Starting phenix.real_space_refine on Thu Mar 5 11:24:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dnh_30783/03_2026/7dnh_30783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dnh_30783/03_2026/7dnh_30783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dnh_30783/03_2026/7dnh_30783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dnh_30783/03_2026/7dnh_30783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dnh_30783/03_2026/7dnh_30783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dnh_30783/03_2026/7dnh_30783.map" } resolution = 3.64 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= 0.002 sd= 1.261 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 13857 2.51 5 N 3628 2.21 5 O 4183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21788 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3743 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 33, 'TRANS': 438} Chain: "A" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3671 Classifications: {'peptide': 463} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 430} Chain: "C" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3743 Classifications: {'peptide': 472} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 438} Chain: "D" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3603 Classifications: {'peptide': 454} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 424} Chain: "E" Number of atoms: 3745 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 472, 3743 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 437} Conformer: "B" Number of residues, atoms: 472, 3743 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 437} bond proxies already assigned to first conformer: 3843 Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1658 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 204} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1625 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 200} Time building chain proxies: 6.04, per 1000 atoms: 0.28 Number of scatterers: 21788 At special positions: 0 Unit cell: (172.634, 179.36, 158.061, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4183 8.00 N 3628 7.00 C 13857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5140 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 50 sheets defined 11.1% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.802A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR B 276 " --> pdb=" O ASP B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 276' Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.763A pdb=" N ALA B 284 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 383 through 394 removed outlier: 3.558A pdb=" N MET B 387 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.432A pdb=" N LEU B 398 " --> pdb=" O ASP B 394 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP B 400 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.803A pdb=" N ASN B 441 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 removed outlier: 4.091A pdb=" N GLN B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.517A pdb=" N MET A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.590A pdb=" N LEU A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A 276 " --> pdb=" O ASP A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 276' Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.631A pdb=" N ASN A 327 " --> pdb=" O CYS A 324 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A 328 " --> pdb=" O TRP A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 328' Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.856A pdb=" N THR A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.555A pdb=" N ASP A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 4.497A pdb=" N LYS A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 removed outlier: 4.138A pdb=" N GLN A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.859A pdb=" N LEU A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.535A pdb=" N LYS C 83 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.880A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.666A pdb=" N ALA C 411 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 442 removed outlier: 4.047A pdb=" N LYS C 442 " --> pdb=" O PRO C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 460 removed outlier: 4.176A pdb=" N GLN C 460 " --> pdb=" O ASP C 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 457 through 460' Processing helix chain 'C' and resid 461 through 472 removed outlier: 3.820A pdb=" N ARG C 465 " --> pdb=" O PHE C 461 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS C 466 " --> pdb=" O PRO C 462 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 471 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 324 through 328 removed outlier: 4.069A pdb=" N ASN D 327 " --> pdb=" O CYS D 324 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN D 328 " --> pdb=" O TRP D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 328' Processing helix chain 'D' and resid 383 through 394 removed outlier: 3.766A pdb=" N TYR D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D 393 " --> pdb=" O TYR D 389 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 removed outlier: 3.611A pdb=" N ASP D 400 " --> pdb=" O ASN D 396 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 461 removed outlier: 3.811A pdb=" N GLN D 460 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.989A pdb=" N LEU D 469 " --> pdb=" O ARG D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.596A pdb=" N LYS E 83 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 84' Processing helix chain 'E' and resid 209 through 214 removed outlier: 3.792A pdb=" N LEU E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN E 214 " --> pdb=" O PHE E 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 209 through 214' Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 233 through 238 removed outlier: 3.530A pdb=" N MET E 237 " --> pdb=" O ASP E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 removed outlier: 3.949A pdb=" N LEU E 275 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR E 276 " --> pdb=" O ASP E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 272 through 276' Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 383 through 394 removed outlier: 3.508A pdb=" N TYR E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 401 removed outlier: 4.580A pdb=" N LEU E 398 " --> pdb=" O ASP E 394 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP E 400 " --> pdb=" O ASN E 396 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP E 401 " --> pdb=" O ILE E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 442 Processing helix chain 'E' and resid 461 through 472 removed outlier: 3.874A pdb=" N LEU E 469 " --> pdb=" O ARG E 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.789A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.661A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG L 188 " --> pdb=" O ASP L 184 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 189' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.663A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.581A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing sheet with id=AA1, first strand: chain 'B' and resid 311 through 312 removed outlier: 6.760A pdb=" N VAL B 374 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 106 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN B 372 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE B 108 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP B 370 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.636A pdb=" N ALA B 44 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 364 " --> pdb=" O MET B 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.930A pdb=" N ILE B 52 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 291 through 296 removed outlier: 4.140A pdb=" N HIS B 259 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER B 296 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL B 257 " --> pdb=" O SER B 296 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 248 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 160 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B 158 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN B 154 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 157 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 72 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 448 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG B 75 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 291 through 296 removed outlier: 4.140A pdb=" N HIS B 259 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER B 296 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL B 257 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 124 removed outlier: 5.120A pdb=" N GLY B 120 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET B 150 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU B 148 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 191 Processing sheet with id=AA8, first strand: chain 'B' and resid 266 through 267 removed outlier: 7.653A pdb=" N LYS B 266 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N VAL C 363 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLU C 368 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG C 110 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP C 370 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE C 108 " --> pdb=" O ASP C 370 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLN C 372 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU C 106 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 374 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 106 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 100 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 38 removed outlier: 7.896A pdb=" N SER C 29 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR C 381 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR C 31 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LYS C 379 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE C 33 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 44 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 42 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 300 through 301 removed outlier: 3.559A pdb=" N GLN A 154 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 97 through 107 removed outlier: 6.713A pdb=" N VAL A 374 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU A 106 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN A 372 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE A 33 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS A 379 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR A 31 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR A 381 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N SER A 29 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 43 through 46 Processing sheet with id=AB5, first strand: chain 'A' and resid 52 through 53 removed outlier: 6.879A pdb=" N ILE A 52 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AB7, first strand: chain 'A' and resid 119 through 124 removed outlier: 4.857A pdb=" N GLY A 120 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET A 150 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU A 148 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 188 through 194 removed outlier: 3.511A pdb=" N PHE A 191 