Starting phenix.real_space_refine on Mon Apr 6 20:15:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dnl_30787/04_2026/7dnl_30787.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dnl_30787/04_2026/7dnl_30787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dnl_30787/04_2026/7dnl_30787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dnl_30787/04_2026/7dnl_30787.map" model { file = "/net/cci-nas-00/data/ceres_data/7dnl_30787/04_2026/7dnl_30787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dnl_30787/04_2026/7dnl_30787.cif" } resolution = 4.19 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= 0.007 sd= 1.018 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 119 5.16 5 C 13900 2.51 5 N 3632 2.21 5 O 4196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21847 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1719 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 209} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1625 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 203} 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: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3743 Classifications: {'peptide': 472} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 437} Time building chain proxies: 4.21, per 1000 atoms: 0.19 Number of scatterers: 21847 At special positions: 0 Unit cell: (187.207, 178.239, 137.883, 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 119 16.00 O 4196 8.00 N 3632 7.00 C 13900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 220 " - pdb=" SG CYS H 134 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 201 " 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: 1.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5158 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 50 sheets defined 12.5% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'L' and resid 127 through 133 removed outlier: 3.644A pdb=" N SER L 133 " --> pdb=" O GLU L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 193 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.685A pdb=" N THR H 92 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.021A pdb=" N TYR B 276 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.606A pdb=" N ALA B 284 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' 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: 3.976A pdb=" N MET B 387 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET B 393 " --> pdb=" O TYR B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.551A pdb=" N ASN B 441 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 460 removed outlier: 4.271A pdb=" N GLN B 460 " --> pdb=" O ASP B 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 460' Processing helix chain 'B' and resid 461 through 472 removed outlier: 3.512A pdb=" N GLY B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 27 removed outlier: 3.815A pdb=" N TYR A 27 " --> pdb=" O THR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 88 through 92 removed outlier: 4.499A pdb=" N PHE A 91 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR A 92 " --> pdb=" O THR A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 92' Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.739A pdb=" N CYS A 225 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.522A pdb=" N TYR A 276 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.753A pdb=" N ASN A 327 " --> pdb=" O CYS A 324 " (cutoff:3.500A) removed outlier: 4.080A 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 383 through 394 removed outlier: 4.123A pdb=" N THR A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.603A pdb=" N TRP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 4.417A pdb=" N LYS A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.870A pdb=" N LEU A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.735A pdb=" N LYS C 83 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.676A pdb=" N CYS C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN C 226 " --> pdb=" O ILE C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 280 through 284 removed outlier: 4.024A pdb=" N ALA C 284 " --> pdb=" O GLY C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 383 through 394 removed outlier: 3.635A pdb=" N MET C 387 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 438 through 442 removed outlier: 3.510A pdb=" N ASN C 441 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS C 442 " --> pdb=" O PRO C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 442' Processing helix chain 'C' and resid 457 through 460 removed outlier: 3.921A 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: 3.591A pdb=" N ARG C 465 " --> pdb=" O PHE C 461 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 466 " --> pdb=" O PRO C 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.703A pdb=" N LEU D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR D 276 " --> pdb=" O ASP D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 276' Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.801A pdb=" N ALA D 284 " --> pdb=" O GLY D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 394 removed outlier: 3.558A pdb=" N MET D 387 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 388 " --> pdb=" O ALA D 384 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 removed outlier: 3.945A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP D 400 " --> pdb=" O ASN D 396 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 395 through 401' Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.832A pdb=" N ASN D 441 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS D 442 " --> pdb=" O PRO D 439 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR D 443 " --> pdb=" O LEU D 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 438 through 443' Processing helix chain 'D' and resid 457 through 461 removed outlier: 3.838A pdb=" N GLN D 460 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 461 " --> pdb=" O LEU D 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 457 through 461' Processing helix chain 'D' and resid 463 through 472 removed outlier: 3.767A pdb=" N GLY D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.526A pdb=" N LYS E 83 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.518A 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 221 through 225 Processing helix chain 'E' and resid 236 through 240 Processing helix chain 'E' and resid 272 through 276 removed outlier: 3.766A pdb=" N TYR E 276 " --> pdb=" O ASP E 273 " (cutoff:3.500A) 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: 3.636A pdb=" N MET E 387 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 388 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 400 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 461 through 472 removed outlier: 3.667A pdb=" N ARG E 465 " --> pdb=" O PHE E 461 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS E 466 " --> pdb=" O PRO E 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.717A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL L 19 " --> pdb=" O ILE L 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.627A pdb=" N GLU L 111 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.536A pdb=" N LEU L 53 " --> pdb=" O TRP L 41 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG L 96 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR L 103 " --> pdb=" O ARG L 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 135 through 145 removed outlier: 4.908A pdb=" N SER L 137 " --> pdb=" O LEU L 187 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU L 187 " --> pdb=" O SER L 137 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL L 139 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU L 185 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE L 141 " --> pdb=" O SER L 183 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER L 183 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN L 143 " --> pdb=" O MET L 181 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET L 181 " --> pdb=" O ASN L 143 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER L 168 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR L 184 " --> pdb=" O LEU L 166 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU L 166 " --> pdb=" O THR L 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 159 through 160 removed outlier: 3.535A pdb=" N GLU L 201 " --> pdb=" O LYS L 153 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS L 200 " --> pdb=" O LYS L 213 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS L 213 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA L 202 " --> pdb=" O ILE L 211 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE L 211 " --> pdb=" O ALA L 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.062A pdb=" N LEU H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA H 98 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY H 35 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL H 36 " --> pdb=" O HIS H 52 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N HIS H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG H 40 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU H 48 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS H 52 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN H 60 " --> pdb=" O HIS H 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.653A pdb=" N LYS H 149 " --> pdb=" O SER H 126 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS H 149 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU H 183 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.653A pdb=" N LYS H 149 " --> pdb=" O SER H 126 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU H 144 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL H 187 " --> pdb=" O LEU H 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.671A pdb=" N LEU B 106 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 99 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 380 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TRP B 101 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N CYS B 378 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N CYS B 103 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN B 376 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 377 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE B 33 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LYS B 379 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR B 31 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N THR B 381 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N SER B 29 " --> pdb=" O THR B 381 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 44 through 46 removed outlier: 3.922A pdb=" N ALA B 44 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 52 through 53 removed outlier: 7.323A pdb=" N ILE B 52 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 248 through 254 removed outlier: 3.949A pdb=" N PHE B 248 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 154 " --> pdb=" O GLN B 254 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 76 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 73 " --> pdb=" O TRP B 446 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 448 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG B 75 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.581A pdb=" N LEU B 148 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU B 146 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 188 through 194 removed outlier: 3.876A pdb=" N TYR B 231 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TRP B 170 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N CYS B 229 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N MET B 200 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 256 through 262 removed outlier: 5.160A pdb=" N VAL B 257 " --> pdb=" O SER B 296 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N SER B 296 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS B 259 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 294 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.723A pdb=" N LYS A 266 " --> pdb=" O PHE B 359 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 97 through 103 Processing sheet with id=AC1, first strand: chain 'A' and resid 97 through 103 removed outlier: 3.622A pdb=" N LEU A 377 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE A 33 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N LYS A 379 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 31 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR A 381 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N SER A 29 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 42 through 46 removed outlier: 3.777A pdb=" N TYR A 369 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 364 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A 342 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 42 through 46 removed outlier: 3.777A pdb=" N TYR A 369 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS E 266 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AC5, first strand: chain 'A' and resid 250 through 254 removed outlier: 3.615A pdb=" N LEU A 250 " --> pdb=" O CYS A 158 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 154 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 157 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 334 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 333 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP A 446 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 75 " --> pdb=" O TRP A 446 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 448 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.760A pdb=" N TYR A 123 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLU A 146 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 188 through 194 removed outlier: 3.690A pdb=" N HIS A 169 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 168 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 231 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 257 through 262 removed outlier: 4.267A pdb=" N HIS A 259 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 294 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 323 through 324 removed outlier: 4.745A pdb=" N TRP C 101 " --> pdb=" O CYS C 324 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C 99 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 380 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TRP C 101 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS C 378 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS C 103 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN C 376 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 374 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 107 " --> pdb=" O GLN C 372 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN C 372 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU C 371 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA C 37 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE C 373 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR C 35 " --> pdb=" O PHE C 373 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE C 375 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 33 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU C 377 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 379 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 455 " --> pdb=" O TYR C 36 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.672A pdb=" N ALA C 44 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 52 through 53 removed outlier: 7.360A pdb=" N ILE C 52 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 446 through 448 removed outlier: 6.745A pdb=" N VAL C 73 " --> pdb=" O TRP C 446 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL C 448 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG C 75 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 331 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 334 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 157 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN C 154 " --> pdb=" O GLN C 254 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 