411 (39242) covalent geometry : angle 0.62401 (53314) hydrogen bonds : bond 0.04229 ( 2439) hydrogen bonds : angle 4.53157 ( 7158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 491 time to evaluate : 1.575 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: B 85 ASP cc_start: 0.7976 (m-30) cc_final: 0.7611 (p0) REVERT: B 198 MET cc_start: 0.9163 (tpp) cc_final: 0.8960 (ttt) REVERT: B 308 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8657 (tp) REVERT: C 277 ASP cc_start: 0.7205 (m-30) cc_final: 0.7001 (m-30) REVERT: C 417 LEU cc_start: 0.8325 (mt) cc_final: 0.7833 (mt) REVERT: D 51 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8608 (p0) REVERT: D 418 GLN cc_start: 0.8852 (tt0) cc_final: 0.8125 (tt0) REVERT: D 454 TYR cc_start: 0.8552 (t80) cc_final: 0.8140 (t80) REVERT: E 187 SER cc_start: 0.8710 (m) cc_final: 0.8082 (t) REVERT: E 191 ASN cc_start: 0.7253 (t0) cc_final: 0.6985 (t0) REVERT: E 193 LEU cc_start: 0.8731 (mp) cc_final: 0.8484 (mt) REVERT: E 194 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8881 (tt) REVERT: E 197 MET cc_start: 0.8799 (mmp) cc_final: 0.8365 (mtp) REVERT: E 284 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8383 (mt-10) REVERT: E 386 ILE cc_start: 0.8866 (mm) cc_final: 0.8536 (pt) REVERT: E 455 MET cc_start: 0.8529 (tpp) cc_final: 0.8209 (tpp) REVERT: F 307 TYR cc_start: 0.8792 (t80) cc_final: 0.8418 (t80) REVERT: F 322 PHE cc_start: 0.8834 (m-80) cc_final: 0.8591 (m-80) REVERT: S 152 ARG cc_start: 0.3983 (tmt170) cc_final: 0.3470 (ptt90) REVERT: T 85 GLU cc_start: 0.6527 (pp20) cc_final: 0.6229 (mm-30) REVERT: T 122 TRP cc_start: 0.8502 (m100) cc_final: 0.7869 (m100) REVERT: T 194 THR cc_start: 0.8333 (p) cc_final: 0.8052 (p) REVERT: T 251 PHE cc_start: 0.7911 (t80) cc_final: 0.7429 (t80) REVERT: T 260 LEU cc_start: 0.8901 (tt) cc_final: 0.8229 (mt) REVERT: V 120 MET cc_start: 0.6693 (ppp) cc_final: 0.6443 (ptp) REVERT: V 130 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6703 (t0) REVERT: W 109 LEU cc_start: 0.9632 (tp) cc_final: 0.9326 (pp) REVERT: W 151 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8452 (tm-30) REVERT: G 26 MET cc_start: 0.8407 (ppp) cc_final: 0.7984 (tmm) REVERT: G 117 ASP cc_start: 0.8188 (t0) cc_final: 0.7446 (t0) REVERT: G 119 TYR cc_start: 0.8860 (m-80) cc_final: 0.8560 (m-80) REVERT: G 172 TYR cc_start: 0.9145 (m-10) cc_final: 0.8750 (m-10) REVERT: G 277 GLU cc_start: 0.8377 (tp30) cc_final: 0.8089 (tt0) REVERT: I 26 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9102 (tp) REVERT: I 29 SER cc_start: 0.8842 (t) cc_final: 0.8537 (m) REVERT: I 50 PHE cc_start: 0.8755 (m-80) cc_final: 0.8488 (m-80) REVERT: I 70 ILE cc_start: 0.6764 (mm) cc_final: 0.6328 (tt) REVERT: J 62 PHE cc_start: 0.8105 (m-10) cc_final: 0.7852 (m-10) REVERT: M 48 TYR cc_start: 0.8415 (m-80) cc_final: 0.8069 (m-80) REVERT: M 57 GLU cc_start: 0.8800 (pt0) cc_final: 0.8206 (tp30) REVERT: N 48 TYR cc_start: 0.8337 (m-80) cc_final: 0.7932 (m-80) REVERT: N 49 MET cc_start: 0.8223 (ppp) cc_final: 0.7822 (ppp) REVERT: N 57 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: O 33 GLN cc_start: 0.9015 (mm110) cc_final: 0.8678 (mm-40) REVERT: O 37 ARG cc_start: 0.8897 (mmt90) cc_final: 0.8348 (mmp80) REVERT: O 46 VAL cc_start: 0.8659 (t) cc_final: 0.8128 (m) REVERT: O 48 TYR cc_start: 0.8067 (m-80) cc_final: 0.7541 (m-80) REVERT: O 49 MET cc_start: 0.8610 (ptm) cc_final: 0.7840 (ppp) REVERT: P 49 MET cc_start: 0.7459 (ptt) cc_final: 0.6976 (ptt) REVERT: P 68 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7424 (m-80) REVERT: Q 44 ARG cc_start: 0.4536 (tpt170) cc_final: 0.4334 (tpm170) REVERT: R 21 MET cc_start: 0.5321 (tmm) cc_final: 0.4909 (tpp) REVERT: R 36 ARG cc_start: 0.7658 (ttt-90) cc_final: 0.7132 (ttt180) REVERT: R 37 HIS cc_start: 0.6619 (t-90) cc_final: 0.6114 (t-90) REVERT: R 41 MET cc_start: 0.8691 (ppp) cc_final: 0.8241 (ppp) REVERT: R 100 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8612 (tm-30) outliers start: 124 outliers final: 85 residues processed: 573 average time/residue: 0.2186 time to fit residues: 215.2781 Evaluate side-chains 555 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 463 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 113 TYR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 135 CYS Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 2 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 366 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 412 optimal weight: 10.0000 chunk 491 optimal weight: 0.9990 chunk 355 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.112248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077908 restraints weight = 104552.725| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.38 r_work: 0.3082 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 39242 Z= 0.174 Angle : 0.619 11.686 53314 Z= 0.320 Chirality : 0.046 0.394 6328 Planarity : 0.004 0.063 7029 Dihedral : 6.153 86.580 5766 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.11 % Favored : 95.87 % Rotamer: Outliers : 3.60 % Allowed : 16.63 % Favored : 79.77 % 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: 0.68 (0.12), residues: 5204 helix: 1.44 (0.10), residues: 2854 sheet: -0.75 (0.23), residues: 526 loop : -0.69 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 146 TYR 0.016 0.001 TYR M 48 PHE 0.028 0.001 PHE I 62 TRP 0.005 0.001 TRP A 471 HIS 0.006 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00403 (39242) covalent geometry : angle 0.61927 (53314) hydrogen bonds : bond 0.04148 ( 2439) hydrogen bonds : angle 4.46408 ( 7158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 487 time to evaluate : 1.535 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: A 390 MET cc_start: 0.9169 (mmm) cc_final: 0.8840 (mmm) REVERT: B 85 ASP cc_start: 0.8084 (m-30) cc_final: 0.7663 (p0) REVERT: B 198 MET cc_start: 0.9207 (tpp) cc_final: 0.8876 (ttt) REVERT: B 308 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8668 (tp) REVERT: C 277 ASP cc_start: 0.7279 (m-30) cc_final: 0.7002 (m-30) REVERT: C 417 LEU cc_start: 0.8341 (mt) cc_final: 0.7834 (mt) REVERT: C 430 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7893 (mtt-85) REVERT: D 418 GLN cc_start: 0.8854 (tt0) cc_final: 0.8120 (tt0) REVERT: D 454 TYR cc_start: 0.8603 (t80) cc_final: 0.8219 (t80) REVERT: E 187 SER cc_start: 0.8796 (m) cc_final: 0.7999 (t) REVERT: E 193 LEU cc_start: 0.8794 (mp) cc_final: 0.8528 (mt) REVERT: E 194 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8897 (tt) REVERT: E 197 MET cc_start: 0.8875 (mmp) cc_final: 0.8364 (mtp) REVERT: E 236 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8582 (mtt) REVERT: E 284 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8409 (mt-10) REVERT: E 312 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8517 (m-30) REVERT: E 386 ILE cc_start: 0.8777 (mm) cc_final: 0.8422 (pt) REVERT: E 455 MET cc_start: 