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 169 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 167 " --> pdb=" O SER A 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 257 through 262 removed outlier: 6.938A pdb=" N THR A 294 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE A 260 " --> pdb=" O PHE A 292 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE A 292 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 346 through 347 removed outlier: 4.050A pdb=" N LYS E 266 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 52 through 53 removed outlier: 7.221A pdb=" N ILE C 52 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 446 through 447 removed outlier: 3.817A pdb=" N ARG C 75 " --> pdb=" O TRP C 446 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 329 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 157 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS C 158 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 250 " --> pdb=" O CYS C 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 189 through 194 removed outlier: 3.516A pdb=" N PHE C 191 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS C 169 " --> pdb=" O PHE C 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 257 through 262 removed outlier: 7.006A pdb=" N THR C 294 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE C 260 " --> pdb=" O PHE C 292 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N PHE C 292 " --> pdb=" O PHE C 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 266 through 267 removed outlier: 7.280A pdb=" N LYS C 266 " --> pdb=" O GLU D 361 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL D 363 " --> pdb=" O LYS C 266 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 377 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE D 33 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LYS D 379 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 31 " --> pdb=" O LYS D 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 266 through 267 removed outlier: 7.280A pdb=" N LYS C 266 " --> pdb=" O GLU D 361 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL D 363 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 42 through 46 removed outlier: 6.544A pdb=" N ASP D 370 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE D 108 " --> pdb=" O ASP D 370 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN D 372 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU D 106 " --> pdb=" O GLN D 372 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL D 374 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 106 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 52 through 53 removed outlier: 7.266A pdb=" N ILE D 52 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 248 through 254 removed outlier: 4.056A pdb=" N PHE D 248 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 160 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN D 154 " --> pdb=" O GLN D 254 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP D 446 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 119 through 124 removed outlier: 5.641A pdb=" N GLY D 120 " --> pdb=" O MET D 150 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET D 150 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU D 148 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 128 through 129 removed outlier: 4.010A pdb=" N ASP D 128 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN D 262 " --> pdb=" O ASP D 128 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL D 257 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N SER D 296 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS D 259 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 294 " --> pdb=" O HIS D 259 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 189 through 194 Processing sheet with id=AD5, first strand: chain 'D' and resid 266 through 267 removed outlier: 6.822A pdb=" N LYS D 266 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N VAL E 363 " --> pdb=" O LYS D 266 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU E 377 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE E 33 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LYS E 379 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR E 31 " --> pdb=" O LYS E 379 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR E 381 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N SER E 29 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 42 through 46 removed outlier: 3.577A pdb=" N ALA E 44 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU E 367 " --> pdb=" O ALA E 44 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 106 through 109 removed outlier: 3.573A pdb=" N GLU E 107 " --> pdb=" O GLN E 372 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP E 370 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 250 through 254 removed outlier: 3.612A pdb=" N VAL E 334 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR E 332 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU E 329 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL E 73 " --> pdb=" O TRP E 446 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL E 448 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG E 75 " --> pdb=" O VAL E 448 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 119 through 124 removed outlier: 3.625A pdb=" N TYR E 123 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU E 146 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 128 through 129 removed outlier: 4.003A pdb=" N ASP E 128 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN E 262 " --> pdb=" O ASP E 128 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS E 259 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 294 " --> pdb=" O HIS E 259 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE E 261 " --> pdb=" O PHE E 292 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AE3, first strand: chain 'E' and resid 170 through 172 Processing sheet with id=AE4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.719A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU L 73 " --> pdb=" O ILE L 21 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.693A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN L 37 " --> pdb=" O GLN L 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 114 through 117 removed outlier: 3.594A pdb=" N ASN L 137 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER L 116 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE L 135 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.673A pdb=" N TRP L 148 " --> pdb=" O ARG L 155 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA L 196 " --> pdb=" O ILE L 205 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.543A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.515A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 45 through 51 removed outlier: 5.192A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.745A pdb=" N SER H 125 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU H 146 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER H 184 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS H 148 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU H 182 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER H 185 " --> pdb=" O HIS H 169 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS H 169 " --> pdb=" O SER H 185 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.745A pdb=" N SER H 125 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU H 146 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER H 184 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS H 148 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU H 182 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.607A pdb=" N VAL H 188 " --> pdb=" O VAL H 141 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 156 through 159 removed outlier: 3.550A pdb=" N LYS H 213 " --> pdb=" O CYS H 200 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 211 " --> pdb=" O VAL H 202 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6783 1.33 - 1.45: 4573 1.45 - 1.57: 10850 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 22371 Sorted by residual: bond pdb=" C GLY L 93 " pdb=" N THR L 94 " ideal model delta sigma weight residual 1.334 1.245 0.090 1.72e-02 3.38e+03 2.73e+01 bond pdb=" C LYS D 434 " pdb=" N GLU D 435 " ideal model delta sigma weight residual 1.331 1.376 -0.044 1.62e-02 3.81e+03 7.50e+00 bond pdb=" C PRO C 408 " pdb=" N PRO C 409 " ideal model delta sigma weight residual 1.334 1.395 -0.062 2.34e-02 1.83e+03 6.91e+00 bond pdb=" C ASP B 80 " pdb=" N PRO B 81 " ideal model delta sigma weight residual 1.334 1.312 0.022 8.40e-03 1.42e+04 6.76e+00 bond pdb=" CA PHE E 260 " pdb=" CB PHE E 260 " ideal model delta sigma weight residual 1.532 1.494 0.038 1.62e-02 3.81e+03 5.63e+00 ... (remaining 22366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 28743 2.16 - 4.31: 1455 4.31 - 6.47: 178 6.47 - 8.63: 41 8.63 - 10.78: 11 Bond angle restraints: 30428 Sorted by residual: angle pdb=" N ALA D 411 " pdb=" CA ALA D 411 " pdb=" C ALA D 411 " ideal model delta sigma weight residual 111.02 119.32 -8.30 1.22e+00 6.72e-01 4.62e+01 angle pdb=" N GLN A 423 " pdb=" CA GLN A 423 " pdb=" C GLN A 423 " ideal model delta sigma weight residual 110.91 117.52 -6.61 1.17e+00 7.31e-01 3.20e+01 angle pdb=" C SER H 177 " pdb=" N ASP H 178 " pdb=" CA ASP H 178 " ideal model delta sigma weight residual 122.61 129.68 -7.07 1.56e+00 4.11e-01 2.05e+01 angle pdb=" C VAL E 63 " pdb=" CA VAL E 63 " pdb=" CB VAL E 63 " ideal model delta sigma weight residual 110.16 114.64 -4.48 1.01e+00 9.80e-01 1.97e+01 angle pdb=" N VAL E 3 " pdb=" CA VAL E 3 " pdb=" C VAL E 3 " ideal model delta sigma weight residual 112.96 108.55 4.41 1.00e+00 1.00e+00 1.95e+01 ... (remaining 30423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11810 17.95 - 35.90: 1267 35.90 - 53.85: 189 53.85 - 71.81: 46 71.81 - 89.76: 16 Dihedral angle restraints: 13328 sinusoidal: 5302 harmonic: 8026 Sorted by residual: dihedral pdb=" CA PRO E 15 " pdb=" C PRO E 15 " pdb=" N VAL E 16 " pdb=" CA VAL E 16 " ideal model delta harmonic sigma weight residual 180.00 138.41 41.59 0 5.00e+00 4.00e-02 6.92e+01 dihedral pdb=" CA TYR B 136 " pdb=" C TYR B 136 " pdb=" N PRO B 137 " pdb=" CA PRO B 137 " ideal model delta harmonic sigma weight residual 180.00 141.48 38.52 0 5.00e+00 4.00e-02 5.94e+01 dihedral pdb=" CA SER A 422 " pdb=" C SER A 422 " pdb=" N GLN A 423 " pdb=" CA GLN A 423 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 13325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2330 0.059 - 0.119: 741 0.119 - 0.178: 183 0.178 - 0.238: 28 0.238 - 0.297: 5 Chirality restraints: 3287 Sorted by residual: chirality pdb=" CB VAL E 201 " pdb=" CA VAL E 201 " pdb=" CG1 VAL E 201 " pdb=" CG2 VAL E 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB VAL C 22 " pdb=" CA VAL C 22 " pdb=" CG1 VAL C 22 " pdb=" CG2 VAL C 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB VAL D 201 " pdb=" CA VAL D 201 " pdb=" CG1 VAL D 201 " pdb=" CG2 VAL D 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3284 not shown) Planarity restraints: 3972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 408 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO E 409 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO E 409 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 409 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 