254 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS C 158 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 250 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 248 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET C 255 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 188 through 194 removed outlier: 3.575A pdb=" N PHE C 191 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS C 169 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TRP C 170 " --> pdb=" O CYS C 229 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N CYS C 229 " --> pdb=" O TRP C 170 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET C 200 " --> pdb=" O LYS C 230 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 257 through 262 removed outlier: 6.863A pdb=" N THR C 294 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N PHE C 260 " --> pdb=" O PHE C 292 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE C 292 " --> pdb=" O PHE C 260 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 266 through 267 removed outlier: 7.441A pdb=" N LYS C 266 " --> pdb=" O GLU D 361 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N VAL D 363 " --> pdb=" O LYS C 266 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 105 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS D 379 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 42 through 46 removed outlier: 3.735A pdb=" N TYR D 369 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 454 through 455 removed outlier: 3.714A pdb=" N SER D 455 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR D 36 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY D 105 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 106 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 311 through 312 removed outlier: 3.650A pdb=" N LEU D 106 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP D 101 " --> pdb=" O CYS D 324 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 52 through 53 removed outlier: 6.906A pdb=" N ILE D 52 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 291 through 296 removed outlier: 3.768A pdb=" N THR D 294 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS D 259 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER D 296 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL D 257 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 250 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN D 254 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN D 154 " --> pdb=" O GLN D 254 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 157 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 329 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 72 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 448 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG D 77 " --> pdb=" O VAL D 448 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 291 through 296 removed outlier: 3.768A pdb=" N THR D 294 " --> pdb=" O HIS D 259 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS D 259 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER D 296 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL D 257 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET D 255 " --> pdb=" O VAL E 300 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 189 through 194 removed outlier: 3.553A pdb=" N GLU D 168 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR D 231 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 266 through 267 removed outlier: 6.960A pdb=" N LYS D 266 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL E 363 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 266 through 267 removed outlier: 6.960A pdb=" N LYS D 266 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL E 363 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 97 through 100 removed outlier: 3.590A pdb=" N ARG E 98 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN E 372 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU E 106 " --> pdb=" O GLN E 372 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL E 374 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 97 through 100 removed outlier: 3.590A pdb=" N ARG E 98 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 377 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE E 33 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LYS E 379 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR E 31 " --> pdb=" O LYS E 379 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR E 381 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N SER E 29 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 52 through 53 removed outlier: 6.833A pdb=" N ILE E 52 " --> pdb=" O LEU E 62 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 250 through 254 removed outlier: 3.737A pdb=" N LEU E 250 " --> pdb=" O CYS E 158 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN E 154 " --> pdb=" O GLN E 254 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU E 329 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL E 76 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 77 " --> pdb=" O VAL E 448 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 118 through 125 removed outlier: 4.851A pdb=" N GLU E 146 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.911A pdb=" N ASP E 128 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN E 262 " --> pdb=" O ASP E 128 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N HIS E 259 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AF5, first strand: chain 'E' and resid 200 through 201 removed outlier: 6.803A pdb=" N MET E 200 " --> pdb=" O LYS E 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 430 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7018 1.35 - 1.47: 5766 1.47 - 1.60: 9484 1.60 - 1.72: 0 1.72 - 1.84: 163 Bond restraints: 22431 Sorted by residual: bond pdb=" C PRO C 408 " pdb=" N PRO C 409 " ideal model delta sigma weight residual 1.336 1.401 -0.065 1.08e-02 8.57e+03 3.65e+01 bond pdb=" C PRO B 432 " pdb=" N PRO B 433 " ideal model delta sigma weight residual 1.328 1.386 -0.057 1.26e-02 6.30e+03 2.07e+01 bond pdb=" N ASN B 177 " pdb=" CA ASN B 177 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.42e-02 4.96e+03 3.83e+00 bond pdb=" C LYS D 434 " pdb=" N GLU D 435 " ideal model delta sigma weight residual 1.331 1.378 -0.048 2.56e-02 1.53e+03 3.47e+00 bond pdb=" C TYR B 12 " pdb=" N LEU B 13 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.83e-02 1.25e+03 3.28e+00 ... (remaining 22426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 29860 2.93 - 5.87: 559 5.87 - 8.80: 79 8.80 - 11.73: 15 11.73 - 14.66: 2 Bond angle restraints: 30515 Sorted by residual: angle pdb=" C LYS A 436 " pdb=" N GLU A 437 " pdb=" CA GLU A 437 " ideal model delta sigma weight residual 121.54 131.53 -9.99 1.91e+00 2.74e-01 2.73e+01 angle pdb=" N VAL C 104 " pdb=" CA VAL C 104 " pdb=" C VAL C 104 " ideal model delta sigma weight residual 113.71 108.82 4.89 9.50e-01 1.11e+00 2.65e+01 angle pdb=" C PRO D 433 " pdb=" N LYS D 434 " pdb=" CA LYS D 434 " ideal model delta sigma weight residual 120.38 127.77 -7.39 1.46e+00 4.69e-01 2.56e+01 angle pdb=" N PRO E 407 " pdb=" CA PRO E 407 " pdb=" C PRO E 407 " ideal model delta sigma weight residual 110.70 116.60 -5.90 1.22e+00 6.72e-01 2.34e+01 angle pdb=" C ALA D 175 " pdb=" N CYS D 176 " pdb=" CA CYS D 176 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 ... (remaining 30510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 11829 17.48 - 34.96: 1258 34.96 - 52.44: 203 52.44 - 69.92: 50 69.92 - 87.40: 24 Dihedral angle restraints: 13364 sinusoidal: 5314 harmonic: 8050 Sorted by residual: dihedral pdb=" CA GLN E 139 " pdb=" C GLN E 139 " pdb=" N PRO E 140 " pdb=" CA PRO E 140 " ideal model delta harmonic sigma weight residual -180.00 -135.78 -44.22 0 5.00e+00 4.00e-02 7.82e+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 180.00 137.97 42.03 0 5.00e+00 4.00e-02 7.07e+01 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 180.00 145.77 34.23 0 5.00e+00 4.00e-02 4.69e+01 ... (remaining 