0.8550 (tpp) cc_final: 0.8152 (tpp) REVERT: E 459 PHE cc_start: 0.7686 (t80) cc_final: 0.7379 (t80) REVERT: F 307 TYR cc_start: 0.8773 (t80) cc_final: 0.8412 (t80) REVERT: F 322 PHE cc_start: 0.8843 (m-80) cc_final: 0.8633 (m-80) REVERT: S 152 ARG cc_start: 0.4083 (tmt170) cc_final: 0.3562 (ptt90) REVERT: T 85 GLU cc_start: 0.6600 (pp20) cc_final: 0.6130 (mm-30) REVERT: T 122 TRP cc_start: 0.8503 (m100) cc_final: 0.7861 (m100) REVERT: T 194 THR cc_start: 0.8345 (p) cc_final: 0.8057 (p) REVERT: T 251 PHE cc_start: 0.7872 (t80) cc_final: 0.7393 (t80) REVERT: T 260 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8265 (mt) REVERT: V 120 MET cc_start: 0.6765 (ppp) cc_final: 0.6490 (ptp) REVERT: V 130 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6740 (t0) REVERT: W 109 LEU cc_start: 0.9630 (tp) cc_final: 0.9252 (pp) REVERT: W 151 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8482 (tm-30) REVERT: G 26 MET cc_start: 0.8468 (ppp) cc_final: 0.8009 (tmm) REVERT: G 117 ASP cc_start: 0.8197 (t0) cc_final: 0.7453 (t0) REVERT: G 119 TYR cc_start: 0.8882 (m-80) cc_final: 0.8598 (m-80) REVERT: G 168 TYR cc_start: 0.8369 (m-10) cc_final: 0.8057 (m-10) REVERT: G 172 TYR cc_start: 0.9135 (m-10) cc_final: 0.8657 (m-10) REVERT: G 277 GLU cc_start: 0.8461 (tp30) cc_final: 0.8196 (tt0) REVERT: I 26 ILE cc_start: 0.9363 (mm) cc_final: 0.9110 (tp) REVERT: I 29 SER cc_start: 0.8868 (t) cc_final: 0.8565 (m) REVERT: I 50 PHE cc_start: 0.8775 (m-80) cc_final: 0.8530 (m-80) REVERT: I 70 ILE cc_start: 0.6712 (mm) cc_final: 0.6250 (tt) REVERT: M 48 TYR cc_start: 0.8424 (m-80) cc_final: 0.8091 (m-80) REVERT: N 49 MET cc_start: 0.8244 (ppp) cc_final: 0.7876 (ppp) REVERT: O 37 ARG cc_start: 0.8901 (mmt90) cc_final: 0.8337 (mmp80) REVERT: O 48 TYR cc_start: 0.8056 (m-80) cc_final: 0.7518 (m-80) REVERT: O 49 MET cc_start: 0.8590 (ptm) cc_final: 0.8377 (ppp) REVERT: P 49 MET cc_start: 0.7476 (ptt) cc_final: 0.6964 (ptt) REVERT: P 68 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: Q 44 ARG cc_start: 0.4510 (tpt170) cc_final: 0.4285 (tpm170) REVERT: R 21 MET cc_start: 0.5599 (tmm) cc_final: 0.5187 (tpp) REVERT: R 36 ARG cc_start: 0.7671 (ttt-90) cc_final: 0.7113 (ttt180) REVERT: R 37 HIS cc_start: 0.6668 (t-90) cc_final: 0.6117 (t-90) REVERT: R 100 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8603 (tm-30) REVERT: R 126 LEU cc_start: 0.9429 (mm) cc_final: 0.9166 (mp) outliers start: 135 outliers final: 103 residues processed: 578 average time/residue: 0.2189 time to fit residues: 216.8069 Evaluate side-chains 575 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 465 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 131 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 135 CYS Chi-restraints excluded: chain T residue 242 LYS Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 107 ARG Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 215 optimal weight: 0.0770 chunk 438 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 95 optimal weight: 9.9990 chunk 305 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 451 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 chunk 502 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.113523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079045 restraints weight = 104100.294| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.38 r_work: 0.3118 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 39242 Z= 0.141 Angle : 0.613 13.068 