406 " -0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO B 407 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 16 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C VAL E 16 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL E 16 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO E 17 " -0.017 2.00e-02 2.50e+03 ... (remaining 3969 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 89 2.41 - 3.03: 12205 3.03 - 3.66: 32144 3.66 - 4.28: 43326 4.28 - 4.90: 72200 Nonbonded interactions: 159964 Sorted by model distance: nonbonded pdb=" O PRO D 409 " pdb=" OG SER D 410 " model vdw 1.791 3.040 nonbonded pdb=" O PRO E 409 " pdb=" OG SER E 410 " model vdw 2.038 3.040 nonbonded pdb=" OG1 THR A 346 " pdb=" O LYS A 360 " model vdw 2.249 3.040 nonbonded pdb=" OG SER E 23 " pdb=" OD1 ASP E 25 " model vdw 2.281 3.040 nonbonded pdb=" O ILE B 425 " pdb=" OG1 THR B 426 " model vdw 2.282 3.040 ... (remaining 159959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 157 or resid 159 through 473)) selection = (chain 'B' and (resid 20 through 157 or resid 159 through 473)) selection = (chain 'C' and (resid 20 through 157 or resid 159 through 473)) selection = (chain 'D' and (resid 20 through 157 or resid 159 through 473)) selection = (chain 'E' and (resid 20 through 157 or resid 159 through 473)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.200 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.008 0.090 22375 Z= 0.398 Angle : 1.085 10.781 30436 Z= 0.608 Chirality : 0.062 0.297 3287 Planarity : 0.008 0.102 3972 Dihedral : 15.006 89.758 8176 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.61 % Favored : 90.21 % Rotamer: Outliers : 0.78 % Allowed : 13.55 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.48 (0.12), residues: 2748 helix: -4.28 (0.17), residues: 179 sheet: -2.45 (0.16), residues: 744 loop : -3.27 (0.11), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 263 TYR 0.021 0.003 TYR D 369 PHE 0.033 0.003 PHE A 454 TRP 0.036 0.002 TRP L 92 HIS 0.010 0.002 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00837 (22371) covalent geometry : angle 1.08487 (30428) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.87569 ( 8) hydrogen bonds : bond 0.31828 ( 387) hydrogen bonds : angle 10.67019 ( 996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 651 time to evaluate : 0.831 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: B 49 TYR cc_start: 0.8718 (m-10) cc_final: 0.8464 (m-10) REVERT: B 126 LYS cc_start: 0.8842 (tmtt) cc_final: 0.8222 (tmtt) REVERT: B 172 LYS cc_start: 0.8408 (tppt) cc_final: 0.7902 (tppt) REVERT: B 210 PHE cc_start: 0.8811 (m-80) cc_final: 0.8502 (m-80) REVERT: B 217 LYS cc_start: 0.8303 (mttm) cc_final: 0.7594 (mttt) REVERT: B 315 ARG cc_start: 0.8442 (tpt90) cc_final: 0.8145 (pmt-80) REVERT: B 451 LYS cc_start: 0.8591 (tppp) cc_final: 0.8103 (mmtt) REVERT: A 25 ASP cc_start: 0.8618 (m-30) cc_final: 0.8304 (m-30) REVERT: A 99 LEU cc_start: 0.9087 (mt) cc_final: 0.8705 (mp) REVERT: A 106 LEU cc_start: 0.9286 (tp) cc_final: 0.8962 (tp) REVERT: A 126 LYS cc_start: 0.8886 (tmtt) cc_final: 0.8573 (tptp) REVERT: A 135 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7103 (ptm160) REVERT: A 153 LYS cc_start: 0.8629 (ptmm) cc_final: 0.8317 (pttm) REVERT: A 217 LYS cc_start: 0.9356 (mttm) cc_final: 0.9063 (mtmt) REVERT: A 291 PHE cc_start: 0.8092 (m-80) cc_final: 0.7660 (m-10) REVERT: A 342 MET cc_start: 0.8397 (mtm) cc_final: 0.7828 (ptm) REVERT: A 418 ARG cc_start: 0.4550 (ptt-90) cc_final: 0.3350 (ptt-90) REVERT: C 71 TYR cc_start: 0.8496 (m-80) cc_final: 0.8050 (m-80) REVERT: C 110 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8007 (mmm-85) REVERT: C 153 LYS cc_start: 0.9310 (ttpp) cc_final: 0.8934 (tttt) REVERT: C 235 LEU cc_start: 0.9525 (mm) cc_final: 0.9251 (mm) REVERT: C 269 GLU cc_start: 0.7926 (mt-10) cc_final: 0.6782 (tt0) REVERT: C 387 MET cc_start: 0.8758 (ttt) cc_final: 0.8355 (tpp) REVERT: C 398 LEU cc_start: 0.9005 (mt) cc_final: 0.8183 (mt) REVERT: C 446 TRP cc_start: 0.8635 (t60) cc_final: 0.8417 (t-100) REVERT: C 453 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8877 (mmtm) REVERT: C 455 SER cc_start: 0.9227 (t) cc_final: 0.8916 (t) REVERT: D 26 GLU cc_start: 0.7814 (tp30) cc_final: 0.7604 (tp30) REVERT: D 50 PHE cc_start: 0.8736 (p90) cc_final: 0.8146 (p90) REVERT: D 71 TYR cc_start: 0.9102 (m-80) cc_final: 0.8885 (m-80) REVERT: D 134 ASN cc_start: 0.8275 (t0) cc_final: 0.7829 (t0) REVERT: D 152 TYR cc_start: 0.7137 (m-10) cc_final: 0.6873 (m-10) REVERT: D 240 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8811 (tm-30) REVERT: D 309 LYS cc_start: 0.9303 (mtmt) cc_final: 0.8741 (ttpp) REVERT: D 399 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8488 (tm-30) REVERT: D 447 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8551 (tm-30) REVERT: D 470 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8899 (tm-30) REVERT: E 65 LYS cc_start: 0.9279 (tttt) cc_final: 0.9074 (tttm) REVERT: E 83 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8649 (mtpp) REVERT: E 84 PHE cc_start: 0.7803 (m-10) cc_final: 0.6987 (t80) REVERT: E 99 LEU cc_start: 0.9461 (mm) cc_final: 0.9150 (mm) REVERT: E 123 TYR cc_start: 0.8947 (m-80) cc_final: 0.8243 (m-80) REVERT: E 146 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6471 (mm-30) REVERT: E 152 TYR cc_start: 0.8198 (m-80) cc_final: 0.7862 (m-10) REVERT: E 154 GLN cc_start: 0.8075 (mp10) cc_final: 0.7756 (mp10) REVERT: E 163 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8954 (mmtp) REVERT: E 217 LYS cc_start: 0.8569 (mttt) cc_final: 0.7962 (ptpp) REVERT: E 244 ASP cc_start: 0.7349 (t70) cc_final: 0.7101 (t70) REVERT: E 303 GLU cc_start: 0.7582 (mp0) cc_final: 0.7134 (mp0) REVERT: E 306 LEU cc_start: 0.9294 (mt) cc_final: 0.9047 (mt) REVERT: E 311 TYR cc_start: 0.8260 (m-80) cc_final: 0.7533 (m-10) REVERT: E 321 ASN cc_start: 0.8977 (t0) cc_final: 0.8534 (t0) REVERT: E 329 LEU cc_start: 0.8931 (mt) cc_final: 0.8622 (mt) REVERT: E 342 MET cc_start: 0.9060 (mmm) cc_final: 0.8672 (mmm) REVERT: E 402 GLN cc_start: 0.8198 (mp10) cc_final: 0.7990 (mp10) REVERT: E 418 ARG cc_start: 0.7902 (tmm160) cc_final: 0.6339 (mtt-85) REVERT: E 451 LYS cc_start: 0.8846 (mptt) cc_final: 0.8586 (mptt) REVERT: L 23 CYS cc_start: 0.4481 (t) cc_final: 0.4133 (t) REVERT: L 142 LYS cc_start: 0.4187 (tttt) cc_final: 0.3778 (tttm) REVERT: L 175 MET cc_start: 0.7868 (ttt) cc_final: 0.7438 (tpt) REVERT: H 104 TYR cc_start: 0.4351 (m-80) cc_final: 0.3545 (m-80) outliers start: 19 outliers final: 15 residues processed: 666 average time/residue: 0.1560 time to fit residues: 158.8084 Evaluate side-chains 483 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 468 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain H residue 20 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN B 112 GLN B 134 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN C 391 HIS ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN D 320 ASN D 328 GLN D 391 HIS E 47 ASN E 56 ASN E 125 ASN E 178 ASN E 179 ASN E 216 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN E 441 ASN L 53 ASN ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100781 restraints weight = 68106.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104312 restraints weight = 28363.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106588 restraints weight = 16622.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108030 restraints weight = 11714.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108918 restraints weight = 9405.530| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22375 Z= 0.240 Angle : 0.732 10.515 30436 Z= 0.378 Chirality : 0.047 0.266 3287 Planarity : 0.006 0.083 3972 Dihedral : 6.231 39.172 3013 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.81 % Allowed : 19.86 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.13), residues: 2748 helix: -3.23 (0.25), residues: 207 sheet: -2.03 (0.17), residues: 737 loop : -2.92 (0.12), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 251 TYR 0.018 0.002 TYR A 389 PHE 0.019 0.002 PHE A 248 TRP 0.031 0.001 TRP L 92 HIS 0.008 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00530 (22371) covalent geometry : angle 0.73194 (30428) SS BOND : bond 0.00433 ( 4) SS BOND : angle 0.88440 ( 8) hydrogen bonds : bond 0.05167 ( 387) hydrogen bonds : angle 7.25528 ( 996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 514 time to evaluate : 0.713 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: B 75 ARG cc_start: 0.8536 (ttt180) cc_final: 0.7981 (ttt-90) REVERT: B 134 ASN cc_start: 0.7478 (t0) cc_final: 0.6906 (t0) REVERT: B 172 LYS cc_start: 0.8183 (tppt) cc_final: 0.7732 (tppt) REVERT: B 250 LEU cc_start: 0.8488 (mt) cc_final: 0.8226 (mp) REVERT: B 315 ARG cc_start: 0.8632 (tpt90) cc_final: 0.8188 (pmt-80) REVERT: B 359 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: A 25 ASP cc_start: 0.8596 (m-30) cc_final: 0.8324 (m-30) REVERT: A 99 LEU cc_start: 0.9175 (mt) cc_final: 0.8909 (mp) REVERT: A 106 LEU cc_start: 0.9433 (tp) cc_final: 0.9224 (tp) REVERT: A 126 LYS cc_start: 0.8673 (tmtt) cc_final: 0.8245 (tptp) REVERT: A 135 ARG cc_start: 0.7607 (mtt180) cc_final: 0.6981 (ptm160) REVERT: A 153 LYS cc_start: 0.8883 (ptmm) cc_final: 0.8517 (pttm) REVERT: A 200 MET cc_start: 0.8740 (mmm) cc_final: 0.8478 (mmm) REVERT: A 217 LYS cc_start: 0.9460 (mttm) cc_final: 0.9113 (mtmt) REVERT: A 247 PHE cc_start: 0.8626 (m-10) cc_final: 0.8201 (m-80) REVERT: A 291 PHE cc_start: 0.8064 (m-80) cc_final: 0.7667 (m-10) REVERT: A 342 MET cc_start: 0.8387 (mtm) cc_final: 0.7738 (ptp) REVERT: A 360 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8167 (ttmm) REVERT: A 367 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7411 (mt-10) REVERT: A 418 ARG cc_start: 0.4247 (ptt-90) cc_final: 0.3215 (ptt-90) REVERT: A 454 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8213 (m-10) REVERT: C 71 TYR cc_start: 0.8805 (m-80) cc_final: 0.8580 (m-80) REVERT: C 110 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.8028 (mmm-85) REVERT: C 151 ASP cc_start: 0.7577 (t0) cc_final: 0.7366 (t0) REVERT: C 153 LYS cc_start: 0.9246 (ttpp) cc_final: 0.8893 (tttt) REVERT: C 208 MET cc_start: 0.8205 (ptp) cc_final: 0.7856 (pmm) REVERT: C 254 GLN cc_start: 0.8786 (pt0) cc_final: 0.8585 (pt0) REVERT: C 255 MET cc_start: 0.8640 (ppp) cc_final: 0.8419 (ppp) REVERT: C 381 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8710 (p) REVERT: C 387 MET cc_start: 0.9052 (ttt) cc_final: 0.8433 (tpp) REVERT: C 446 TRP cc_start: 0.8660 (t60) cc_final: 0.8416 (t-100) REVERT: C 453 LYS cc_start: 0.9133 (mmtp) cc_final: 0.8852 (mmtm) REVERT: D 26 GLU cc_start: 0.7907 (tp30) cc_final: 0.7680 (tp30) REVERT: D 71 TYR cc_start: 0.9075 (m-80) cc_final: 0.8573 (m-80) REVERT: D 146 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: D 208 MET cc_start: 0.8188 (ptt) cc_final: 0.7747 (ptp) REVERT: D 237 MET cc_start: 0.8930 (mtm) cc_final: 0.8546 (mtt) REVERT: D 269 GLU cc_start: 0.8210 (tp30) cc_final: 0.7944 (tp30) REVERT: D 302 SER cc_start: 0.8931 (p) cc_final: 0.8375 (p) REVERT: D 309 LYS cc_start: 0.9112 (mtmt) cc_final: 0.8709 (ttpp) REVERT: D 426 THR cc_start: 0.8549 (m) cc_final: 0.8292 (p) REVERT: D 447 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8491 (tm-30) REVERT: D 453 LYS cc_start: 0.9159 (mmmt) cc_final: 0.8901 (mmmm) REVERT: D 470 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8947 (tm-30) REVERT: E 