13361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2462 0.059 - 0.119: 660 0.119 - 0.178: 167 0.178 - 0.237: 16 0.237 - 0.296: 2 Chirality restraints: 3307 Sorted by residual: chirality pdb=" CB ILE H 53 " pdb=" CA ILE H 53 " pdb=" CG1 ILE H 53 " pdb=" CG2 ILE H 53 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB VAL E 16 " pdb=" CA VAL E 16 " pdb=" CG1 VAL E 16 " pdb=" CG2 VAL E 16 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL C 201 " pdb=" CA VAL C 201 " pdb=" CG1 VAL C 201 " pdb=" CG2 VAL C 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3304 not shown) Planarity restraints: 3973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 408 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO E 409 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO E 409 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 409 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 112 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO B 113 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 431 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.30e+00 pdb=" N PRO E 432 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 432 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 432 " 0.037 5.00e-02 4.00e+02 ... (remaining 3970 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 50 2.38 - 3.01: 11270 3.01 - 3.64: 32674 3.64 - 4.27: 45296 4.27 - 4.90: 73133 Nonbonded interactions: 162423 Sorted by model distance: nonbonded pdb=" O PRO D 409 " pdb=" OG SER D 410 " model vdw 1.747 3.040 nonbonded pdb=" OG1 THR D 426 " pdb=" NE2 GLN D 428 " model vdw 2.009 3.120 nonbonded pdb=" O PRO E 409 " pdb=" OG SER E 410 " model vdw 2.025 3.040 nonbonded pdb=" O PRO C 407 " pdb=" OG SER C 410 " model vdw 2.139 3.040 nonbonded pdb=" OG SER A 455 " pdb=" OD1 ASP A 457 " model vdw 2.282 3.040 ... (remaining 162418 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 473) selection = (chain 'B' and resid 20 through 473) selection = (chain 'C' and resid 20 through 473) selection = chain 'D' selection = (chain 'E' and resid 20 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 18.650 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22436 Z= 0.264 Angle : 1.033 14.664 30525 Z= 0.575 Chirality : 0.058 0.296 3307 Planarity : 0.007 0.101 3973 Dihedral : 14.876 87.397 8191 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.30 % Favored : 92.60 % Rotamer: Outliers : 0.57 % Allowed : 8.64 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -4.29 (0.13), residues: 2755 helix: -3.72 (0.21), residues: 188 sheet: -2.31 (0.17), residues: 701 loop : -3.18 (0.11), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 99 TYR 0.024 0.002 TYR B 417 PHE 0.028 0.002 PHE E 256 TRP 0.011 0.001 TRP H 55 HIS 0.008 0.002 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00510 (22431) covalent geometry : angle 1.03291 (30515) SS BOND : bond 0.00388 ( 5) SS BOND : angle 1.61586 ( 10) hydrogen bonds : bond 0.32119 ( 404) hydrogen bonds : angle 10.98117 ( 1074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 770 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 LEU cc_start: 0.8517 (tp) cc_final: 0.8248 (mm) REVERT: B 20 LYS cc_start: 0.9412 (pttp) cc_final: 0.9110 (ptpp) REVERT: B 36 TYR cc_start: 0.9256 (t80) cc_final: 0.8914 (t80) REVERT: B 70 GLN cc_start: 0.9038 (mt0) cc_final: 0.8662 (mp10) REVERT: B 80 ASP cc_start: 0.9449 (t70) cc_final: 0.9014 (t0) REVERT: B 83 LYS cc_start: 0.9305 (mmtm) cc_final: 0.9075 (mmtm) REVERT: B 128 ASP cc_start: 0.9177 (m-30) cc_final: 0.8714 (m-30) REVERT: B 150 MET cc_start: 0.9318 (pmm) cc_final: 0.8841 (pmm) REVERT: B 163 LYS cc_start: 0.9438 (tppp) cc_final: 0.9206 (tppp) REVERT: B 242 TYR cc_start: 0.9160 (m-80) cc_final: 0.8925 (m-10) REVERT: B 248 PHE cc_start: 0.8382 (t80) cc_final: 0.7625 (t80) REVERT: B 255 MET cc_start: 0.8370 (tmm) cc_final: 0.7899 (tmm) REVERT: B 260 PHE cc_start: 0.9208 (m-80) cc_final: 0.8890 (m-80) REVERT: B 323 ILE cc_start: 0.9510 (mp) cc_final: 0.9221 (mp) REVERT: B 324 CYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8384 (t) REVERT: B 345 CYS cc_start: 0.8690 (p) cc_final: 0.8469 (p) REVERT: B 387 MET cc_start: 0.9583 (mtp) cc_final: 0.9372 (mtt) REVERT: B 449 ASN cc_start: 0.9102 (t0) cc_final: 0.8237 (t0) REVERT: B 452 GLU cc_start: 0.9224 (pm20) cc_final: 0.8975 (pm20) REVERT: A 121 HIS cc_start: 0.9112 (t-90) cc_final: 0.8876 (t70) REVERT: A 127 PHE cc_start: 0.9197 (t80) cc_final: 0.8993 (t80) REVERT: A 128 ASP cc_start: 0.9172 (m-30) cc_final: 0.8671 (m-30) REVERT: A 131 GLU cc_start: 0.6762 (mp0) cc_final: 0.6513 (mp0) REVERT: A 159 LEU cc_start: 0.9469 (mm) cc_final: 0.9157 (mm) REVERT: A 233 ASP cc_start: 0.9144 (t0) cc_final: 0.8698 (t70) REVERT: A 236 LYS cc_start: 0.9340 (tttp) cc_final: 0.9125 (ttmm) REVERT: A 237 MET cc_start: 0.8846 (mtp) cc_final: 0.8501 (mtp) REVERT: A 246 LEU cc_start: 0.9750 (mp) cc_final: 0.9541 (mp) REVERT: A 259 HIS cc_start: 0.9225 (m-70) cc_final: 0.8714 (m-70) REVERT: A 267 LEU cc_start: 0.9132 (tp) cc_final: 0.8899 (mp) REVERT: A 282 ASN cc_start: 0.9375 (m110) cc_final: 0.8692 (t0) REVERT: A 309 LYS cc_start: 0.9449 (mttp) cc_final: 0.9054 (mmmm) REVERT: A 311 TYR cc_start: 0.9178 (m-80) cc_final: 0.8657 (m-80) REVERT: A 320 ASN cc_start: 0.8480 (t0) cc_final: 0.8135 (t0) REVERT: A 359 PHE cc_start: 0.9069 (m-80) cc_final: 0.8431 (m-10) REVERT: A 418 ARG cc_start: 0.4403 (mtm-85) cc_final: 0.2535 (mpp80) REVERT: C 83 LYS cc_start: 0.9421 (mmtp) cc_final: 0.9064 (mtpt) REVERT: C 107 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7957 (tp30) REVERT: C 150 MET cc_start: 0.8910 (mmm) cc_final: 0.8689 (mmm) REVERT: C 154 GLN cc_start: 0.9348 (mm110) cc_final: 0.8621 (mt0) REVERT: C 159 LEU cc_start: 0.9438 (mm) cc_final: 0.9115 (mm) REVERT: C 163 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8685 (ttpt) REVERT: C 170 TRP cc_start: 0.9372 (m100) cc_final: 0.8916 (m100) REVERT: C 192 ASN cc_start: 0.8848 (m110) cc_final: 0.8377 (t0) REVERT: C 196 GLU cc_start: 0.8480 (pp20) cc_final: 0.8186 (pp20) REVERT: C 197 ASP cc_start: 0.8279 (p0) cc_final: 0.7788 (p0) REVERT: C 200 MET cc_start: 0.9313 (mmm) cc_final: 0.9007 (mmm) REVERT: C 208 MET cc_start: 0.8434 (ptp) cc_final: 0.6691 (mpp) REVERT: C 209 ASP cc_start: 0.9040 (m-30) cc_final: 0.8637 (m-30) REVERT: C 230 LYS cc_start: 0.9275 (mppt) cc_final: 0.8838 (mppt) REVERT: C 236 LYS cc_start: 0.9492 (tttt) cc_final: 0.8948 (tppt) REVERT: C 246 LEU cc_start: 0.9508 (tp) cc_final: 0.9073 (tp) REVERT: C 248 PHE cc_start: 0.7810 (t80) cc_final: 0.7443 (t80) REVERT: C 255 MET cc_start: 0.8583 (ppp) cc_final: 0.8017 (tmm) REVERT: C 274 ASP cc_start: 0.9578 (p0) cc_final: 0.9354 (p0) REVERT: C 368 GLU cc_start: 0.9190 (tt0) cc_final: 0.8684 (tt0) REVERT: C 376 GLN cc_start: 0.8730 (tt0) cc_final: 0.8509 (tm-30) REVERT: C 385 GLU cc_start: 0.9428 (pm20) cc_final: 0.9211 (pm20) REVERT: C 387 MET cc_start: 0.9456 (mtm) cc_final: 0.9106 (mtt) REVERT: C 394 ASP cc_start: 0.9174 (t0) cc_final: 0.8765 (t70) REVERT: C 438 ASP cc_start: 0.8852 (m-30) cc_final: 0.8507 (t70) REVERT: C 451 LYS cc_start: 0.9221 (mttt) cc_final: 0.8776 (mttp) REVERT: D 34 TYR cc_start: 0.9343 (m-80) cc_final: 0.8951 (m-10) REVERT: D 63 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9037 (m) REVERT: D 71 TYR cc_start: 0.9029 (m-80) cc_final: 0.8685 (m-80) REVERT: D 78 LEU cc_start: 0.9427 (tt) cc_final: 0.9216 (tt) REVERT: D 153 LYS cc_start: 0.9061 (tmmt) cc_final: 0.8617 (ttpt) REVERT: D 189 GLU cc_start: 0.9166 (tp30) cc_final: 0.8506 (mp0) REVERT: D 196 GLU cc_start: 0.8558 (pt0) cc_final: 0.8358 (tt0) REVERT: D 210 PHE cc_start: 0.9257 (m-80) cc_final: 0.8771 (m-80) REVERT: D 231 TYR cc_start: 0.9299 (t80) cc_final: 0.9020 (t80) REVERT: D 255 MET cc_start: 0.8806 (ptm) cc_final: 0.8335 (ppp) REVERT: D 303 GLU cc_start: 0.9352 (tm-30) cc_final: 0.9078 (tm-30) REVERT: D 320 ASN cc_start: 0.8790 (t0) cc_final: 0.8571 (t0) REVERT: D 321 ASN cc_start: 0.9415 (t0) cc_final: 0.9107 (t0) REVERT: D 344 LEU cc_start: 0.9318 (mt) cc_final: 0.8863 (mt) REVERT: D 351 GLU cc_start: 0.9459 (mm-30) cc_final: 0.8911 (mm-30) REVERT: D 