53314 Z= 0.315 Chirality : 0.046 0.520 6328 Planarity : 0.004 0.063 7029 Dihedral : 6.079 84.729 5766 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.19 % Favored : 95.79 % Rotamer: Outliers : 3.12 % Allowed : 17.45 % Favored : 79.42 % 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: 5204 helix: 1.47 (0.10), residues: 2856 sheet: -0.68 (0.23), residues: 520 loop : -0.58 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 146 TYR 0.022 0.001 TYR E 454 PHE 0.041 0.001 PHE O 62 TRP 0.005 0.001 TRP A 471 HIS 0.004 0.001 HIS R 37 Details of bonding type rmsd covalent geometry : bond 0.00327 (39242) covalent geometry : angle 0.61279 (53314) hydrogen bonds : bond 0.04003 ( 2439) hydrogen bonds : angle 4.39576 ( 7158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 501 time to evaluate : 1.549 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: A 41 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.8109 (tpp-160) REVERT: A 390 MET cc_start: 0.9157 (mmm) cc_final: 0.8774 (mmm) REVERT: B 85 ASP cc_start: 0.7990 (m-30) cc_final: 0.7614 (p0) REVERT: B 198 MET cc_start: 0.9141 (tpp) cc_final: 0.8853 (ttt) REVERT: B 410 PHE cc_start: 0.8250 (m-80) cc_final: 0.7930 (m-80) REVERT: C 417 LEU cc_start: 0.8260 (mt) cc_final: 0.7763 (mt) REVERT: C 430 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7860 (mtt-85) REVERT: D 454 TYR cc_start: 0.8611 (t80) cc_final: 0.8193 (t80) REVERT: D 455 MET cc_start: 0.7751 (mmm) cc_final: 0.6538 (mmm) REVERT: E 187 SER cc_start: 0.8765 (m) cc_final: 0.7990 (t) REVERT: E 193 LEU cc_start: 0.8716 (mp) cc_final: 0.8391 (mt) REVERT: E 197 MET cc_start: 0.8868 (mmp) cc_final: 0.8386 (mtp) REVERT: E 284 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8405 (mt-10) REVERT: E 285 MET cc_start: 0.9064 (tpp) cc_final: 0.8841 (tpp) REVERT: E 303 MET cc_start: 0.9118 (tpp) cc_final: 0.8807 (ttt) REVERT: E 312 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8520 (m-30) REVERT: E 386 ILE cc_start: 0.8708 (mm) cc_final: 0.8362 (pt) REVERT: E 455 MET cc_start: 0.8547 (tpp) cc_final: 0.8147 (tpp) REVERT: F 307 TYR cc_start: 0.8697 (t80) cc_final: 0.8285 (t80) REVERT: T 85 GLU cc_start: 0.6635 (pp20) cc_final: 0.6149 (mm-30) REVERT: T 122 TRP cc_start: 0.8493 (m100) cc_final: 0.7843 (m100) REVERT: T 194 THR cc_start: 0.8350 (p) cc_final: 0.8063 (p) REVERT: T 251 PHE cc_start: 0.7782 (t80) cc_final: 0.7273 (t80) REVERT: T 260 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8202 (mt) REVERT: V 120 MET cc_start: 0.6897 (ppp) cc_final: 0.6605 (ptp) REVERT: V 130 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6747 (t0) REVERT: W 109 LEU cc_start: 0.9608 (tp) cc_final: 0.9323 (pp) REVERT: W 112 ARG cc_start: 0.8167 (mmt-90) cc_final: 0.7947 (mmt-90) REVERT: W 151 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8485 (tm-30) REVERT: G 26 MET cc_start: 0.8465 (ppp) cc_final: 0.7987 (tmm) REVERT: G 117 ASP cc_start: 0.8141 (t0) cc_final: 0.7348 (t0) REVERT: G 119 TYR cc_start: 0.8870 (m-80) cc_final: 0.8617 (m-80) REVERT: G 172 TYR cc_start: 0.9136 (m-10) cc_final: 0.8592 (m-10) REVERT: G 277 GLU cc_start: 0.8458 (tp30) cc_final: 0.8206 (tt0) REVERT: I 26 ILE cc_start: 0.9321 (mm) cc_final: 0.9035 (tp) REVERT: I 29 SER cc_start: 0.8852 (t) cc_final: 0.8572 (m) REVERT: I 70 ILE cc_start: 0.6728 (mm) cc_final: 0.6230 (tt) REVERT: M 48 TYR cc_start: 0.8397 (m-80) cc_final: 0.8066 (m-80) REVERT: M 57 GLU cc_start: 0.8858 (pt0) cc_final: 0.8090 (tp30) REVERT: N 49 MET cc_start: 0.8171 (ppp) cc_final: 0.7946 (ppp) REVERT: O 37 ARG cc_start: 0.8901 (mmt90) cc_final: 0.8344 (mmp80) REVERT: O 55 PHE cc_start: 0.8612 (m-80) cc_final: 0.8310 (m-80) REVERT: P 68 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: R 21 MET cc_start: 0.5637 (tmm) cc_final: 0.5232 (tpp) REVERT: R 36 ARG cc_start: 0.7669 (ttt-90) cc_final: 0.7115 (ttt180) REVERT: R 37 HIS cc_start: 0.6467 (t-90) cc_final: 0.5942 (t-90) REVERT: R 41 MET cc_start: 0.8602 (ppp) cc_final: 0.8172 (ppp) REVERT: R 100 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8559 (tm-30) REVERT: R 119 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8685 (pp) REVERT: R 126 LEU cc_start: 0.9478 (mm) cc_final: 0.9187 (mp) outliers start: 117 outliers final: 92 residues processed: 573 average time/residue: 0.2239 time to fit residues: 218.4711 Evaluate side-chains 568 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 471 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 131 ILE Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 135 CYS Chi-restraints excluded: chain T residue 242 LYS Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 262 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 417 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 441 optimal weight: 8.9990 chunk 303 optimal weight: 9.9990 chunk 392 optimal weight: 50.0000 chunk 506 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN E 191 ASN F 195 HIS T 121 ASN ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.112371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.075355 restraints weight = 104793.265| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.45 r_work: 0.3099 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 39242 Z= 0.186 Angle : 0.642 13.504 53314 Z= 0.329 Chirality : 0.047 0.618 6328 Planarity : 0.004 0.063 7029 Dihedral : 6.056 82.552 5766 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.52 % Favored : 95.47 % Rotamer: Outliers : 3.20 % Allowed : 17.91 % Favored : 78.89 % 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: 5204 helix: 1.47 (0.10), residues: 2885 sheet: -0.69 (0.23), residues: 518 loop : -0.61 (0.15), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 146 TYR 0.016 0.001 TYR A 491 PHE 0.037 0.002 PHE N 62 TRP 0.004 0.001 TRP A 471 HIS 0.005 0.001 HIS F 324 Details of bonding type rmsd covalent geometry : bond 0.00435 (39242) covalent geometry : angle 0.64204 (53314) hydrogen bonds : bond 0.04062 ( 2439) hydrogen bonds : angle 4.42419 ( 7158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 493 time to evaluate : 1.639 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: A 41 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.8142 (tpp-160) REVERT: B 85 ASP cc_start: 0.7970 (m-30) cc_final: 0.7650 (p0) REVERT: B 198 MET cc_start: 0.9168 (tpp) cc_final: 0.8816 (ttt) REVERT: B 410 PHE cc_start: 0.8307 (m-80) cc_final: 0.7988 (m-80) REVERT: C 277 ASP cc_start: 0.7173 (m-30) cc_final: 0.6918 (m-30) REVERT: C 417 LEU cc_start: 0.8326 (mt) cc_final: 0.7827 (mt) REVERT: C 430 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7916 (mtt-85) REVERT: D 418 GLN cc_start: 0.8898 (tt0) cc_final: 0.8224 (tt0) REVERT: D 454 TYR cc_start: 0.8636 (t80) cc_final: 0.8221 (t80) REVERT: D 455 MET cc_start: 0.7806 (mmm) cc_final: 0.6670 (mmm) REVERT: E 193 LEU cc_start: 0.8684 (mp) cc_final: 0.8414 (mt) REVERT: E 197 MET cc_start: 0.8824 (mmp) cc_final: 0.8384 (mtp) REVERT: E 284 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8406 (mt-10) REVERT: E 303 MET cc_start: 0.9062 (tpp) cc_final: 0.8788 (ttp) REVERT: E 312 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: E 386 ILE cc_start: 0.8747 (mm) cc_final: 0.8393 (pt) REVERT: E 455 MET cc_start: 0.8624 (tpp) cc_final: 0.8218 (tpp) REVERT: F 307 TYR cc_start: 0.8701 (t80) cc_final: 0.8360 (t80) REVERT: S 110 GLN cc_start: 0.8820 (pm20) cc_final: 0.8447 (pm20) REVERT: S 139 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6827 (mt) REVERT: T 85 GLU cc_start: 0.6530 (pp20) cc_final: 0.6090 (mm-30) REVERT: T 122 TRP cc_start: 0.8510 (m100) cc_final: 0.7880 (m100) REVERT: T 194 THR cc_start: 0.8371 (p) cc_final: 0.8078 (p) REVERT: T 251 PHE cc_start: 0.7833 (t80) cc_final: 0.7308 (t80) REVERT: T 260 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8196 (mt) REVERT: V 120 MET cc_start: 0.6926 (ppp) cc_final: 0.6608 (ptp) REVERT: V 130 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6765 (t0) REVERT: W 109 LEU cc_start: 0.9621 (tp) cc_final: 0.9302 (pp) REVERT: W 151 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8493 (tm-30) REVERT: G 26 MET cc_start: 0.8505 (ppp) cc_final: 0.8030 (tmm) REVERT: G 117 ASP cc_start: 0.8160 (t0) cc_final: 0.7349 (t0) REVERT: G 119 TYR cc_start: 0.8909 (m-80) cc_final: 0.8615 (m-80) REVERT: G 172 TYR cc_start: 0.9138 (m-10) cc_final: 0.8543 (m-10) REVERT: I 26 ILE cc_start: 0.9364 (mm) cc_final: 0.9078 (tp) REVERT: I 29 SER cc_start: 0.8889 (t) cc_final: 0.8588 (m) REVERT: J 62 PHE cc_start: 0.7843 (m-10) cc_final: 0.7611 (m-10) REVERT: M 48 TYR cc_start: 0.8433 (m-80) cc_final: 0.8115 (m-80) REVERT: M 57 GLU cc_start: 0.8848 (pt0) cc_final: 0.8090 (tp30) REVERT: N 49 MET cc_start: 0.8224 (ppp) cc_final: 0.7946 (ppp) REVERT: N 62 PHE cc_start: 0.8453 (m-10) cc_final: 0.8237 (m-10) REVERT: O 37 ARG cc_start: 0.8903 (mmt90) cc_final: 0.8345 (mmp80) REVERT: O 55 PHE cc_start: 0.8648 (m-80) cc_final: 0.8332 (m-80) REVERT: P 68 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: R 21 MET cc_start: 0.5658 (tmm) cc_final: 0.5236 (tpp) REVERT: R 36 ARG cc_start: 0.7634 (ttt-90) cc_final: 0.7079 (ttt180) REVERT: R 37 HIS cc_start: 0.6671 (t-90) cc_final: 0.6155 (t-90) REVERT: R 100 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8551 (tm-30) REVERT: R 119 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8724 (pp) REVERT: R 121 LYS cc_start: 0.8566 (tppt) cc_final: 0.8292 (mmtp) REVERT: R 126 LEU cc_start: 0.9494 (mm) cc_final: 0.9183 (mp) outliers start: 120 outliers final: 98 residues processed: 569 average time/residue: 0.1974 time to fit residues: 192.9610 Evaluate side-chains 573 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 469 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 131 ILE Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 242 LYS Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 32 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 341 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 487 optimal weight: 8.9990 chunk 101 optimal weight: 0.0060 chunk 116 optimal weight: 0.6980 chunk 491 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.112918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076032 restraints weight = 103969.842| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.43 r_work: 0.3115 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 39242 Z= 0.160 Angle : 0.641 13.726 53314 Z= 