65 LYS cc_start: 0.9081 (tttt) cc_final: 0.8879 (tttp) REVERT: E 83 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8584 (mmtm) REVERT: E 84 PHE cc_start: 0.7934 (m-10) cc_final: 0.6978 (t80) REVERT: E 123 TYR cc_start: 0.8976 (m-80) cc_final: 0.8209 (m-80) REVERT: E 146 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6332 (mm-30) REVERT: E 152 TYR cc_start: 0.8194 (m-80) cc_final: 0.7766 (m-10) REVERT: E 153 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7964 (pttm) REVERT: E 163 LYS cc_start: 0.9062 (mmtm) cc_final: 0.8572 (mmtp) REVERT: E 196 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8085 (mm-30) REVERT: E 217 LYS cc_start: 0.8365 (mttt) cc_final: 0.7761 (ptpt) REVERT: E 244 ASP cc_start: 0.6919 (t70) cc_final: 0.6136 (t70) REVERT: E 306 LEU cc_start: 0.9505 (mt) cc_final: 0.9098 (mt) REVERT: E 311 TYR cc_start: 0.8261 (m-80) cc_final: 0.7509 (m-10) REVERT: E 321 ASN cc_start: 0.9095 (t0) cc_final: 0.8518 (t0) REVERT: E 329 LEU cc_start: 0.8767 (mt) cc_final: 0.8546 (mt) REVERT: E 342 MET cc_start: 0.8608 (mmm) cc_final: 0.7802 (mmm) REVERT: E 418 ARG cc_start: 0.7955 (tmm160) cc_final: 0.6342 (mtt-85) REVERT: L 23 CYS cc_start: 0.5935 (t) cc_final: 0.5621 (t) REVERT: L 139 PHE cc_start: 0.3411 (p90) cc_final: 0.3023 (p90) REVERT: L 175 MET cc_start: 0.7231 (ttt) cc_final: 0.6811 (tpt) REVERT: L 181 LEU cc_start: 0.5171 (OUTLIER) cc_final: 0.4303 (tt) REVERT: H 60 TYR cc_start: 0.6405 (m-80) cc_final: 0.5636 (m-80) REVERT: H 104 TYR cc_start: 0.4421 (m-80) cc_final: 0.3922 (m-80) outliers start: 93 outliers final: 64 residues processed: 568 average time/residue: 0.1419 time to fit residues: 125.7657 Evaluate side-chains 511 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 441 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 190 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 251 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 272 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 chunk 136 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 320 ASN D 47 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN D 391 HIS E 460 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 79 GLN ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.140101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102175 restraints weight = 53201.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105408 restraints weight = 24538.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107499 restraints weight = 15074.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108817 restraints weight = 10978.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.109650 restraints weight = 8994.087| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22375 Z= 0.193 Angle : 0.682 8.382 30436 Z= 0.347 Chirality : 0.046 0.179 3287 Planarity : 0.005 0.069 3972 Dihedral : 5.667 36.658 2999 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.87 % Allowed : 21.13 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.14), residues: 2748 helix: -2.57 (0.29), residues: 201 sheet: -1.79 (0.17), residues: 732 loop : -2.76 (0.12), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 98 TYR 0.019 0.002 TYR C 354 PHE 0.025 0.002 PHE B 127 TRP 0.028 0.001 TRP L 92 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00431 (22371) covalent geometry : angle 0.68176 (30428) SS BOND : bond 0.00352 ( 4) SS BOND : angle 0.65982 ( 8) hydrogen bonds : bond 0.04126 ( 387) hydrogen bonds : angle 6.43897 ( 996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 487 time to evaluate : 0.823 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: B 49 TYR cc_start: 0.8827 (m-10) cc_final: 0.8456 (m-10) REVERT: B 75 ARG cc_start: 0.8587 (ttt180) cc_final: 0.8039 (ttt-90) REVERT: B 126 LYS cc_start: 0.8929 (tmtt) cc_final: 0.8471 (tptp) REVERT: B 131 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6420 (mt-10) REVERT: B 134 ASN cc_start: 0.7404 (t0) cc_final: 0.6969 (t0) REVERT: B 172 LYS cc_start: 0.8113 (tppt) cc_final: 0.7746 (tppt) REVERT: B 196 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: B 315 ARG cc_start: 0.8629 (tpt90) cc_final: 0.8190 (pmt-80) REVERT: A 25 ASP cc_start: 0.8588 (m-30) cc_final: 0.8352 (m-30) REVERT: A 99 LEU cc_start: 0.9135 (mt) cc_final: 0.8875 (mp) REVERT: A 106 LEU cc_start: 0.9445 (tp) cc_final: 0.9172 (tp) REVERT: A 126 LYS cc_start: 0.8633 (tmtt) cc_final: 0.8165 (tptp) REVERT: A 135 ARG cc_start: 0.7599 (mtt180) cc_final: 0.6975 (ptm160) REVERT: A 148 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 153 LYS cc_start: 0.8851 (ptmm) cc_final: 0.8486 (pttm) REVERT: A 200 MET cc_start: 0.8776 (mmm) cc_final: 0.8535 (mmm) REVERT: A 208 MET cc_start: 0.8083 (ptp) cc_final: 0.7144 (ptp) REVERT: A 217 LYS cc_start: 0.9449 (mttm) cc_final: 0.9115 (mtmt) REVERT: A 242 TYR cc_start: 0.8899 (m-80) cc_final: 0.8557 (m-80) REVERT: A 360 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8231 (ttpt) REVERT: A 367 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7506 (mt-10) REVERT: A 418 ARG cc_start: 0.4267 (ptt-90) cc_final: 0.3268 (ptt-90) REVERT: A 454 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8213 (m-10) REVERT: C 50 PHE cc_start: 0.8279 (p90) cc_final: 0.7953 (p90) REVERT: C 65 LYS cc_start: 0.9269 (ttpp) cc_final: 0.8852 (ttmm) REVERT: C 71 TYR cc_start: 0.8781 (m-80) cc_final: 0.8328 (m-80) REVERT: C 153 LYS cc_start: 0.9223 (ttpp) cc_final: 0.8648 (tttt) REVERT: C 208 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7756 (ptp) REVERT: C 235 LEU cc_start: 0.9511 (mm) cc_final: 0.9137 (mm) REVERT: C 242 TYR cc_start: 0.8859 (m-80) cc_final: 0.8647 (m-10) REVERT: C 255 MET cc_start: 0.8764 (ppp) cc_final: 0.8472 (ppp) REVERT: C 332 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9272 (p) REVERT: C 381 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8628 (p) REVERT: C 382 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9138 (tt) REVERT: C 387 MET cc_start: 0.9068 (ttt) cc_final: 0.8333 (tpp) REVERT: C 446 TRP cc_start: 0.8652 (t60) cc_final: 0.8404 (t-100) REVERT: C 453 LYS cc_start: 0.9153 (mmtp) cc_final: 0.8849 (mmtm) REVERT: D 26 GLU cc_start: 0.7962 (tp30) cc_final: 0.7727 (tp30) REVERT: D 71 TYR cc_start: 0.9072 (m-80) cc_final: 0.8465 (m-80) REVERT: D 127 PHE cc_start: 0.8721 (t80) cc_final: 0.8225 (t80) REVERT: D 146 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: D 200 MET cc_start: 0.8162 (tpp) cc_final: 0.7899 (tpp) REVERT: D 208 MET cc_start: 0.8152 (ptt) cc_final: 0.7849 (ptp) REVERT: D 237 MET cc_start: 0.8985 (mtm) cc_final: 0.8618 (mtt) REVERT: D 269 GLU cc_start: 0.8350 (tp30) cc_final: 0.8032 (tp30) REVERT: D 302 SER cc_start: 0.8759 (p) cc_final: 0.8473 (p) REVERT: D 309 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8743 (ttmm) REVERT: D 370 ASP cc_start: 0.8827 (t0) cc_final: 0.8172 (t0) REVERT: D 372 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: D 393 MET cc_start: 0.8894 (mmm) cc_final: 0.8644 (tpp) REVERT: D 426 THR cc_start: 0.8555 (m) cc_final: 0.8185 (p) REVERT: D 447 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8518 (tm-30) REVERT: D 453 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8926 (mmmm) REVERT: D 470 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8981 (tm-30) REVERT: E 65 LYS cc_start: 0.9010 (tttt) cc_final: 0.8663 (tttp) REVERT: E 83 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8614 (mmtm) REVERT: E 84 PHE cc_start: 0.7688 (m-10) cc_final: 0.7034 (t80) REVERT: E 92 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.7417 (p90) REVERT: E 123 TYR cc_start: 0.9034 (m-80) cc_final: 0.8079 (m-80) REVERT: E 163 LYS cc_start: 0.9044 (mmtm) cc_final: 0.8822 (mmtp) REVERT: E 196 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7944 (mm-30) REVERT: E 214 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8397 (mm-40) REVERT: E 217 LYS cc_start: 0.8374 (mttt) cc_final: 0.7785 (ptpp) REVERT: E 244 ASP cc_start: 0.6794 (t70) cc_final: 0.6517 (t70) REVERT: E 303 GLU cc_start: 0.8049 (mp0) cc_final: 0.7466 (mp0) REVERT: E 306 LEU cc_start: 0.9516 (mt) cc_final: 0.9121 (mt) REVERT: E 311 TYR cc_start: 0.8188 (m-80) cc_final: 0.7497 (m-10) REVERT: E 321 ASN cc_start: 0.9120 (t0) cc_final: 0.8457 (t0) REVERT: E 342 MET cc_start: 0.8552 (mmm) cc_final: 0.7845 (mmm) REVERT: E 393 MET cc_start: 0.9208 (tmm) cc_final: 0.8946 (tmm) REVERT: E 418 ARG cc_start: 0.7959 (tmm160) cc_final: 0.6473 (mtt-85) REVERT: L 175 MET cc_start: 0.7401 (ttt) cc_final: 0.6805 (tpt) REVERT: L 181 LEU cc_start: 0.5026 (OUTLIER) cc_final: 0.4214 (tt) REVERT: H 20 ILE cc_start: 0.4416 (OUTLIER) cc_final: 0.3767 (tp) REVERT: H 104 TYR cc_start: 0.4524 (m-80) cc_final: 0.3898 (m-80) outliers start: 119 outliers final: 78 residues processed: 555 average time/residue: 0.1403 time to fit residues: 123.8332 Evaluate side-chains 531 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 441 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 211 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 320 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN D 391 HIS D 428 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 82 HIS ** 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 = 0.3842 r_free = 0.3842 target = 0.140641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101479 restraints weight = 66239.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104956 restraints weight = 28085.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107197 restraints weight = 16591.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108605 restraints weight = 11800.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109408 restraints weight = 9520.502| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22375 Z= 0.231 Angle : 0.693 9.372 30436 Z= 0.352 Chirality : 0.046 0.180 3287 Planarity : 0.005 0.064 3972 Dihedral : 5.589 35.681 2997 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.77 % Allowed : 21.87 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.14), residues: 2748 helix: -2.05 (0.32), residues: 196 sheet: -1.69 (0.18), residues: 732 loop : -2.64 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 252 TYR 0.019 0.002 TYR C 354 PHE 0.023 0.002 PHE E 127 TRP 0.028 0.001 TRP L 92 HIS 0.004 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00516 (22371) covalent geometry : angle 0.69255 (30428) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.77162 ( 8) hydrogen bonds : bond 0.03862 ( 387) hydrogen bonds : angle 6.20509 ( 996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 462 time to evaluate : 0.846 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: B 49 TYR cc_start: 0.8849 (m-10) cc_final: 0.8486 (m-10) REVERT: B 126 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8496 (tptp) REVERT: B 134 ASN cc_start: 0.7549 (t0) cc_final: 0.7032 (t0) REVERT: B 148 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 172 LYS cc_start: 0.8100 (tppt) cc_final: 0.7700 (tppt) REVERT: B 196 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: B 315 ARG cc_start: 0.8667 (tpt90) cc_final: 0.8200 (pmt-80) REVERT: A 25 ASP cc_start: 0.8622 (m-30) cc_final: 0.8365 (m-30) REVERT: A 99 LEU cc_start: 0.9207 (mt) cc_final: 0.8926 (mp) REVERT: A 106 LEU cc_start: 0.9450 (tp) cc_final: 0.9182 (tp) REVERT: A 126 LYS cc_start: 0.8637 (tmtt) cc_final: 0.8160 (tptp) REVERT: A 135 ARG cc_start: 0.7621 (mtt180) cc_final: 0.6996 (ptm160) REVERT: A 148 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8402 (mm) REVERT: A 153 LYS cc_start: 