360 LYS cc_start: 0.9598 (mttt) cc_final: 0.9345 (tppt) REVERT: D 369 TYR cc_start: 0.8717 (m-80) cc_final: 0.8516 (m-10) REVERT: D 372 GLN cc_start: 0.8174 (mp-120) cc_final: 0.7738 (mp10) REVERT: D 378 CYS cc_start: 0.8984 (m) cc_final: 0.8328 (t) REVERT: D 387 MET cc_start: 0.9425 (ppp) cc_final: 0.9081 (ppp) REVERT: D 390 ILE cc_start: 0.9820 (OUTLIER) cc_final: 0.9619 (mp) REVERT: D 393 MET cc_start: 0.9298 (tpp) cc_final: 0.8977 (tmm) REVERT: D 397 ILE cc_start: 0.9678 (mp) cc_final: 0.9422 (mp) REVERT: D 399 GLU cc_start: 0.9274 (pp20) cc_final: 0.9021 (pp20) REVERT: D 401 TRP cc_start: 0.9483 (m-10) cc_final: 0.9235 (m-10) REVERT: D 417 TYR cc_start: 0.9014 (m-80) cc_final: 0.8746 (m-80) REVERT: D 443 TYR cc_start: 0.9463 (m-80) cc_final: 0.9103 (m-80) REVERT: D 449 ASN cc_start: 0.9220 (t0) cc_final: 0.8730 (t0) REVERT: D 470 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8572 (tt0) REVERT: E 47 ASN cc_start: 0.9309 (t0) cc_final: 0.9106 (t0) REVERT: E 52 ILE cc_start: 0.8793 (mm) cc_final: 0.8593 (pt) REVERT: E 80 ASP cc_start: 0.9386 (t0) cc_final: 0.9170 (t0) REVERT: E 83 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9118 (mmmt) REVERT: E 121 HIS cc_start: 0.9045 (t-90) cc_final: 0.8272 (t-170) REVERT: E 125 ASN cc_start: 0.9462 (t0) cc_final: 0.9061 (p0) REVERT: E 135 ARG cc_start: 0.8669 (mmt90) cc_final: 0.7963 (mtp85) REVERT: E 150 MET cc_start: 0.8695 (mtm) cc_final: 0.8426 (mtm) REVERT: E 156 GLN cc_start: 0.8330 (mt0) cc_final: 0.8036 (mt0) REVERT: E 172 LYS cc_start: 0.8335 (tptm) cc_final: 0.8074 (tppt) REVERT: E 194 ILE cc_start: 0.9750 (mt) cc_final: 0.9370 (tp) REVERT: E 229 CYS cc_start: 0.9054 (m) cc_final: 0.8226 (p) REVERT: E 234 TYR cc_start: 0.9352 (m-80) cc_final: 0.8958 (m-10) REVERT: E 251 ARG cc_start: 0.9428 (ptt90) cc_final: 0.8751 (ptt90) REVERT: E 259 HIS cc_start: 0.9225 (m-70) cc_final: 0.8820 (m-70) REVERT: E 311 TYR cc_start: 0.9166 (m-80) cc_final: 0.8713 (m-80) REVERT: E 314 GLN cc_start: 0.9315 (mt0) cc_final: 0.8604 (pm20) REVERT: E 344 LEU cc_start: 0.8185 (tp) cc_final: 0.7876 (tp) REVERT: E 354 TYR cc_start: 0.8560 (t80) cc_final: 0.8299 (t80) REVERT: E 367 GLU cc_start: 0.8642 (tt0) cc_final: 0.8175 (tt0) REVERT: E 387 MET cc_start: 0.9161 (tmm) cc_final: 0.8678 (tpp) REVERT: E 399 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9222 (tm-30) REVERT: E 400 ASP cc_start: 0.9110 (p0) cc_final: 0.8844 (p0) outliers start: 14 outliers final: 3 residues processed: 778 average time/residue: 0.1408 time to fit residues: 171.9984 Evaluate side-chains 569 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 563 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 134 ASN B 169 HIS B 226 ASN B 305 GLN B 327 ASN B 423 GLN A 57 ASN A 192 ASN A 254 GLN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 319 HIS C 365 HIS D 47 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN ** D 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 125 ASN E 154 GLN E 192 ASN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 GLN E 376 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.137395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094263 restraints weight = 55616.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097398 restraints weight = 28099.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.099461 restraints weight = 17735.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.100787 restraints weight = 12887.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101663 restraints weight = 10331.312| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 22436 Z= 0.263 Angle : 0.730 9.648 30525 Z= 0.381 Chirality : 0.047 0.165 3307 Planarity : 0.006 0.086 3973 Dihedral : 6.124 61.174 2998 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.91 % Favored : 92.05 % Rotamer: Outliers : 0.20 % Allowed : 6.60 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -3.66 (0.14), residues: 2755 helix: -2.24 (0.28), residues: 195 sheet: -1.93 (0.17), residues: 728 loop : -2.84 (0.12), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 418 TYR 0.025 0.002 TYR A 369 PHE 0.033 0.002 PHE E 454 TRP 0.017 0.001 TRP H 194 HIS 0.010 0.002 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00568 (22431) covalent geometry : angle 0.73013 (30515) SS BOND : bond 0.00260 ( 5) SS BOND : angle 1.35887 ( 10) hydrogen bonds : bond 0.05253 ( 404) hydrogen bonds : angle 7.79475 ( 1074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 654 time to evaluate : 0.867 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: H 36 VAL cc_start: 0.7095 (m) cc_final: 0.6555 (t) REVERT: B 20 LYS cc_start: 0.9345 (pttp) cc_final: 0.9028 (ptpp) REVERT: B 36 TYR cc_start: 0.9427 (t80) cc_final: 0.9127 (t80) REVERT: B 80 ASP cc_start: 0.9537 (t70) cc_final: 0.9018 (t70) REVERT: B 82 ASN cc_start: 0.9186 (m-40) cc_final: 0.8977 (m-40) REVERT: B 163 LYS cc_start: 0.9471 (tppp) cc_final: 0.9236 (tppp) REVERT: B 242 TYR cc_start: 0.9188 (m-80) cc_final: 0.8656 (m-10) REVERT: B 248 PHE cc_start: 0.8361 (t80) cc_final: 0.7611 (t80) REVERT: B 255 MET cc_start: 0.8373 (tmm) cc_final: 0.8002 (tmm) REVERT: B 347 GLU cc_start: 0.9167 (pp20) cc_final: 0.8670 (pp20) REVERT: B 378 CYS cc_start: 0.8331 (m) cc_final: 0.8107 (m) REVERT: B 387 MET cc_start: 0.9596 (mtp) cc_final: 0.9346 (mtp) REVERT: B 452 GLU cc_start: 0.9187 (pm20) cc_final: 0.8782 (pm20) REVERT: A 127 PHE cc_start: 0.9257 (t80) cc_final: 0.8348 (t80) REVERT: A 128 ASP cc_start: 0.9201 (m-30) cc_final: 0.8294 (m-30) REVERT: A 159 LEU cc_start: 0.9465 (mm) cc_final: 0.9156 (mm) REVERT: A 166 THR cc_start: 0.9210 (p) cc_final: 0.8534 (p) REVERT: A 200 MET cc_start: 0.9350 (mmt) cc_final: 0.9107 (mmt) REVERT: A 208 MET cc_start: 0.8084 (pmm) cc_final: 0.7158 (pmm) REVERT: A 237 MET cc_start: 0.8763 (mtp) cc_final: 0.8543 (mmm) REVERT: A 244 ASP cc_start: 0.8223 (m-30) cc_final: 0.8008 (m-30) REVERT: A 250 LEU cc_start: 0.9532 (mm) cc_final: 0.9265 (mm) REVERT: A 253 GLU cc_start: 0.9224 (pm20) cc_final: 0.8860 (pm20) REVERT: A 309 LYS cc_start: 0.9387 (mttp) cc_final: 0.8965 (mmmm) REVERT: A 311 TYR cc_start: 0.9219 (m-80) cc_final: 0.8694 (m-80) REVERT: A 320 ASN cc_start: 0.8481 (t0) cc_final: 0.7951 (t0) REVERT: A 359 PHE cc_start: 0.9259 (m-80) cc_final: 0.8641 (m-10) REVERT: A 372 GLN cc_start: 0.8937 (mt0) cc_final: 0.8319 (mp-120) REVERT: A 387 MET cc_start: 0.9238 (ptp) cc_final: 0.8949 (ptp) REVERT: C 107 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7876 (tp30) REVERT: C 128 ASP cc_start: 0.9227 (m-30) cc_final: 0.8965 (m-30) REVERT: C 150 MET cc_start: 0.8955 (mmm) cc_final: 0.8695 (mmm) REVERT: C 154 GLN cc_start: 0.9288 (mm110) cc_final: 0.8602 (mt0) REVERT: C 156 GLN cc_start: 0.8519 (mt0) cc_final: 0.8178 (mt0) REVERT: C 159 LEU cc_start: 0.9331 (mm) cc_final: 0.9098 (mm) REVERT: C 160 ILE cc_start: 0.9351 (mp) cc_final: 0.9124 (mp) REVERT: C 192 ASN cc_start: 0.8902 (m110) cc_final: 0.8565 (t0) REVERT: C 196 GLU cc_start: 0.8431 (pp20) cc_final: 0.8048 (pp20) REVERT: C 208 MET cc_start: 0.8972 (ptp) cc_final: 0.6945 (mpp) REVERT: C 209 ASP cc_start: 0.8998 (m-30) cc_final: 0.8733 (m-30) REVERT: C 229 CYS cc_start: 0.8688 (p) cc_final: 0.8431 (p) REVERT: C 236 LYS cc_start: 0.9531 (tttt) cc_final: 0.8896 (tppt) REVERT: C 237 MET cc_start: 0.9383 (tpp) cc_final: 0.9079 (mmt) REVERT: C 248 PHE cc_start: 0.7294 (t80) cc_final: 0.6799 (t80) REVERT: C 274 ASP cc_start: 0.9574 (p0) cc_final: 0.9236 (p0) REVERT: C 296 SER cc_start: 0.7072 (p) cc_final: 0.6679 (t) REVERT: C 347 GLU cc_start: 0.9186 (pm20) cc_final: 0.8986 (pm20) REVERT: C 367 GLU cc_start: 0.7367 (tp30) cc_final: 0.6909 (tp30) REVERT: C 368 GLU cc_start: 0.8785 (tt0) cc_final: 0.8486 (tt0) REVERT: C 378 CYS cc_start: 0.6903 (m) cc_final: 0.4240 (m) REVERT: C 387 MET cc_start: 0.9541 (mtm) cc_final: 0.9154 (mtt) REVERT: C 394 ASP cc_start: 0.9159 (t0) cc_final: 0.8865 (t70) REVERT: C 400 ASP cc_start: 0.9104 (p0) cc_final: 0.8830 (p0) REVERT: C 402 GLN cc_start: 0.9500 (mt0) cc_final: 0.9095 (mp10) REVERT: C 451 LYS cc_start: 0.9332 (mttt) cc_final: 0.8920 (mttp) REVERT: C 452 GLU cc_start: 0.5102 (tp30) cc_final: 0.4864 (mm-30) REVERT: D 34 TYR cc_start: 0.9300 (m-80) cc_final: 0.8919 (m-10) REVERT: D 71 TYR cc_start: 0.9024 (m-80) cc_final: 0.8526 (m-80) REVERT: D 78 LEU cc_start: 0.9480 (tt) cc_final: 0.9187 (tt) REVERT: D 126 LYS cc_start: 0.9314 (tmmt) cc_final: 0.9111 (tmtt) REVERT: D 150 MET cc_start: 0.8903 (pmm) cc_final: 0.8674 (pmm) REVERT: D 153 LYS cc_start: 0.8850 (tmmt) cc_final: 0.8043 (pttt) REVERT: D 154 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8583 (pp30) REVERT: D 168 GLU cc_start: 0.9211 (pm20) cc_final: 0.8923 (pm20) REVERT: D 210 PHE cc_start: 0.9342 (m-80) cc_final: 0.8987 (m-80) REVERT: D 217 LYS cc_start: 0.9552 (ptpp) cc_final: 0.8895 (pttt) REVERT: D 229 CYS cc_start: 0.7990 (p) cc_final: 0.7552 (p) REVERT: D 231 TYR cc_start: 0.9128 (t80) cc_final: 0.8272 (t80) REVERT: D 234 TYR cc_start: 0.9216 (m-80) cc_final: 0.8743 (m-80) REVERT: D 240 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8764 (tm-30) REVERT: D 255 MET cc_start: 0.8893 (ptm) cc_final: 0.8155 (ppp) REVERT: D 287 GLN cc_start: 0.8167 (mt0) cc_final: 0.7768 (tt0) REVERT: D 303 GLU cc_start: 0.9373 (tm-30) cc_final: 0.9100 (tm-30) REVERT: D 306 LEU cc_start: 0.9626 (mm) cc_final: 0.9331 (mm) REVERT: D 320 ASN cc_start: 0.9030 (t0) cc_final: 0.8815 (t0) REVERT: D 321 ASN cc_start: 0.9530 (t0) cc_final: 0.9103 (t0) REVERT: D 360 LYS cc_start: 0.9634 (mttt) cc_final: 0.9377 (ttmm) REVERT: D 369 TYR cc_start: 0.8892 (m-80) cc_final: 0.8512 (m-10) REVERT: D 393 MET cc_start: 0.9324 (tpp) cc_final: 0.9121 (mmm) REVERT: D 401 TRP cc_start: 0.9533 (m-10) cc_final: 0.9311 (m-10) REVERT: D 417 TYR cc_start: 0.8870 (m-80) cc_final: 0.8542 (m-80) REVERT: D 443 TYR cc_start: 0.9495 (m-80) cc_final: 0.9196 (m-80) REVERT: D 444 THR cc_start: 0.8700 (p) cc_final: 0.8019 (p) REVERT: D 470 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8394 (tt0) REVERT: E 125 ASN cc_start: 0.9580 (t0) cc_final: 0.8939 (p0) REVERT: E 150 MET cc_start: 0.8610 (mtm) cc_final: 0.8363 (mtm) REVERT: E 172 LYS cc_start: 0.8446 (tptm) cc_final: 0.8119 (tppt) REVERT: E 200 MET cc_start: 0.9300 (mmm) cc_final: 0.8242 (tpp) REVERT: E 208 MET cc_start: 0.9004 (ppp) cc_final: 0.8686 (ppp) REVERT: E 224 ILE cc_start: 0.9748 (pt) cc_final: 0.9071 (mm) REVERT: E 234 TYR cc_start: 0.9328 (m-80) cc_final: 0.8746 (m-10) REVERT: E 251 ARG cc_start: 0.9202 (ptt90) cc_final: 0.8355 (ptt90) REVERT: E 254 GLN cc_start: 0.9278 (pt0) cc_final: 0.8881 (pm20) REVERT: E 259 HIS cc_start: 0.9136 (m-70) cc_final: 0.8490 (m-70) REVERT: E 311 TYR cc_start: 0.9145 (m-80) cc_final: 0.8825 (m-80) REVERT: E 314 GLN cc_start: 0.9318 (mt0) cc_final: 0.8641 (pm20) REVERT: E 338 ARG cc_start: 0.9472 (mtt-85) cc_final: 0.8811 (mtp85) REVERT: E 369 TYR cc_start: 0.9144 (m-80) cc_final: 0.8850 (m-80) REVERT: E 387 MET cc_start: 0.9109 (tmm) cc_final: 0.8616 (tpp) REVERT: E 398 LEU cc_start: 0.9571 (tp) cc_final: 0.9370 (tp) REVERT: E 399 GLU cc_start: 0.9584 (tm-30) cc_final: 0.9337 (tm-30) REVERT: E 400 ASP cc_start: 0.8932 (p0) cc_final: 0.8583 (p0) outliers start: 5 outliers final: 1 residues processed: 658 average time/residue: 0.1365 time to fit residues: 144.6691 Evaluate side-chains 511 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 509 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 6 optimal weight: 40.0000 chunk 4 optimal weight: 9.9990 chunk 262 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 50.0000 chunk 85 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN A 154 GLN A 254 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 169 HIS ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS C 321 ASN C 460 GLN D 57 ASN D 82 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 GLN D 460 GLN E 154 GLN E 192 ASN ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 ASN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.136190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.091993 restraints weight = 55458.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095007 restraints weight = 28343.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097000 restraints weight = 18127.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.098372 restraints weight = 13333.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099161 restraints weight = 10845.302| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 22436 Z= 0.255 Angle : 0.702 10.658 30525 Z= 0.363 Chirality : 0.047 0.159 3307 Planarity : 0.006 0.078 3973 Dihedral : 5.953 67.540 2998 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.04 % Allowed : 6.16 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -3.38 (0.14), residues: 2755 helix: -1.75 (0.31), residues: 202 sheet: -1.67 (0.18), residues: 714 loop : -2.71 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 418 TYR 0.034 0.002 TYR A 36 PHE 0.025 0.002 PHE E 454 TRP 0.012 0.001 TRP D 446 HIS 0.008 0.002 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00551 (22431) covalent geometry : angle 0.70144 (30515) SS BOND : bond 0.00321 ( 5) SS BOND : angle 1.22241 ( 10) hydrogen bonds : bond 0.04330 ( 404) hydrogen bonds : angle 7.27091 ( 1074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 613 time to evaluate : 0.795 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: L 21 MET cc_start: 0.6077 (mmm) cc_final: 0.5845 (mtt) REVERT: H 36 VAL cc_start: 0.6410 (m) cc_final: 0.5857 (t) REVERT: B 20 LYS cc_start: 0.9413 (pttp) cc_final: 0.9131 (ptpp) REVERT: B 36 TYR cc_start: 0.9426 (t80) cc_final: 0.9165 (t80) REVERT: B 71 TYR cc_start: 0.9010 (m-80) cc_final: 0.8772 (m-10) REVERT: B 80 ASP cc_start: 0.9308 (t70) cc_final: 0.8950 (t70) REVERT: B 83 LYS cc_start: 0.9016 (mppt) cc_final: 0.8754 (mmtm) REVERT: B 84 PHE cc_start: 0.8708 (t80) cc_final: 0.8333 (t80) REVERT: B 110 ARG cc_start: 0.7090 (ttt90) cc_final: 0.6854 (tpp80) REVERT: B 128 ASP cc_start: 0.9238 (m-30) cc_final: 0.8942 (m-30) REVERT: B 237 MET cc_start: 0.9004 (mtt) cc_final: 0.8783 (mtt) REVERT: B 242 TYR cc_start: 0.9178 (m-10) cc_final: 0.8966 (m-10) REVERT: B 248 PHE cc_start: 0.8280 (t80) cc_final: 0.7721 (t80) REVERT: B 255 MET cc_start: 0.8480 (tmm) cc_final: 0.8114 (tmm) REVERT: B 262 ASN cc_start: 0.9347 (p0) cc_final: 0.9107 (p0) REVERT: B 337 THR cc_start: 0.9590 (p) cc_final: 0.9132 (p) REVERT: B 338 ARG cc_start: 0.8836 (mtt90) cc_final: 0.8408 (mtt90) REVERT: B 347 GLU cc_start: 0.9082 (pp20) cc_final: 0.8576 (pp20) REVERT: B 387 MET cc_start: 0.9582 (mtp) cc_final: 0.9283 (mtp) REVERT: B 452 GLU cc_start: 0.9159 (pm20) cc_final: 0.8795 (pm20) REVERT: A 127 PHE cc_start: 0.9232 (t80) cc_final: 0.8417 (t80) REVERT: A 128 ASP cc_start: 0.9218 (m-30) cc_final: 0.8377 (m-30) REVERT: A 151 ASP cc_start: 0.8837 (t0) cc_final: 0.8622 (t0) REVERT: A 159 LEU cc_start: 0.9493 (mm) cc_final: 0.9217 (mm) REVERT: A 168 GLU cc_start: 0.8954 (pm20) cc_final: 0.8651 (pm20) REVERT: A 236 LYS cc_start: 0.9464 (tttp) cc_final: 0.9241 (ttmm) REVERT: A 237 MET cc_start: 0.8914 (mtp) cc_final: 0.8557 (mmm) REVERT: A 244 ASP cc_start: 0.8126 (m-30) cc_final: 0.7791 (m-30) REVERT: A 250 LEU cc_start: 0.9607 (mm) cc_final: 0.9297 (mm) REVERT: A 309 LYS cc_start: 0.9374 (mttp) cc_final: 0.8950 (mmmm) REVERT: A 311 TYR cc_start: 0.9212 (m-80) cc_final: 0.8628 (m-80) REVERT: A 320 ASN cc_start: 0.8434 (t0) cc_final: 0.7880 (t0) REVERT: A 359 PHE cc_start: 0.9248 (m-80) cc_final: 0.8720 (m-10) REVERT: A 387 MET cc_start: 0.9250 (ptp) cc_final: 0.8944 (ptp) REVERT: C 128 ASP cc_start: 0.9276 (m-30) cc_final: 0.9021 (m-30) REVERT: C 150 MET cc_start: 0.9032 (mmm) cc_final: 0.8716 (mmm) REVERT: C 151 ASP cc_start: 0.7947 (p0) cc_final: 0.7669 (p0) REVERT: C 154 GLN cc_start: 0.9099 (mm110) cc_final: 0.8889 (mt0) REVERT: C 156 GLN cc_start: 0.8601 (mt0) cc_final: 0.8112 (mp10) REVERT: C 159 LEU cc_start: 0.9317 (mm) cc_final: 0.9065 (mm) REVERT: C 160 ILE cc_start: 0.9375 (mp) cc_final: 0.9088 (mp) REVERT: C 192 ASN cc_start: 0.8884 (m110) cc_final: 0.8549 (t0) REVERT: C 208 MET cc_start: 0.9174 (ptp) cc_final: 0.7855 (ptp) REVERT: C 229 CYS cc_start: 0.8589 (p) cc_final: 0.8304 (p) REVERT: C 236 LYS cc_start: 