0.327 Chirality : 0.047 0.643 6328 Planarity : 0.004 0.069 7029 Dihedral : 5.975 84.401 5763 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.23 % Favored : 95.75 % Rotamer: Outliers : 2.83 % Allowed : 18.60 % Favored : 78.57 % 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: 0.76 (0.12), residues: 5204 helix: 1.46 (0.10), residues: 2887 sheet: -0.68 (0.23), residues: 530 loop : -0.61 (0.16), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 178 TYR 0.023 0.001 TYR E 454 PHE 0.034 0.001 PHE H 62 TRP 0.006 0.001 TRP T 122 HIS 0.005 0.001 HIS R 37 Details of bonding type rmsd covalent geometry : bond 0.00373 (39242) covalent geometry : angle 0.64078 (53314) hydrogen bonds : bond 0.04019 ( 2439) hydrogen bonds : angle 4.39130 ( 7158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10408 Ramachandran restraints generated. 5204 Oldfield, 0 Emsley, 5204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 495 time to evaluate : 1.632 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: A 94 MET cc_start: 0.8480 (tpp) cc_final: 0.8243 (tpt) REVERT: B 85 ASP cc_start: 0.7953 (m-30) cc_final: 0.7662 (p0) REVERT: B 198 MET cc_start: 0.9129 (tpp) cc_final: 0.8814 (ttt) REVERT: B 410 PHE cc_start: 0.8301 (m-80) cc_final: 0.7984 (m-80) REVERT: C 417 LEU cc_start: 0.8327 (mt) cc_final: 0.7837 (mt) REVERT: C 430 ARG cc_start: 0.8118 (mtt-85) cc_final: 0.7905 (mtt-85) REVERT: D 418 GLN cc_start: 0.8892 (tt0) cc_final: 0.8226 (tt0) REVERT: D 454 TYR cc_start: 0.8643 (t80) cc_final: 0.8243 (t80) REVERT: D 455 MET cc_start: 0.7744 (mmm) cc_final: 0.6629 (mmm) REVERT: E 193 LEU cc_start: 0.8693 (mp) cc_final: 0.8367 (mt) REVERT: E 197 MET cc_start: 0.8813 (mmp) cc_final: 0.8384 (mtp) REVERT: E 284 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8406 (mt-10) REVERT: E 303 MET cc_start: 0.9045 (tpp) cc_final: 0.8782 (ttp) REVERT: E 312 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8475 (m-30) REVERT: E 386 ILE cc_start: 0.8744 (mm) cc_final: 0.8405 (pt) REVERT: E 455 MET cc_start: 0.8607 (tpp) cc_final: 0.8218 (tpp) REVERT: E 459 PHE cc_start: 0.7541 (t80) cc_final: 0.7299 (t80) REVERT: F 307 TYR cc_start: 0.8659 (t80) cc_final: 0.8316 (t80) REVERT: S 110 GLN cc_start: 0.8964 (pm20) cc_final: 0.8675 (pm20) REVERT: S 139 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6893 (mt) REVERT: T 85 GLU cc_start: 0.6588 (pp20) cc_final: 0.6078 (mm-30) REVERT: T 122 TRP cc_start: 0.8489 (m100) cc_final: 0.7842 (m100) REVERT: T 194 THR cc_start: 0.8338 (p) cc_final: 0.8042 (p) REVERT: T 251 PHE cc_start: 0.7817 (t80) cc_final: 0.7285 (t80) REVERT: T 260 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8220 (mt) REVERT: V 120 MET cc_start: 0.7066 (ppp) cc_final: 0.6798 (ptt) REVERT: V 130 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6746 (t0) REVERT: W 109 LEU cc_start: 0.9614 (tp) cc_final: 0.9293 (pp) REVERT: W 151 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8509 (tm-30) REVERT: G 26 MET cc_start: 0.8503 (ppp) cc_final: 0.8021 (tmm) REVERT: G 117 ASP cc_start: 0.8113 (t0) cc_final: 0.7287 (t0) REVERT: G 119 TYR cc_start: 0.8867 (m-80) cc_final: 0.8620 (m-80) REVERT: G 172 TYR cc_start: 0.9073 (m-10) cc_final: 0.8434 (m-10) REVERT: I 29 SER cc_start: 0.8873 (t) cc_final: 0.8599 (m) REVERT: J 62 PHE cc_start: 0.7833 (m-10) cc_final: 0.7560 (m-10) REVERT: M 48 TYR cc_start: 0.8426 (m-80) cc_final: 0.8132 (m-80) REVERT: N 49 MET cc_start: 0.8257 (ppp) cc_final: 0.8029 (ppp) REVERT: O 37 ARG cc_start: 0.8906 (mmt90) cc_final: 0.8344 (mmp80) REVERT: O 55 PHE cc_start: 0.8730 (m-80) cc_final: 0.8387 (m-80) REVERT: P 68 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: Q 49 MET cc_start: 0.8642 (ppp) cc_final: 0.8436 (pmm) REVERT: R 21 MET cc_start: 0.5577 (tmm) cc_final: 0.5192 (tpp) REVERT: R 36 ARG cc_start: 0.7671 (ttt-90) cc_final: 0.7104 (ttt180) REVERT: R 37 HIS cc_start: 0.6453 (t-90) cc_final: 0.5968 (t-90) REVERT: R 41 MET cc_start: 0.8642 (ppp) cc_final: 0.8297 (ppp) REVERT: R 100 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8586 (tm-30) REVERT: R 121 LYS cc_start: 0.8614 (tppt) cc_final: 0.8378 (mmtp) REVERT: R 126 LEU cc_start: 0.9497 (mm) cc_final: 0.9165 (mp) outliers start: 106 outliers final: 89 residues processed: 567 average time/residue: 0.2104 time to fit residues: 205.4935 Evaluate side-chains 564 residues out of total 4192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 470 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 312 ASP Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 410 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 442 ASN Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 131 ILE Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain T residue 80 LEU Chi-restraints excluded: chain T residue 125 LEU Chi-restraints excluded: chain T residue 242 LYS Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain U residue 39 GLU Chi-restraints excluded: chain V residue 130 ASP Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain W residue 117 HIS Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 68 PHE Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 81 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 402 optimal weight: 0.4980 chunk 327 optimal weight: 10.0000 chunk 318 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 395 optimal weight: 50.0000 chunk 7 optimal weight: 0.5980 chunk 263 optimal weight: 0.0000 chunk 174 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 467 optimal weight: 5.9990 chunk 488 optimal weight: 6.9990 overall best weight: 0.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN E 195 HIS F 195 HIS ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 149 HIS ** K 33 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 = 0.3996 r_free = 0.3996 target = 0.114513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080459 restraints weight = 104277.011| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.37 r_work: 0.3148 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 39242 Z= 0.128 Angle : 0.626 13.740 53314 Z= 0.319 Chirality : 0.047 0.574 6328 Planarity : 0.004 0.065 7029 Dihedral : 5.936 83.310 5763 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.02 % Rotamer: Outliers : 2.48 % Allowed : 19.40 % Favored : 78.12 % 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: 5204 helix: 1.51 (0.10), residues: 2855 sheet: -0.68 (0.22), residues: 550 loop : -0.61 (0.16), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 178 TYR 0.018 0.001 TYR A 491 PHE 0.033 0.001 PHE H 62 TRP 0.004 0.001 TRP C 471 HIS 0.006 0.001 HIS R 37 Details of bonding type rmsd covalent geometry : bond 0.00288 (39242) covalent geometry : angle 0.62557 (53314) hydrogen bonds : bond 0.03889 ( 2439) hydrogen bonds : angle 4.33655 ( 7158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10648.02 seconds wall clock time: 182 minutes 34.39 seconds (10954.39 seconds total)