0.8850 (ptmm) cc_final: 0.8484 (pttm) REVERT: A 200 MET cc_start: 0.8812 (mmm) cc_final: 0.8565 (mmm) REVERT: A 208 MET cc_start: 0.7805 (ptp) cc_final: 0.6650 (ptp) REVERT: A 217 LYS cc_start: 0.9441 (mttm) cc_final: 0.9130 (mtmt) REVERT: A 242 TYR cc_start: 0.8777 (m-80) cc_final: 0.7273 (m-80) REVERT: A 244 ASP cc_start: 0.8937 (m-30) cc_final: 0.8716 (m-30) REVERT: A 291 PHE cc_start: 0.8054 (m-80) cc_final: 0.7679 (m-10) REVERT: A 367 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7469 (mt-10) REVERT: A 418 ARG cc_start: 0.4309 (ptt-90) cc_final: 0.3300 (ptt-90) REVERT: A 454 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: C 4 TRP cc_start: 0.6844 (OUTLIER) cc_final: 0.5725 (m-10) REVERT: C 71 TYR cc_start: 0.8729 (m-80) cc_final: 0.8360 (m-80) REVERT: C 153 LYS cc_start: 0.9207 (ttpp) cc_final: 0.8938 (tttt) REVERT: C 208 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7758 (ptp) REVERT: C 242 TYR cc_start: 0.8872 (m-10) cc_final: 0.8064 (m-80) REVERT: C 255 MET cc_start: 0.8750 (ppp) cc_final: 0.8481 (ppp) REVERT: C 332 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9300 (p) REVERT: C 354 TYR cc_start: 0.8109 (t80) cc_final: 0.7901 (t80) REVERT: C 361 GLU cc_start: 0.7640 (mp0) cc_final: 0.7133 (mp0) REVERT: C 379 LYS cc_start: 0.9008 (pttt) cc_final: 0.8623 (ptmt) REVERT: C 381 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8627 (p) REVERT: C 382 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9100 (tt) REVERT: C 387 MET cc_start: 0.9107 (ttt) cc_final: 0.8334 (tpp) REVERT: C 393 MET cc_start: 0.9248 (tpp) cc_final: 0.8204 (tpp) REVERT: C 446 TRP cc_start: 0.8673 (t60) cc_final: 0.8403 (t-100) REVERT: C 453 LYS cc_start: 0.9139 (mmtp) cc_final: 0.8822 (mmtm) REVERT: D 26 GLU cc_start: 0.8007 (tp30) cc_final: 0.7781 (tp30) REVERT: D 71 TYR cc_start: 0.9142 (m-80) cc_final: 0.8563 (m-80) REVERT: D 200 MET cc_start: 0.8214 (tpp) cc_final: 0.7923 (tpp) REVERT: D 237 MET cc_start: 0.9006 (mtm) cc_final: 0.8644 (mtt) REVERT: D 269 GLU cc_start: 0.8356 (tp30) cc_final: 0.7924 (tp30) REVERT: D 302 SER cc_start: 0.8738 (p) cc_final: 0.8314 (p) REVERT: D 309 LYS cc_start: 0.9183 (mtmt) cc_final: 0.8815 (ttmm) REVERT: D 320 ASN cc_start: 0.9498 (OUTLIER) cc_final: 0.8788 (t0) REVERT: D 370 ASP cc_start: 0.8872 (t0) cc_final: 0.8370 (t0) REVERT: D 372 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: D 426 THR cc_start: 0.8557 (m) cc_final: 0.8306 (p) REVERT: D 457 ASP cc_start: 0.8064 (t0) cc_final: 0.7844 (t0) REVERT: D 470 GLN cc_start: 0.9280 (tm-30) cc_final: 0.8988 (tm-30) REVERT: E 65 LYS cc_start: 0.9073 (tttt) cc_final: 0.8784 (tttp) REVERT: E 83 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8643 (mmtm) REVERT: E 84 PHE cc_start: 0.7682 (m-10) cc_final: 0.6988 (t80) REVERT: E 92 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7359 (p90) REVERT: E 123 TYR cc_start: 0.9093 (m-80) cc_final: 0.8174 (m-80) REVERT: E 146 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6823 (mm-30) REVERT: E 163 LYS cc_start: 0.9036 (mmtm) cc_final: 0.8792 (mmtp) REVERT: E 196 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8037 (mm-30) REVERT: E 214 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8156 (mm-40) REVERT: E 244 ASP cc_start: 0.6955 (t70) cc_final: 0.6660 (t70) REVERT: E 303 GLU cc_start: 0.8082 (mp0) cc_final: 0.7430 (mp0) REVERT: E 306 LEU cc_start: 0.9494 (mt) cc_final: 0.9255 (mt) REVERT: E 311 TYR cc_start: 0.8250 (m-80) cc_final: 0.7514 (m-10) REVERT: E 321 ASN cc_start: 0.9106 (t0) cc_final: 0.8456 (t0) REVERT: E 342 MET cc_start: 0.8581 (mmm) cc_final: 0.7931 (mmm) REVERT: E 418 ARG cc_start: 0.7904 (tmm160) cc_final: 0.6480 (mtt-85) REVERT: L 98 PHE cc_start: 0.7805 (m-10) cc_final: 0.7564 (m-10) REVERT: L 175 MET cc_start: 0.7493 (ttt) cc_final: 0.6931 (tpt) REVERT: L 181 LEU cc_start: 0.4949 (OUTLIER) cc_final: 0.4235 (tt) REVERT: H 20 ILE cc_start: 0.4371 (OUTLIER) cc_final: 0.3740 (tp) REVERT: H 157 VAL cc_start: 0.5529 (t) cc_final: 0.5295 (t) outliers start: 141 outliers final: 99 residues processed: 553 average time/residue: 0.1357 time to fit residues: 120.6865 Evaluate side-chains 547 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 434 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 4 TRP Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 70 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN B 305 GLN A 112 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN D 112 GLN D 376 GLN E 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102664 restraints weight = 52118.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105883 restraints weight = 24035.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107940 restraints weight = 14757.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.109278 restraints weight = 10755.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110110 restraints weight = 8784.979| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22375 Z= 0.175 Angle : 0.662 9.099 30436 Z= 0.334 Chirality : 0.046 0.284 3287 Planarity : 0.005 0.061 3972 Dihedral : 5.354 34.957 2997 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 5.69 % Allowed : 23.01 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.14), residues: 2748 helix: -1.76 (0.33), residues: 197 sheet: -1.55 (0.18), residues: 722 loop : -2.50 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 252 TYR 0.014 0.001 TYR C 354 PHE 0.021 0.002 PHE L 98 TRP 0.027 0.001 TRP L 92 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00393 (22371) covalent geometry : angle 0.66199 (30428) SS BOND : bond 0.00352 ( 4) SS BOND : angle 0.71326 ( 8) hydrogen bonds : bond 0.03596 ( 387) hydrogen bonds : angle 5.91009 ( 996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 480 time to evaluate : 0.834 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: B 49 TYR cc_start: 0.8839 (m-10) cc_final: 0.8452 (m-10) REVERT: B 75 ARG cc_start: 0.8665 (ttt180) cc_final: 0.8150 (ttt-90) REVERT: B 126 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8513 (tptp) REVERT: B 134 ASN cc_start: 0.7817 (t0) cc_final: 0.7270 (t0) REVERT: B 148 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7926 (mm) REVERT: B 154 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: B 172 LYS cc_start: 0.8071 (tppt) cc_final: 0.7683 (tppt) REVERT: B 196 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: B 315 ARG cc_start: 0.8649 (tpt90) cc_final: 0.8203 (pmt-80) REVERT: B 342 MET cc_start: 0.8490 (tpp) cc_final: 0.8114 (tpt) REVERT: A 25 ASP cc_start: 0.8619 (m-30) cc_final: 0.8358 (m-30) REVERT: A 106 LEU cc_start: 0.9455 (tp) cc_final: 0.9201 (tp) REVERT: A 126 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8190 (tptp) REVERT: A 135 ARG cc_start: 0.7632 (mtt180) cc_final: 0.6980 (ptm160) REVERT: A 148 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 153 LYS cc_start: 0.8834 (ptmm) cc_final: 0.8473 (pttm) REVERT: A 200 MET cc_start: 0.8837 (mmm) cc_final: 0.8565 (mmm) REVERT: A 217 LYS cc_start: 0.9482 (mttm) cc_final: 0.8905 (ptmt) REVERT: A 251 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8288 (ptp90) REVERT: A 291 PHE cc_start: 0.8034 (m-80) cc_final: 0.7663 (m-10) REVERT: A 418 ARG cc_start: 0.4383 (ptt-90) cc_final: 0.3555 (ptt-90) REVERT: A 454 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: C 71 TYR cc_start: 0.8746 (m-80) cc_final: 0.8389 (m-80) REVERT: C 153 LYS cc_start: 0.9185 (ttpp) cc_final: 0.8632 (ttpt) REVERT: C 208 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7687 (ptp) REVERT: C 210 PHE cc_start: 0.8851 (m-10) cc_final: 0.8604 (m-10) REVERT: C 242 TYR cc_start: 0.8946 (m-10) cc_final: 0.8119 (m-80) REVERT: C 255 MET cc_start: 0.8842 (ppp) cc_final: 0.8585 (ppp) REVERT: C 303 GLU cc_start: 0.8268 (tt0) cc_final: 0.8039 (tt0) REVERT: C 332 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9286 (p) REVERT: C 354 TYR cc_start: 0.8105 (t80) cc_final: 0.7794 (t80) REVERT: C 361 GLU cc_start: 0.7636 (mp0) cc_final: 0.7208 (mp0) REVERT: C 379 LYS cc_start: 0.9008 (pttt) cc_final: 0.8615 (ptmt) REVERT: C 380 ILE cc_start: 0.8517 (tp) cc_final: 0.8314 (tt) REVERT: C 381 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8621 (p) REVERT: C 382 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8905 (tt) REVERT: C 387 MET cc_start: 0.9073 (ttt) cc_final: 0.8296 (tpp) REVERT: C 393 MET cc_start: 0.9228 (tpp) cc_final: 0.8265 (tpp) REVERT: C 446 TRP cc_start: 0.8729 (t60) cc_final: 0.8410 (t-100) REVERT: C 453 LYS cc_start: 0.9119 (mmtp) cc_final: 0.8800 (mmtm) REVERT: D 26 GLU cc_start: 0.7992 (tp30) cc_final: 0.7769 (tp30) REVERT: D 71 TYR cc_start: 0.9131 (m-80) cc_final: 0.8544 (m-80) REVERT: D 146 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: D 154 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: D 200 MET cc_start: 0.8128 (tpp) cc_final: 0.7761 (tpp) REVERT: D 237 MET cc_start: 0.8986 (mtm) cc_final: 0.8633 (mtt) REVERT: D 269 GLU cc_start: 0.8312 (tp30) cc_final: 0.7901 (tp30) REVERT: D 309 LYS cc_start: 0.9124 (mtmt) cc_final: 0.8788 (ttpp) REVERT: D 320 ASN cc_start: 0.9474 (OUTLIER) cc_final: 0.8782 (t0) REVERT: D 370 ASP cc_start: 0.8945 (t0) cc_final: 0.8474 (t0) REVERT: D 372 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: D 426 THR cc_start: 0.8506 (m) cc_final: 0.8225 (p) REVERT: D 470 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8993 (tm-30) REVERT: E 65 LYS cc_start: 0.9065 (tttt) cc_final: 0.8748 (tttp) REVERT: E 83 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8631 (mmtm) REVERT: E 84 PHE cc_start: 0.7626 (m-10) cc_final: 0.6817 (t80) REVERT: E 92 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7339 (p90) REVERT: E 123 TYR cc_start: 0.9076 (m-80) cc_final: 0.8179 (m-80) REVERT: E 146 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6756 (mm-30) REVERT: E 163 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8774 (mmtp) REVERT: E 196 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7804 (mm-30) REVERT: E 208 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7435 (ptp) REVERT: E 214 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8394 (mm-40) REVERT: E 244 ASP cc_start: 0.7002 (t70) cc_final: 0.6690 (t70) REVERT: E 303 GLU cc_start: 0.8063 (mp0) cc_final: 0.7409 (mp0) REVERT: E 306 LEU cc_start: 0.9480 (mt) cc_final: 0.9218 (mt) REVERT: E 311 TYR cc_start: 0.8180 (m-80) cc_final: 0.7502 (m-10) REVERT: E 321 ASN cc_start: 0.9127 (t0) cc_final: 0.8404 (t0) REVERT: E 393 MET cc_start: 0.9159 (tmm) cc_final: 0.8904 (tmm) REVERT: E 418 ARG cc_start: 0.7883 (tmm160) cc_final: 0.6560 (mtt-85) REVERT: L 175 MET cc_start: 0.7456 (ttt) cc_final: 0.6954 (tpt) REVERT: H 20 ILE cc_start: 0.4413 (OUTLIER) cc_final: 0.3781 (tp) outliers start: 139 outliers final: 95 residues processed: 569 average time/residue: 0.1408 time to fit residues: 126.8927 Evaluate side-chains 563 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 451 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 42 optimal weight: 0.0040 chunk 181 optimal weight: 10.0000 chunk 64 optimal weight: 0.0050 chunk 167 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 86 optimal weight: 0.0020 chunk 83 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 chunk 243 optimal weight: 20.0000 overall best weight: 1.0214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 305 GLN B 358 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 GLN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN C 320 ASN D 177 ASN D 376 GLN ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN H 201 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.143777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105643 restraints weight = 56469.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109108 restraints weight = 25103.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111316 restraints weight = 15047.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.112723 restraints weight = 10762.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113600 restraints weight = 8702.947| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22375 Z= 0.109 Angle : 0.652 11.619 30436 Z= 0.320 Chirality : 0.045 0.280 3287 Planarity : 0.005 0.074 3972 Dihedral : 4.897 33.259 2996 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.30 % Allowed : 24.41 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.15), residues: 2748 helix: -1.64 (0.33), residues: 200 sheet: -1.41 (0.18), residues: 741 loop : -2.27 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 252 TYR 0.013 0.001 TYR E 417 PHE 0.021 0.001 PHE L 98 TRP 0.024 0.001 TRP L 92 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00250 (22371) covalent geometry : angle 0.65211 (30428) SS BOND : bond 0.00330 ( 4) SS BOND : angle 0.69122 ( 8) hydrogen bonds : bond 0.03222 ( 387) hydrogen bonds : angle 5.47233 ( 996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 540 time to evaluate : 0.728 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 49 TYR cc_start: 0.8845 (m-10) cc_final: 0.8433 (m-10) REVERT: B 75 ARG cc_start: 0.8608 (ttt180) cc_final: 0.7920 (ttt-90) REVERT: B 126 LYS cc_start: 0.8454 (tmtt) cc_final: 0.8236 (tptp) REVERT: B 134 ASN cc_start: 0.7805 (t0) cc_final: 0.7307 (t0) REVERT: B 148 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7858 (mm) REVERT: B 172 LYS cc_start: 0.7960 (tppt) cc_final: 0.7544 (tppt) REVERT: B 315 ARG cc_start: 0.8706 (tpt90) cc_final: 0.8236 (pmt-80) REVERT: B 422 SER cc_start: 0.8438 (t) cc_final: 0.8044 (m) REVERT: A 25 ASP cc_start: 0.8607 (m-30) cc_final: 0.8353 (m-30) REVERT: A 106 LEU cc_start: 0.9443 (tp) cc_final: 0.9231 (tp) REVERT: A 126 LYS cc_start: 0.8555 (tmtt) cc_final: 0.8104 (tptp) REVERT: A 134 ASN cc_start: 0.7848 (t0) cc_final: 0.7647 (t0) REVERT: A 135 ARG cc_start: 0.7695 (mtt180) cc_final: 0.6910 (ptm160) REVERT: A 145 ARG cc_start: 0.8825 (mtm180) cc_final: 0.8472 (mtm180) REVERT: A 153 LYS cc_start: 0.8795 (ptmm) cc_final: 0.8361 (pttm) REVERT: A 200 MET cc_start: 0.8845 (mmm) cc_final: 0.8585 (mmm) REVERT: A 217 LYS cc_start: 0.9478 (mttm) cc_final: 0.8873 (ptmt) REVERT: A 247 PHE cc_start: 0.8617 (m-10) cc_final: 0.8352 (m-80) REVERT: A 291 PHE cc_start: 0.8037 (m-80) cc_final: 0.7702 (m-10) REVERT: A 379 LYS cc_start: 0.8826 (pttp) cc_final: 0.8603 (ptmt) REVERT: A 393 MET cc_start: 0.8212 (mmm) cc_final: 0.7926 (mmm) REVERT: A 418 ARG cc_start: 0.4427 (ptt-90) cc_final: 0.1921 (mpp80) REVERT: A 454 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.7950 (m-10) REVERT: C 71 TYR cc_start: 0.8944 (m-80) cc_final: 0.8682 (m-80) REVERT: C 150 MET cc_start: 0.8957 (pmm) cc_final: 0.8374 (pmm) REVERT: C 208 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7535 (ptp) REVERT: C 242 TYR cc_start: 0.8922 (m-10) cc_final: 0.8043 (m-80) REVERT: C 255 MET cc_start: 0.8872 (ppp) cc_final: 0.8497 (ppp) REVERT: C 306 LEU cc_start: 0.9567 (mm) cc_final: 0.9215 (mm) REVERT: C 354 TYR cc_start: 0.8030 (t80) cc_final: 0.7707 (t80) REVERT: C 361 GLU cc_start: 0.7641 (mp0) cc_final: 0.7101 (mp0) REVERT: C 379 LYS cc_start: 0.9004 (pttt) cc_final: 0.8589 (ptmt) REVERT: C 382 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8955 (tt) REVERT: C 387 MET cc_start: 0.9089 (ttt) cc_final: 0.8304 (tpp) REVERT: C 393 MET cc_start: 0.9213 (tpp) cc_final: 0.8198 (tpp) REVERT: C 446 TRP cc_start: 0.8675 (t60) cc_final: 0.8376 (t-100) REVERT: C 453 LYS cc_start: 0.9095 (mmtp) cc_final: 0.8779 (mmtm) REVERT: D 26 GLU cc_start: 0.7996 (tp30) cc_final: 0.7726 (tp30) REVERT: D 71 TYR cc_start: 0.9102 (m-80) cc_final: 0.8457 (m-80) REVERT: D 107 GLU cc_start: 0.8509 (tp30) cc_final: 0.8286 (tp30) REVERT: D 127 PHE cc_start: 0.8564 (t80) cc_final: 0.8058 (t80) REVERT: D 146 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: D 154 GLN cc_start: 0.8600 (pt0) cc_final: 0.7893 (pt0) REVERT: D 200 MET cc_start: 0.8031 (tpp) cc_final: 0.7627 (tpp) REVERT: D 208 MET cc_start: 0.7770 (pmm) cc_final: 0.7562 (pmm) REVERT: D 237 MET cc_start: 0.8924 (mtm) cc_final: 0.8644 (mtt) REVERT: D 253 GLU cc_start: 0.7971 (pm20) cc_final: 0.7659 (pm20) REVERT: D 269 GLU cc_start: 0.8269 (tp30) cc_final: 0.7860 (tp30) REVERT: D 309 LYS cc_start: 0.9209 (mtmt) cc_final: 0.8959 (ttmm) REVERT: D 320 ASN cc_start: 0.9443 (OUTLIER) cc_final: 0.8971 (t0) REVERT: D 370 ASP cc_start: 0.8819 (t0) cc_final: 0.8402 (t0) REVERT: D 372 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: D 457 ASP cc_start: 0.7964 (t0) cc_final: 0.7748 (t0) REVERT: D 470 GLN cc_start: 0.9275 (tm-30) cc_final: 0.9023 (tm-30) REVERT: E 65 LYS cc_start: 0.9057 (tttt) cc_final: 0.8727 (tttp) REVERT: E 83 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8557 (mmtm) REVERT: E 84 PHE cc_start: 0.7533 (m-10) cc_final: 0.6885 (t80) REVERT: E 92 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7254 (p90) REVERT: E 123 TYR cc_start: 0.9012 (m-80) cc_final: 0.8018 (m-80) REVERT: E 146 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6776 (mm-30) REVERT: E 196 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7879 (mm-30) REVERT: E 219 ASP cc_start: 0.8188 (p0) cc_final: 0.7532 (p0) REVERT: E 303 GLU cc_start: 0.8026 (mp0) cc_final: 0.7383 (mp0) REVERT: E 306 LEU cc_start: 0.9503 (mt) cc_final: 0.9237 (mt) REVERT: E 311 TYR cc_start: 0.8083 (m-80) cc_final: 0.7480 (m-10) REVERT: E 321 ASN cc_start: 0.9101 (t0) cc_final: 0.8499 (t0) REVERT: E 393 MET cc_start: 0.9147 (tmm) cc_final: 0.8864 (tmm) REVERT: E 418 ARG cc_start: 0.7874 (tmm160) cc_final: 0.6663 (mtt-85) REVERT: L 61 ARG cc_start: 0.6837 (ptt-90) cc_final: 0.6448 (ptp-170) REVERT: L 175 MET cc_start: 0.7452 (ttt) cc_final: 0.7018 (tpt) REVERT: H 20 ILE cc_start: 0.4580 (OUTLIER) cc_final: 0.3801 (tp) REVERT: H 78 THR cc_start: 0.6804 (t) cc_final: 0.6508 (m) outliers start: 105 outliers final: 65 residues processed: 606 average time/residue: 0.1425 time to fit residues: 135.9196 Evaluate side-chains 551 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 477 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 155 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 0.0770 chunk 200 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 259 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 238 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 GLN C 320 ASN D 376 GLN E 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.141634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102999 restraints weight = 66944.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106618 restraints weight = 27901.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108936 restraints weight = 16260.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110408 restraints weight = 11394.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111353 restraints weight = 9101.484| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22375 Z= 0.166 Angle : 0.669 11.477 30436 Z= 0.330 Chirality : 0.046 0.254 3287 Planarity : 0.005 0.077 3972 Dihedral : 4.936 31.894 2995 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 5.65 % Allowed : 24.32 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.15), residues: 2748 helix: -1.53 (0.33), residues: 201 sheet: -1.34 (0.18), residues: 733 loop : -2.23 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 252 TYR 0.012 0.001 TYR B 152 PHE 0.018 0.001 PHE L 139 TRP 0.022 0.001 TRP L 92 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd covalent geometry : bond 0.00378 (22371) covalent geometry : angle 0.66851 (30428) SS BOND : bond 0.00222 ( 4) SS BOND : angle 1.32239 ( 8) hydrogen bonds : bond 0.03347 ( 387) hydrogen bonds : angle 5.51757 ( 996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 487 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8848 (m-10) cc_final: 0.8426 (m-10) REVERT: B 75 ARG cc_start: 0.8630 (ttt180) cc_final: 0.8121 (ttt-90) REVERT: B 126 LYS cc_start: 0.8636 (tmtt) cc_final: 0.8370 (tptp) REVERT: B 129 ASP cc_start: 0.7498 (t0) cc_final: 0.7287 (t0) REVERT: B 134 ASN cc_start: 0.7877 (t0) cc_final: 0.7371 (t0) REVERT: B 148 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7866 (mm) REVERT: B 172 LYS cc_start: 0.8035 (tppt) cc_final: 0.7665 (tppt) REVERT: B 291 PHE cc_start: 0.8547 (m-80) cc_final: 0.8140 (m-80) REVERT: B 315 ARG cc_start: 0.8735 (tpt90) cc_final: 0.8257 (pmt-80) REVERT: B 422 SER cc_start: 0.8503 (t) cc_final: 0.8099 (m) REVERT: A 25 ASP cc_start: 0.8612 (m-30) cc_final: 0.8362 (m-30) REVERT: A 106 LEU cc_start: 0.9445 (tp) cc_final: 0.9196 (tp) REVERT: A 126 LYS cc_start: 0.8651 (tmtt) cc_final: 0.8148 (tptp) REVERT: A 134 ASN cc_start: 0.7906 (t0) cc_final: 0.7629 (t0) REVERT: A 135 ARG cc_start: 0.7621 (mtt180) cc_final: 0.6872 (ptm160) REVERT: A 145 ARG cc_start: 0.8801 (mtm180) cc_final: 0.8442 (mtm180) REVERT: A 148 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8497 (mm) REVERT: A 153 LYS cc_start: 0.8772 (ptmm) cc_final: 0.8367 (pttm) REVERT: A 200 MET cc_start: 0.8878 (mmm) cc_final: 0.8569 (mmm) REVERT: A 217 LYS cc_start: 0.9479 (mttm) cc_final: 0.8902 (ptmt) REVERT: A 246 LEU cc_start: 0.9042 (mt) cc_final: 0.8788 (tp) REVERT: A 291 PHE cc_start: 0.8044 (m-80) cc_final: 0.7678 (m-10) REVERT: A 379 LYS cc_start: 0.8868 (pttp) cc_final: 0.8501 (ptmt) REVERT: A 418 ARG cc_start: 0.4298 (OUTLIER) cc_final: 0.1879 (mpp80) REVERT: A 454 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8164 (m-10) REVERT: C 150 MET cc_start: 0.8852 (pmm) cc_final: 0.8287 (pmm) REVERT: C 208 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7704 (ptp) REVERT: C 255 MET cc_start: 0.8868 (ppp) cc_final: 0.8535 (ppp) REVERT: C 354 TYR cc_start: 0.8097 (t80) cc_final: 0.7794 (t80) REVERT: C 361 GLU cc_start: 0.7516 (mp0) cc_final: 0.7149 (mt-10) REVERT: C 379 LYS cc_start: 0.9023 (pttt) cc_final: 0.8622 (ptmt) REVERT: C 381 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8608 (p) REVERT: C 382 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8846 (tt) REVERT: C 387 MET cc_start: 0.9092 (ttt) cc_final: 0.8293 (tpp) REVERT: C 393 MET cc_start: 0.9226 (tpp) cc_final: 0.8732 (tpp) REVERT: C 446 TRP cc_start: 0.8718 (t60) cc_final: 0.8382 (t-100) REVERT: C 453 LYS cc_start: 0.9081 (mmtp) cc_final: 0.8763 (mmtm) REVERT: D 26 GLU cc_start: 0.8019 (tp30) cc_final: 0.7771 (tp30) REVERT: D 71 TYR cc_start: 0.9167 (m-80) cc_final: 0.8554 (m-80) REVERT: D 136 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: D 146 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: D 154 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: D 200 MET cc_start: 0.8148 (tpp) cc_final: 0.7760 (tpp) REVERT: D 237 MET cc_start: 0.9054 (mtm) cc_final: 0.8772 (mtt) REVERT: D 253 GLU cc_start: 0.8096 (pm20) cc_final: 0.7708 (pm20) REVERT: D 269 GLU cc_start: 0.8313 (tp30) cc_final: 0.7934 (tp30) REVERT: D 287 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7321 (mm-40) REVERT: D 309 LYS cc_start: 0.9218 (mtmt) cc_final: 0.8938 (ttpp) REVERT: D 320 ASN cc_start: 0.9343 (OUTLIER) cc_final: 0.8768 (t0) REVERT: D 370 ASP cc_start: 0.8820 (t0) cc_final: 0.8411 (t0) REVERT: D 372 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: D 470 GLN cc_start: 0.9261 (tm-30) cc_final: 0.9009 (tm-30) REVERT: E 65 LYS cc_start: 0.9035 (tttt) cc_final: 0.8683 (tttp) REVERT: E 83 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8569 (mmtm) REVERT: E 84 PHE cc_start: 0.7584 (m-10) cc_final: 0.6857 (t80) REVERT: E 92 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7314 (p90) REVERT: E 123 TYR cc_start: 0.9013 (m-80) cc_final: 0.8367 (m-80) REVERT: E 196 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7808 (mm-30) REVERT: E 219 ASP cc_start: 0.8369 (p0) cc_final: 0.8164 (p0) REVERT: E 252 ARG cc_start: 0.7590 (ttm110) cc_final: 0.7327 (ttm-80) REVERT: E 303 GLU cc_start: 0.8047 (mp0) cc_final: 0.7417 (mp0) REVERT: E 306 LEU cc_start: 0.9511 (mt) cc_final: 0.9278 (mt) REVERT: E 311 TYR cc_start: 0.8206 (m-80) cc_final: 0.7471 (m-10) REVERT: E 321 ASN cc_start: 0.9098 (t0) cc_final: 0.8363 (t0) REVERT: E 393 MET cc_start: 0.9222 (tmm) cc_final: 0.8970 (tmm) REVERT: E 418 ARG cc_start: 0.7930 (tmm160) cc_final: 0.6669 (mtt-85) REVERT: L 61 ARG cc_start: 0.6855 (ptt-90) cc_final: 0.6467 (ptp-170) REVERT: L 175 MET cc_start: 0.7470 (ttt) cc_final: 0.7038 (tpt) REVERT: H 20 ILE cc_start: 0.4488 (OUTLIER) cc_final: 0.3755 (tp) outliers start: 138 outliers final: 102 residues processed: 573 average time/residue: 0.1379 time to fit residues: 125.9398 Evaluate side-chains 579 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 462 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 442 LYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 61 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 14 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 235 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN D 177 ASN E 154 GLN L 198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101622 restraints weight = 53445.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104805 restraints weight = 24715.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106827 restraints weight = 15166.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.108120 restraints weight = 11061.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108942 restraints weight = 9055.948| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 22375 Z= 0.248 Angle : 0.728 10.274 30436 Z= 0.365 Chirality : 0.047 0.228 3287 Planarity : 0.005 0.073 3972 Dihedral : 5.347 31.735 2995 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 6.35 % Allowed : 24.00 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.15), residues: 2748 helix: -1.50 (0.32), residues: 201 sheet: -1.45 (0.18), residues: 755 loop : -2.26 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 263 TYR 0.015 0.002 TYR E 231 PHE 0.023 0.002 PHE A 247 TRP 0.019 0.001 TRP C 4 HIS 0.006 0.001 HIS C 319 Details of bonding type rmsd covalent geometry : bond 0.00556 (22371) covalent geometry : angle 0.72751 (30428) SS BOND : bond 0.00266 ( 4) SS BOND : angle 1.06039 ( 8) hydrogen bonds : bond 0.03684 ( 387) hydrogen bonds : angle 5.74221 ( 996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 455 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8886 (m-10) cc_final: 0.8581 (m-10) REVERT: B 126 LYS cc_start: 0.8663 (tmtt) cc_final: 0.8426 (tptp) REVERT: B 129 ASP cc_start: 0.7661 (t0) cc_final: 0.7451 (t0) REVERT: B 134 ASN cc_start: 0.7903 (t0) cc_final: 0.7307 (t0) REVERT: B 145 ARG cc_start: 0.8237 (mtm180) cc_final: 0.8013 (mtm180) REVERT: B 148 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7929 (mm) REVERT: B 315 ARG cc_start: 0.8742 (tpt90) cc_final: 0.8210 (pmt-80) REVERT: A 25 ASP cc_start: 0.8573 (m-30) cc_final: 0.8315 (m-30) REVERT: A 106 LEU cc_start: 0.9462 (tp) cc_final: 0.8983 (tp) REVERT: A 107 GLU cc_start: 0.8258 (tp30) cc_final: 0.8023 (tp30) REVERT: A 126 LYS cc_start: 0.8766 (tmtt) cc_final: 0.8241 (tptp) REVERT: A 135 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7038 (ptm160) REVERT: A 145 ARG cc_start: 0.8945 (mtm180) cc_final: 0.8517 (mtm180) REVERT: A 148 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8393 (mm) REVERT: A 153 LYS cc_start: 0.8695 (ptmm) cc_final: 0.8252 (pttp) REVERT: A 200 MET cc_start: 0.8884 (mmm) cc_final: 0.8540 (mmm) REVERT: A 217 LYS cc_start: 0.9464 (mttm) cc_final: 0.8916 (ptmt) REVERT: A 244 ASP cc_start: 0.8890 (m-30) cc_final: 0.8677 (m-30) REVERT: A 291 PHE cc_start: 0.8053 (m-80) cc_final: 0.7649 (m-10) REVERT: A 418 ARG cc_start: 0.4412 (OUTLIER) cc_final: 0.1616 (ppt170) REVERT: A 454 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8151 (m-10) REVERT: C 4 TRP cc_start: 0.6782 (OUTLIER) cc_final: 0.5535 (m-10) REVERT: C 110 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7745 (mmm-85) REVERT: C 150 MET cc_start: 0.8836 (pmm) cc_final: 0.8264 (pmm) REVERT: C 153 LYS cc_start: 0.9449 (tttt) cc_final: 0.9208 (tttt) REVERT: C 208 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8094 (ptp) REVERT: C 255 MET cc_start: 0.8877 (ppp) cc_final: 0.8556 (ppp) REVERT: C 354 TYR cc_start: 0.8167 (t80) cc_final: 0.7830 (t80) REVERT: C 361 GLU cc_start: 0.7698 (mp0) cc_final: 0.7139 (mp0) REVERT: C 379 LYS cc_start: 0.9089 (pttt) cc_final: 0.8706 (ptmt) REVERT: C 380 ILE cc_start: 0.8528 (tp) cc_final: 0.8319 (tt) REVERT: C 381 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8725 (p) REVERT: C 382 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8850 (tt) REVERT: C 387 MET cc_start: 0.9095 (ttt) cc_final: 0.8279 (tpp) REVERT: C 393 MET cc_start: 0.9267 (tpp) cc_final: 0.8675 (tpp) REVERT: C 446 TRP cc_start: 0.8743 (t60) cc_final: 0.8417 (t-100) REVERT: C 453 LYS cc_start: 0.9064 (mmtp) cc_final: 0.8699 (mmtm) REVERT: D 26 GLU cc_start: 0.8030 (tp30) cc_final: 0.7769 (tp30) REVERT: D 71 TYR cc_start: 0.9212 (m-80) cc_final: 0.8630 (m-80) REVERT: D 107 GLU cc_start: 0.8626 (tp30) cc_final: 0.8151 (tp30) REVERT: D 136 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7091 (m-80) REVERT: D 146 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: D 154 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: D 237 MET cc_start: 0.9095 (mtm) cc_final: 0.8807 (mtt) REVERT: D 253 GLU cc_start: 0.8257 (pm20) cc_final: 0.7937 (pm20) REVERT: D 287 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7439 (mm-40) REVERT: D 309 LYS cc_start: 0.9301 (mtmt) cc_final: 0.9001 (ttpp) REVERT: D 320 ASN cc_start: 0.9325 (OUTLIER) cc_final: 0.8753 (t0) REVERT: D 370 ASP cc_start: 0.8862 (t0) cc_final: 0.8440 (t0) REVERT: D 372 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: D 470 GLN cc_start: 0.9304 (tm-30) cc_final: 0.9021 (tm-30) REVERT: E 65 LYS cc_start: 0.9079 (tttt) cc_final: 0.8778 (tttp) REVERT: E 83 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8601 (mmtm) REVERT: E 84 PHE cc_start: 0.7597 (m-10) cc_final: 0.6745 (t80) REVERT: E 92 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7450 (p90) REVERT: E 93 ASN cc_start: 0.8831 (t0) cc_final: 0.8493 (t0) REVERT: E 123 TYR cc_start: 0.9075 (m-80) cc_final: 0.8428 (m-80) REVERT: E 152 TYR cc_start: 0.8124 (m-80) cc_final: 0.7773 (m-80) REVERT: E 196 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8210 (mm-30) REVERT: E 208 MET cc_start: 0.8459 (ptp) cc_final: 0.7877 (ptp) REVERT: E 217 LYS cc_start: 0.8411 (mttt) cc_final: 0.7885 (ptpt) REVERT: E 311 TYR cc_start: 0.8292 (m-80) cc_final: 0.7493 (m-10) REVERT: E 321 ASN cc_start: 0.9110 (t0) cc_final: 0.8426 (t0) REVERT: E 393 MET cc_start: 0.9198 (tmm) cc_final: 0.8968 (tmm) REVERT: E 418 ARG cc_start: 0.7933 (tmm160) cc_final: 0.6619 (mtt-85) REVERT: L 61 ARG cc_start: 0.6976 (ptt-90) cc_final: 0.6539 (ptp-170) REVERT: L 175 MET cc_start: 0.7509 (ttt) cc_final: 0.7086 (tpt) REVERT: H 20 ILE cc_start: 0.4757 (OUTLIER) cc_final: 0.4132 (tp) REVERT: H 43 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6595 (tt0) outliers start: 155 outliers final: 115 residues processed: 559 average time/residue: 0.1324 time to fit residues: 118.8017 Evaluate side-chains 570 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 438 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 4 TRP Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 252 ARG Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 54 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 258 optimal weight: 30.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN D 177 ASN E 154 GLN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.102860 restraints weight = 52324.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.106080 restraints weight = 24251.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108120 restraints weight = 14886.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.109413 restraints weight = 10845.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110241 restraints weight = 8887.459| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22375 Z= 0.180 Angle : 0.696 10.660 30436 Z= 0.346 Chirality : 0.046 0.238 3287 Planarity : 0.005 0.070 3972 Dihedral : 5.199 31.834 2995 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.53 % Allowed : 24.98 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.15), residues: 2748 helix: -1.39 (0.33), residues: 200 sheet: -1.40 (0.18), residues: 744 loop : -2.22 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 263 TYR 0.012 0.001 TYR E 231 PHE 0.017 0.001 PHE L 139 TRP 0.021 0.001 TRP L 92 HIS 0.006 0.001 HIS C 319 Details of bonding type rmsd covalent geometry : bond 0.00409 (22371) covalent geometry : angle 0.69544 (30428) SS BOND : bond 0.00388 ( 4) SS BOND : angle 1.08824 ( 8) hydrogen bonds : bond 0.03465 ( 387) hydrogen bonds : angle 5.63001 ( 996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 466 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8909 (m-10) cc_final: 0.8632 (m-10) REVERT: B 75 ARG cc_start: 0.8649 (ttt180) cc_final: 0.8181 (ttt-90) REVERT: B 126 LYS cc_start: 0.8600 (tmtt) cc_final: 0.8396 (tptp) REVERT: B 129 ASP cc_start: 0.7629 (t0) cc_final: 0.7429 (t0) REVERT: B 134 ASN cc_start: 0.7908 (t0) cc_final: 0.7319 (t0) REVERT: B 148 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7990 (mm) REVERT: B 315 ARG cc_start: 0.8741 (tpt90) cc_final: 0.8225 (pmt-80) REVERT: A 25 ASP cc_start: 0.8552 (m-30) cc_final: 0.8291 (m-30) REVERT: A 106 LEU cc_start: 0.9469 (tp) cc_final: 0.9208 (tp) REVERT: A 126 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8186 (tptp) REVERT: A 130 THR cc_start: 0.6206 (p) cc_final: 0.5950 (p) REVERT: A 135 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7030 (ptm160) REVERT: A 145 ARG cc_start: 0.8889 (mtm180) cc_final: 0.8486 (mtm180) REVERT: A 146 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6376 (mm-30) REVERT: A 148 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 153 LYS cc_start: 0.8704 (ptmm) cc_final: 0.8266 (pttp) REVERT: A 200 MET cc_start: 0.8871 (mmm) cc_final: 0.8551 (mmm) REVERT: A 217 LYS cc_start: 0.9461 (mttm) cc_final: 0.8950 (ptmt) REVERT: A 244 ASP cc_start: 0.8857 (m-30) cc_final: 0.8655 (m-30) REVERT: A 291 PHE cc_start: 0.8092 (m-80) cc_final: 0.7686 (m-10) REVERT: A 379 LYS cc_start: 0.8915 (pttp) cc_final: 0.8634 (ptmt) REVERT: A 454 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8082 (m-10) REVERT: C 150 MET cc_start: 0.8911 (pmm) cc_final: 0.8377 (pmm) REVERT: C 208 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8036 (ptp) REVERT: C 255 MET cc_start: 0.8821 (ppp) cc_final: 0.8562 (ppp) REVERT: C 354 TYR cc_start: 0.8084 (t80) cc_final: 0.7785 (t80) REVERT: C 361 GLU cc_start: 0.7713 (mp0) cc_final: 0.7136 (mp0) REVERT: C 379 LYS cc_start: 0.9048 (pttt) cc_final: 0.8694 (ptmt) REVERT: C 381 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8783 (p) REVERT: C 382 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8781 (tt) REVERT: C 387 MET cc_start: 0.9097 (ttt) cc_final: 0.8240 (tpp) REVERT: C 393 MET cc_start: 0.9263 (tpp) cc_final: 0.8698 (tpp) REVERT: C 446 TRP cc_start: 0.8763 (t60) cc_final: 0.8391 (t-100) REVERT: C 453 LYS cc_start: 0.9049 (mmtp) cc_final: 0.8687 (mmtm) REVERT: D 26 GLU cc_start: 0.8057 (tp30) cc_final: 0.7813 (tp30) REVERT: D 71 TYR cc_start: 0.9188 (m-80) cc_final: 0.8592 (m-80) REVERT: D 107 GLU cc_start: 0.8632 (tp30) cc_final: 0.8038 (tp30) REVERT: D 136 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7054 (m-80) REVERT: D 146 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: D 154 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: D 200 MET cc_start: 0.8174 (tpp) cc_final: 0.7835 (tpp) REVERT: D 237 MET cc_start: 0.9076 (mtm) cc_final: 0.8772 (mtt) REVERT: D 253 GLU cc_start: 0.8202 (pm20) cc_final: 0.7805 (pm20) REVERT: D 269 GLU cc_start: 0.8155 (tp30) cc_final: 0.7807 (tp30) REVERT: D 287 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7337 (mm-40) REVERT: D 309 LYS cc_start: 0.9314 (mtmt) cc_final: 0.9012 (ttpp) REVERT: D 320 ASN cc_start: 0.9314 (OUTLIER) cc_final: 0.8712 (t0) REVERT: D 370 ASP cc_start: 0.8848 (t0) cc_final: 0.8379 (t0) REVERT: D 372 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: D 470 GLN cc_start: 0.9273 (tm-30) cc_final: 0.9020 (tm-30) REVERT: E 65 LYS cc_start: 0.9143 (tttt) cc_final: 0.8820 (tttp) REVERT: E 83 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8587 (mmtm) REVERT: E 84 PHE cc_start: 0.7614 (m-10) cc_final: 0.6838 (t80) REVERT: E 92 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7506 (p90) REVERT: E 123 TYR cc_start: 0.9030 (m-80) cc_final: 0.8404 (m-80) REVERT: E 196 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8339 (mm-30) REVERT: E 217 LYS cc_start: 0.8394 (mttt) cc_final: 0.7864 (ptpt) REVERT: E 303 GLU cc_start: 0.8058 (mp0) cc_final: 0.7822 (mp0) REVERT: E 311 TYR cc_start: 0.8265 (m-80) cc_final: 0.7490 (m-10) REVERT: E 321 ASN cc_start: 0.9107 (t0) cc_final: 0.8379 (t0) REVERT: E 418 ARG cc_start: 0.7892 (tmm160) cc_final: 0.6626 (mtt-85) REVERT: L 61 ARG cc_start: 0.6752 (ptt-90) cc_final: 0.6368 (ptp-170) REVERT: L 98 PHE cc_start: 0.7421 (m-10) cc_final: 0.7163 (m-10) REVERT: L 175 MET cc_start: 0.7501 (ttt) cc_final: 0.7050 (tpt) REVERT: H 20 ILE cc_start: 0.4800 (OUTLIER) cc_final: 0.4188 (tp) REVERT: H 43 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.6605 (tt0) outliers start: 135 outliers final: 112 residues processed: 554 average time/residue: 0.1333 time to fit residues: 118.4944 Evaluate side-chains 570 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 443 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 169 HIS Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 165 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 234 optimal weight: 30.0000 chunk 181 optimal weight: 0.4980 chunk 249 optimal weight: 40.0000 chunk 265 optimal weight: 1.9990 chunk 239 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN E 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.101864 restraints weight = 67517.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105434 restraints weight = 28075.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.107708 restraints weight = 16359.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.109165 restraints weight = 11510.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.109976 restraints weight = 9213.111| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22375 Z= 0.186 Angle : 0.701 10.088 30436 Z= 0.348 Chirality : 0.046 0.234 3287 Planarity : 0.005 0.069 3972 Dihedral : 5.182 31.368 2995 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 5.41 % Allowed : 25.39 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.15), residues: 2748 helix: -1.39 (0.33), residues: 202 sheet: -1.37 (0.18), residues: 732 loop : -2.19 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 263 TYR 0.012 0.001 TYR E 231 PHE 0.023 0.002 PHE L 139 TRP 0.021 0.001 TRP L 92 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00424 (22371) covalent geometry : angle 0.70078 (30428) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.89409 ( 8) hydrogen bonds : bond 0.03437 ( 387) hydrogen bonds : angle 5.61916 ( 996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 438 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 TYR cc_start: 0.8892 (m-10) cc_final: 0.8657 (m-10) REVERT: B 75 ARG cc_start: 0.8650 (ttt180) cc_final: 0.8193 (ttt-90) REVERT: B 126 LYS cc_start: 0.8584 (tmtt) cc_final: 0.8346 (tptp) REVERT: B 129 ASP cc_start: 0.7569 (t0) cc_final: 0.6949 (t0) REVERT: B 131 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6430 (mp0) REVERT: B 134 ASN cc_start: 0.7643 (t0) cc_final: 0.7092 (t0) REVERT: B 145 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7649 (mtm-85) REVERT: B 148 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7971 (mm) REVERT: B 315 ARG cc_start: 0.8736 (tpt90) cc_final: 0.8289 (pmt-80) REVERT: A 25 ASP cc_start: 0.8551 (m-30) cc_final: 0.8289 (m-30) REVERT: A 106 LEU cc_start: 0.9466 (tp) cc_final: 0.9200 (tp) REVERT: A 126 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8184 (tptp) REVERT: A 130 THR cc_start: 0.6228 (p) cc_final: 0.5968 (p) REVERT: A 135 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7023 (ptm160) REVERT: A 145 ARG cc_start: 0.8875 (mtm180) cc_final: 0.8465 (mtm180) REVERT: A 146 GLU cc_start: 0.6626 (mm-30) cc_final: 0.6382 (mm-30) REVERT: A 148 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8366 (mm) REVERT: A 153 LYS cc_start: 0.8681 (ptmm) cc_final: 0.8234 (pttp) REVERT: A 200 MET cc_start: 0.8874 (mmm) cc_final: 0.8553 (mmm) REVERT: A 217 LYS cc_start: 0.9461 (mttm) cc_final: 0.8955 (ptmt) REVERT: A 291 PHE cc_start: 0.8082 (m-80) cc_final: 0.7674 (m-10) REVERT: A 379 LYS cc_start: 0.8930 (pttp) cc_final: 0.8650 (ptmt) REVERT: A 393 MET cc_start: 0.7841 (mmm) cc_final: 0.7601 (mmm) REVERT: A 418 ARG cc_start: 0.4360 (OUTLIER) cc_final: 0.1567 (ppt170) REVERT: A 454 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8112 (m-10) REVERT: C 150 MET cc_start: 0.8911 (pmm) cc_final: 0.8376 (pmm) REVERT: C 208 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8194 (ptp) REVERT: C 255 MET cc_start: 0.8814 (ppp) cc_final: 0.8561 (ppp) REVERT: C 354 TYR cc_start: 0.8081 (t80) cc_final: 0.7688 (t80) REVERT: C 361 GLU cc_start: 0.7544 (mp0) cc_final: 0.7013 (mp0) REVERT: C 379 LYS cc_start: 0.9091 (pttt) cc_final: 0.8745 (ptmt) REVERT: C 381 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8790 (p) REVERT: C 382 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8791 (tt) REVERT: C 387 MET cc_start: 0.9114 (ttt) cc_final: 0.8242 (tpp) REVERT: C 393 MET cc_start: 0.9252 (tpp) cc_final: 0.8664 (tpp) REVERT: C 446 TRP cc_start: 0.8772 (t60) cc_final: 0.8385 (t-100) REVERT: C 453 LYS cc_start: 0.9049 (mmtp) cc_final: 0.8685 (mmtm) REVERT: D 26 GLU cc_start: 0.8053 (tp30) cc_final: 0.7792 (tp30) REVERT: D 71 TYR cc_start: 0.9197 (m-80) cc_final: 0.8601 (m-80) REVERT: D 107 GLU cc_start: 0.8639 (tp30) cc_final: 0.8036 (tp30) REVERT: D 136 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7061 (m-80) REVERT: D 146 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: D 154 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: D 200 MET cc_start: 0.8185 (tpp) cc_final: 0.7837 (tpp) REVERT: D 237 MET cc_start: 0.9081 (mtm) cc_final: 0.8787 (mtt) REVERT: D 253 GLU cc_start: 0.8207 (pm20) cc_final: 0.7818 (pm20) REVERT: D 269 GLU cc_start: 0.8157 (tp30) cc_final: 0.7773 (tp30) REVERT: D 287 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7393 (mm-40) REVERT: D 309 LYS cc_start: 0.9317 (mtmt) cc_final: 0.9010 (ttpp) REVERT: D 370 ASP cc_start: 0.8834 (t0) cc_final: 0.8375 (t0) REVERT: D 372 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: D 470 GLN cc_start: 0.9281 (tm-30) cc_final: 0.9025 (tm-30) REVERT: E 65 LYS cc_start: 0.9133 (tttt) cc_final: 0.8852 (tttp) REVERT: E 83 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8588 (mmtm) REVERT: E 84 PHE cc_start: 0.7624 (m-10) cc_final: 0.6835 (t80) REVERT: E 92 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7556 (p90) REVERT: E 123 TYR cc_start: 0.9035 (m-80) cc_final: 0.8409 (m-80) REVERT: E 152 TYR cc_start: 0.8097 (m-80) cc_final: 0.7753 (m-80) REVERT: E 196 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8066 (mm-30) REVERT: E 299 ILE cc_start: 0.9290 (pt) cc_final: 0.9073 (pt) REVERT: E 303 GLU cc_start: 0.8203 (mp0) cc_final: 0.7810 (mp0) REVERT: E 311 TYR cc_start: 0.8275 (m-80) cc_final: 0.7502 (m-10) REVERT: E 321 ASN cc_start: 0.9103 (t0) cc_final: 0.8401 (t0) REVERT: E 418 ARG cc_start: 0.7834 (tmm160) cc_final: 0.6593 (mtt-85) REVERT: L 61 ARG cc_start: 0.6762 (ptt-90) cc_final: 0.6315 (ptp-170) REVERT: L 175 MET cc_start: 0.7493 (ttt) cc_final: 0.7127 (tpt) REVERT: H 20 ILE cc_start: 0.4785 (OUTLIER) cc_final: 0.4179 (tp) REVERT: H 43 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6477 (tt0) outliers start: 132 outliers final: 113 residues processed: 529 average time/residue: 0.1362 time to fit residues: 115.2635 Evaluate side-chains 561 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 433 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 56 ASN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 287 GLN Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 372 GLN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 8 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 269 optimal weight: 30.0000 chunk 211 optimal weight: 4.9990 chunk 120 optimal weight: 40.0000 chunk 273 optimal weight: 9.9990 chunk 47 optimal weight: 0.2980 chunk 240 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.139684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100995 restraints weight = 63887.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.104531 restraints weight = 27236.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106790 restraints weight = 16046.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108211 restraints weight = 11356.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109018 restraints weight = 9143.830| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22375 Z= 0.173 Angle : 0.697 9.800 30436 Z= 0.344 Chirality : 0.046 0.237 3287 Planarity : 0.005 0.070 3972 Dihedral : 5.126 31.060 2995 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.45 % Allowed : 25.43 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.46 % Cis-general : 0.04 % Twisted Proline : 0.55 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.15), residues: 2748 helix: -1.35 (0.33), residues: 207 sheet: -1.37 (0.18), residues: 721 loop : -2.14 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 263 TYR 0.012 0.001 TYR E 231 PHE 0.023 0.002 PHE L 139 TRP 0.021 0.001 TRP L 92 HIS 0.004 0.001 HIS B 121 Details of bonding type rmsd covalent geometry : bond 0.00396 (22371) covalent geometry : angle 0.69699 (30428) SS BOND : bond 0.00379 ( 4) SS BOND : angle 0.97745 ( 8) hydrogen bonds : bond 0.03389 ( 387) hydrogen bonds : angle 5.54954 ( 996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5083.42 seconds wall clock time: 87 minutes 58.91 seconds (5278.91 seconds total)