0.9497 (tttt) cc_final: 0.8889 (tppt) REVERT: C 248 PHE cc_start: 0.7459 (t80) cc_final: 0.6976 (t80) REVERT: C 255 MET cc_start: 0.8946 (ppp) cc_final: 0.8682 (ppp) REVERT: C 296 SER cc_start: 0.7012 (p) cc_final: 0.6775 (t) REVERT: C 347 GLU cc_start: 0.9259 (pm20) cc_final: 0.8689 (pp20) REVERT: C 367 GLU cc_start: 0.7652 (tp30) cc_final: 0.7180 (tp30) REVERT: C 368 GLU cc_start: 0.8925 (tt0) cc_final: 0.8639 (tt0) REVERT: C 394 ASP cc_start: 0.9274 (t0) cc_final: 0.8868 (t70) REVERT: C 400 ASP cc_start: 0.9064 (p0) cc_final: 0.8532 (p0) REVERT: C 402 GLN cc_start: 0.9530 (mt0) cc_final: 0.9251 (mp10) REVERT: C 451 LYS cc_start: 0.9262 (mttt) cc_final: 0.8872 (mttp) REVERT: D 34 TYR cc_start: 0.9319 (m-80) cc_final: 0.8955 (m-80) REVERT: D 65 LYS cc_start: 0.9359 (ttpt) cc_final: 0.9129 (tttt) REVERT: D 69 LEU cc_start: 0.9418 (mt) cc_final: 0.9064 (mp) REVERT: D 71 TYR cc_start: 0.9024 (m-80) cc_final: 0.8472 (m-80) REVERT: D 126 LYS cc_start: 0.9351 (tmmt) cc_final: 0.9030 (tmtt) REVERT: D 150 MET cc_start: 0.8860 (pmm) cc_final: 0.8562 (pmm) REVERT: D 153 LYS cc_start: 0.8880 (tmmt) cc_final: 0.8013 (pttt) REVERT: D 156 GLN cc_start: 0.8276 (mt0) cc_final: 0.7914 (mt0) REVERT: D 210 PHE cc_start: 0.9340 (m-80) cc_final: 0.8910 (m-80) REVERT: D 229 CYS cc_start: 0.7805 (p) cc_final: 0.7269 (p) REVERT: D 231 TYR cc_start: 0.9068 (t80) cc_final: 0.8250 (t80) REVERT: D 234 TYR cc_start: 0.9206 (m-80) cc_final: 0.8773 (m-80) REVERT: D 244 ASP cc_start: 0.8368 (p0) cc_final: 0.8163 (p0) REVERT: D 255 MET cc_start: 0.8903 (ptm) cc_final: 0.8108 (ppp) REVERT: D 321 ASN cc_start: 0.9544 (t0) cc_final: 0.9083 (t0) REVERT: D 342 MET cc_start: 0.9052 (mmt) cc_final: 0.7993 (mmt) REVERT: D 360 LYS cc_start: 0.9668 (mttt) cc_final: 0.9401 (ttmm) REVERT: D 369 TYR cc_start: 0.8986 (m-80) cc_final: 0.8569 (m-10) REVERT: D 401 TRP cc_start: 0.9542 (m-10) cc_final: 0.9312 (m-10) REVERT: D 417 TYR cc_start: 0.8872 (m-80) cc_final: 0.8617 (m-80) REVERT: D 470 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8606 (tt0) REVERT: E 127 PHE cc_start: 0.8790 (t80) cc_final: 0.7743 (t80) REVERT: E 200 MET cc_start: 0.9326 (mmm) cc_final: 0.8398 (tpp) REVERT: E 224 ILE cc_start: 0.9778 (pt) cc_final: 0.9163 (mm) REVERT: E 234 TYR cc_start: 0.9313 (m-80) cc_final: 0.9073 (m-10) REVERT: E 246 LEU cc_start: 0.9611 (mm) cc_final: 0.9281 (mm) REVERT: E 254 GLN cc_start: 0.9286 (pt0) cc_final: 0.8901 (pm20) REVERT: E 259 HIS cc_start: 0.8944 (m-70) cc_final: 0.8692 (m-70) REVERT: E 311 TYR cc_start: 0.9245 (m-80) cc_final: 0.8957 (m-80) REVERT: E 314 GLN cc_start: 0.9319 (mt0) cc_final: 0.8589 (pm20) REVERT: E 324 CYS cc_start: 0.9201 (p) cc_final: 0.8834 (p) REVERT: E 338 ARG cc_start: 0.9436 (mtt-85) cc_final: 0.8892 (mtp85) REVERT: E 399 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9360 (tm-30) REVERT: E 400 ASP cc_start: 0.8833 (p0) cc_final: 0.8526 (p0) REVERT: E 416 THR cc_start: 0.8955 (t) cc_final: 0.8303 (t) REVERT: E 451 LYS cc_start: 0.9392 (mttm) cc_final: 0.8676 (mmmm) outliers start: 1 outliers final: 0 residues processed: 614 average time/residue: 0.1336 time to fit residues: 131.8763 Evaluate side-chains 492 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 36 optimal weight: 50.0000 chunk 107 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 112 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 327 ASN B 460 GLN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 356 ASN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 HIS E 156 GLN E 305 GLN E 341 ASN ** E 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.135491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091632 restraints weight = 55599.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094592 restraints weight = 28415.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.096540 restraints weight = 18199.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.097876 restraints weight = 13410.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.098677 restraints weight = 10914.855| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 22436 Z= 0.261 Angle : 0.697 9.328 30525 Z= 0.360 Chirality : 0.047 0.161 3307 Planarity : 0.006 0.092 3973 Dihedral : 5.905 64.506 2998 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -3.24 (0.14), residues: 2755 helix: -1.68 (0.32), residues: 210 sheet: -1.58 (0.19), residues: 713 loop : -2.61 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 418 TYR 0.028 0.002 TYR A 36 PHE 0.022 0.002 PHE A 291 TRP 0.034 0.002 TRP C 401 HIS 0.010 0.002 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00567 (22431) covalent geometry : angle 0.69725 (30515) SS BOND : bond 0.00215 ( 5) SS BOND : angle 0.94783 ( 10) hydrogen bonds : bond 0.03886 ( 404) hydrogen bonds : angle 6.99973 ( 1074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 611 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 MET cc_start: 0.5992 (mmm) cc_final: 0.5688 (mtt) REVERT: H 36 VAL cc_start: 0.5937 (m) cc_final: 0.5326 (t) REVERT: B 20 LYS cc_start: 0.9440 (pttp) cc_final: 0.9154 (ptpp) REVERT: B 36 TYR cc_start: 0.9434 (t80) cc_final: 0.9166 (t80) REVERT: B 78 LEU cc_start: 0.9589 (mm) cc_final: 0.9372 (mm) REVERT: B 84 PHE cc_start: 0.8652 (t80) cc_final: 0.8293 (t80) REVERT: B 128 ASP cc_start: 0.9201 (m-30) cc_final: 0.8885 (m-30) REVERT: B 237 MET cc_start: 0.9022 (mtt) cc_final: 0.8751 (mtt) REVERT: B 242 TYR cc_start: 0.9183 (m-10) cc_final: 0.8975 (m-10) REVERT: B 248 PHE cc_start: 0.8301 (t80) cc_final: 0.7636 (t80) REVERT: B 255 MET cc_start: 0.8570 (tmm) cc_final: 0.8179 (tmm) REVERT: B 262 ASN cc_start: 0.9450 (p0) cc_final: 0.9226 (p0) REVERT: B 347 GLU cc_start: 0.9020 (pp20) cc_final: 0.8529 (pp20) REVERT: B 387 MET cc_start: 0.9577 (mtp) cc_final: 0.9262 (mtp) REVERT: B 393 MET cc_start: 0.8996 (ttm) cc_final: 0.8623 (ttm) REVERT: B 403 PHE cc_start: 0.8371 (m-80) cc_final: 0.8132 (m-80) REVERT: B 452 GLU cc_start: 0.9212 (pm20) cc_final: 0.8786 (pm20) REVERT: A 127 PHE cc_start: 0.9280 (t80) cc_final: 0.8508 (t80) REVERT: A 128 ASP cc_start: 0.9203 (m-30) cc_final: 0.8353 (m-30) REVERT: A 148 LEU cc_start: 0.8681 (tp) cc_final: 0.8384 (tp) REVERT: A 153 LYS cc_start: 0.9377 (ptmm) cc_final: 0.8791 (ttpp) REVERT: A 244 ASP cc_start: 0.8210 (m-30) cc_final: 0.7886 (m-30) REVERT: A 255 MET cc_start: 0.8766 (ptt) cc_final: 0.8076 (ptt) REVERT: A 309 LYS cc_start: 0.9336 (mttp) cc_final: 0.9082 (mmmm) REVERT: A 320 ASN cc_start: 0.8416 (t0) cc_final: 0.7860 (t0) REVERT: A 359 PHE cc_start: 0.9210 (m-80) cc_final: 0.8753 (m-10) REVERT: A 387 MET cc_start: 0.9234 (ptp) cc_final: 0.8977 (ptp) REVERT: A 402 GLN cc_start: 0.8882 (tp40) cc_final: 0.7879 (pp30) REVERT: A 418 ARG cc_start: 0.4688 (mpp-170) cc_final: 0.3216 (mpt-90) REVERT: C 107 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7771 (tp30) REVERT: C 128 ASP cc_start: 0.9308 (m-30) cc_final: 0.9086 (m-30) REVERT: C 151 ASP cc_start: 0.7821 (p0) cc_final: 0.7570 (p0) REVERT: C 154 GLN cc_start: 0.9165 (mm110) cc_final: 0.8728 (mt0) REVERT: C 156 GLN cc_start: 0.8549 (mt0) cc_final: 0.8173 (mt0) REVERT: C 159 LEU cc_start: 0.9346 (mm) cc_final: 0.9081 (mm) REVERT: C 160 ILE cc_start: 0.9310 (mp) cc_final: 0.9007 (mp) REVERT: C 192 ASN cc_start: 0.8977 (m110) cc_final: 0.8614 (m-40) REVERT: C 208 MET cc_start: 0.9106 (ptp) cc_final: 0.7437 (ptp) REVERT: C 209 ASP cc_start: 0.9020 (m-30) cc_final: 0.8803 (m-30) REVERT: C 229 CYS cc_start: 0.8391 (p) cc_final: 0.8034 (p) REVERT: C 236 LYS cc_start: 0.9407 (tttt) cc_final: 0.8772 (tppt) REVERT: C 248 PHE cc_start: 0.7454 (t80) cc_final: 0.7039 (t80) REVERT: C 253 GLU cc_start: 0.9443 (mm-30) cc_final: 0.8835 (mm-30) REVERT: C 296 SER cc_start: 0.7082 (p) cc_final: 0.6728 (t) REVERT: C 342 MET cc_start: 0.7015 (mmm) cc_final: 0.6574 (mmm) REVERT: C 347 GLU cc_start: 0.9288 (pm20) cc_final: 0.8693 (pp20) REVERT: C 368 GLU cc_start: 0.8541 (tt0) cc_final: 0.7798 (tt0) REVERT: C 394 ASP cc_start: 0.9303 (t0) cc_final: 0.8955 (t70) REVERT: C 451 LYS cc_start: 0.9281 (mttt) cc_final: 0.8815 (mttp) REVERT: D 34 TYR cc_start: 0.9336 (m-80) cc_final: 0.8980 (m-80) REVERT: D 69 LEU cc_start: 0.9397 (mt) cc_final: 0.9133 (mp) REVERT: D 71 TYR cc_start: 0.8972 (m-80) cc_final: 0.8330 (m-80) REVERT: D 121 HIS cc_start: 0.9214 (t70) cc_final: 0.8888 (t70) REVERT: D 126 LYS cc_start: 0.9341 (tmmt) cc_final: 0.9076 (tmtt) REVERT: D 150 MET cc_start: 0.8724 (pmm) cc_final: 0.8456 (pmm) REVERT: D 153 LYS cc_start: 0.8981 (tmmt) cc_final: 0.8036 (pttt) REVERT: D 168 GLU cc_start: 0.8934 (pm20) cc_final: 0.8323 (pm20) REVERT: D 210 PHE cc_start: 0.9337 (m-80) cc_final: 0.8868 (m-80) REVERT: D 229 CYS cc_start: 0.7809 (p) cc_final: 0.7257 (p) REVERT: D 231 TYR cc_start: 0.9011 (t80) cc_final: 0.8333 (t80) REVERT: D 234 TYR cc_start: 0.9174 (m-80) cc_final: 0.8665 (m-80) REVERT: D 242 TYR cc_start: 0.8332 (m-10) cc_final: 0.8108 (m-10) REVERT: D 247 PHE cc_start: 0.8785 (m-10) cc_final: 0.8323 (m-80) REVERT: D 255 MET cc_start: 0.8905 (ptm) cc_final: 0.8257 (ppp) REVERT: D 306 LEU cc_start: 0.9661 (mm) cc_final: 0.9307 (mm) REVERT: D 321 ASN cc_start: 0.9537 (t0) cc_final: 0.9204 (t0) REVERT: D 342 MET cc_start: 0.9077 (mmt) cc_final: 0.8029 (mmt) REVERT: D 360 LYS cc_start: 0.9684 (mttt) cc_final: 0.9457 (ttmm) REVERT: D 369 TYR cc_start: 0.8819 (m-80) cc_final: 0.8599 (m-10) REVERT: D 401 TRP cc_start: 0.9538 (m-10) cc_final: 0.9319 (m-10) REVERT: D 417 TYR cc_start: 0.8862 (m-80) cc_final: 0.8638 (m-80) REVERT: D 443 TYR cc_start: 0.9335 (m-80) cc_final: 0.9098 (m-80) REVERT: D 470 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8479 (tt0) REVERT: E 107 GLU cc_start: 0.8707 (tp30) cc_final: 0.8325 (tp30) REVERT: E 127 PHE cc_start: 0.8752 (t80) cc_final: 0.7721 (t80) REVERT: E 200 MET cc_start: 0.9376 (mmm) cc_final: 0.8470 (tpp) REVERT: E 208 MET cc_start: 0.8769 (ppp) cc_final: 0.8315 (ppp) REVERT: E 224 ILE cc_start: 0.9775 (pt) cc_final: 0.9154 (mm) REVERT: E 234 TYR cc_start: 0.9335 (m-80) cc_final: 0.9050 (m-10) REVERT: E 254 GLN cc_start: 0.9224 (pt0) cc_final: 0.8841 (pm20) REVERT: E 314 GLN cc_start: 0.9339 (mt0) cc_final: 0.8679 (pm20) REVERT: E 324 CYS cc_start: 0.9246 (p) cc_final: 0.8808 (p) REVERT: E 338 ARG cc_start: 0.9352 (mtt-85) cc_final: 0.8772 (mtp85) REVERT: E 368 GLU cc_start: 0.9171 (pt0) cc_final: 0.8717 (pm20) REVERT: E 399 GLU cc_start: 0.9588 (tm-30) cc_final: 0.9360 (tm-30) REVERT: E 400 ASP cc_start: 0.8816 (p0) cc_final: 0.8461 (p0) REVERT: E 451 LYS cc_start: 0.9357 (mttm) cc_final: 0.8921 (mtpp) outliers start: 2 outliers final: 0 residues processed: 613 average time/residue: 0.1332 time to fit residues: 130.4671 Evaluate side-chains 479 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 7 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 50.0000 chunk 63 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN A 112 GLN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN E 305 GLN E 341 ASN E 358 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.091463 restraints weight = 55283.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094447 restraints weight = 28575.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.096387 restraints weight = 18409.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.097555 restraints weight = 13589.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098379 restraints weight = 11229.310| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 22436 Z= 0.250 Angle : 0.696 9.619 30525 Z= 0.359 Chirality : 0.047 0.208 3307 Planarity : 0.006 0.095 3973 Dihedral : 5.873 62.862 2998 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -3.13 (0.15), residues: 2755 helix: -1.37 (0.34), residues: 203 sheet: -1.51 (0.19), residues: 697 loop : -2.54 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 98 TYR 0.022 0.002 TYR A 36 PHE 0.023 0.002 PHE D 307 TRP 0.049 0.002 TRP B 312 HIS 0.008 0.002 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00547 (22431) covalent geometry : angle 0.69539 (30515) SS BOND : bond 0.00213 ( 5) SS BOND : angle 0.98486 ( 10) hydrogen bonds : bond 0.03705 ( 404) hydrogen bonds : angle 6.84670 ( 1074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 615 time to evaluate : 0.849 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: L 21 MET cc_start: 0.5919 (mmm) cc_final: 0.5508 (mtt) REVERT: H 36 VAL cc_start: 0.6177 (m) cc_final: 0.5683 (t) REVERT: B 20 LYS cc_start: 0.9364 (pttp) cc_final: 0.9106 (ptpp) REVERT: B 36 TYR cc_start: 0.9445 (t80) cc_final: 0.9182 (t80) REVERT: B 71 TYR cc_start: 0.8973 (m-10) cc_final: 0.8702 (m-10) REVERT: B 78 LEU cc_start: 0.9584 (mm) cc_final: 0.9365 (mm) REVERT: B 84 PHE cc_start: 0.8703 (t80) cc_final: 0.8342 (t80) REVERT: B 128 ASP cc_start: 0.9197 (m-30) cc_final: 0.8902 (m-30) REVERT: B 237 MET cc_start: 0.8996 (mtt) cc_final: 0.8791 (mtt) REVERT: B 242 TYR cc_start: 0.9196 (m-10) cc_final: 0.8937 (m-10) REVERT: B 248 PHE cc_start: 0.8279 (t80) cc_final: 0.7649 (t80) REVERT: B 255 MET cc_start: 0.8604 (tmm) cc_final: 0.8245 (tmm) REVERT: B 262 ASN cc_start: 0.9438 (p0) cc_final: 0.9181 (p0) REVERT: B 266 LYS cc_start: 0.9147 (ptpt) cc_final: 0.8787 (ptpt) REVERT: B 347 GLU cc_start: 0.8993 (pp20) cc_final: 0.8516 (pp20) REVERT: B 387 MET cc_start: 0.9582 (mtp) cc_final: 0.9253 (mtp) REVERT: B 393 MET cc_start: 0.9068 (ttm) cc_final: 0.8806 (ttm) REVERT: B 403 PHE cc_start: 0.8435 (m-80) cc_final: 0.8195 (m-80) REVERT: B 452 GLU cc_start: 0.9224 (pm20) cc_final: 0.8791 (pm20) REVERT: A 67 SER cc_start: 0.9369 (t) cc_final: 0.8995 (m) REVERT: A 127 PHE cc_start: 0.9283 (t80) cc_final: 0.8415 (t80) REVERT: A 128 ASP cc_start: 0.9244 (m-30) cc_final: 0.8285 (m-30) REVERT: A 148 LEU cc_start: 0.8685 (tp) cc_final: 0.8428 (tp) REVERT: A 153 LYS cc_start: 0.9332 (ptmm) cc_final: 0.8667 (ttpp) REVERT: A 166 THR cc_start: 0.9245 (p) cc_final: 0.8595 (p) REVERT: A 222 ILE cc_start: 0.9379 (tp) cc_final: 0.9162 (tp) REVERT: A 229 CYS cc_start: 0.8504 (p) cc_final: 0.8300 (p) REVERT: A 237 MET cc_start: 0.8920 (mtp) cc_final: 0.8589 (mmm) REVERT: A 244 ASP cc_start: 0.8156 (m-30) cc_final: 0.7832 (m-30) REVERT: A 255 MET cc_start: 0.8728 (ptt) cc_final: 0.8185 (ptt) REVERT: A 262 ASN cc_start: 0.8715 (p0) cc_final: 0.8169 (p0) REVERT: A 309 LYS cc_start: 0.9406 (mttp) cc_final: 0.9162 (mmmm) REVERT: A 320 ASN cc_start: 0.8398 (t0) cc_final: 0.7841 (t0) REVERT: A 331 VAL cc_start: 0.9849 (t) cc_final: 0.9609 (p) REVERT: A 387 MET cc_start: 0.9235 (ptp) cc_final: 0.8988 (ptp) REVERT: A 402 GLN cc_start: 0.8964 (tp40) cc_final: 0.7967 (pp30) REVERT: A 451 LYS cc_start: 0.8694 (mttt) cc_final: 0.8444 (mtpt) REVERT: C 107 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7781 (tp30) REVERT: C 128 ASP cc_start: 0.9291 (m-30) cc_final: 0.9073 (m-30) REVERT: C 151 ASP cc_start: 0.7680 (p0) cc_final: 0.7348 (p0) REVERT: C 154 GLN cc_start: 0.9103 (mm110) cc_final: 0.8658 (mt0) REVERT: C 156 GLN cc_start: 0.8576 (mt0) cc_final: 0.8206 (mt0) REVERT: C 157 LEU cc_start: 0.9494 (pt) cc_final: 0.9294 (pt) REVERT: C 160 ILE cc_start: 0.9357 (mp) cc_final: 0.9094 (mp) REVERT: C 208 MET cc_start: 0.9137 (ptp) cc_final: 0.7368 (ptp) REVERT: C 229 CYS cc_start: 0.8478 (p) cc_final: 0.8124 (p) REVERT: C 234 TYR cc_start: 0.9145 (m-80) cc_final: 0.8868 (m-10) REVERT: C 236 LYS cc_start: 0.9399 (tttt) cc_final: 0.8836 (tppt) REVERT: C 246 LEU cc_start: 0.9449 (tp) cc_final: 0.9238 (tp) REVERT: C 248 PHE cc_start: 0.7548 (t80) cc_final: 0.7072 (t80) REVERT: C 253 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8982 (mm-30) REVERT: C 296 SER cc_start: 0.7150 (p) cc_final: 0.6459 (t) REVERT: C 342 MET cc_start: 0.6995 (mmm) cc_final: 0.6406 (mmm) REVERT: C 347 GLU cc_start: 0.9336 (pm20) cc_final: 0.8702 (pp20) REVERT: C 367 GLU cc_start: 0.8077 (tt0) cc_final: 0.7852 (tt0) REVERT: C 368 GLU cc_start: 0.8069 (tt0) cc_final: 0.7564 (tt0) REVERT: C 394 ASP cc_start: 0.9306 (t0) cc_final: 0.8982 (t70) REVERT: C 402 GLN cc_start: 0.9556 (mt0) cc_final: 0.9227 (mp10) REVERT: C 451 LYS cc_start: 0.9267 (mttt) cc_final: 0.8566 (mptp) REVERT: D 34 TYR cc_start: 0.9347 (m-80) cc_final: 0.9032 (m-80) REVERT: D 65 LYS cc_start: 0.9422 (ttpt) cc_final: 0.9089 (tptm) REVERT: D 69 LEU cc_start: 0.9349 (mt) cc_final: 0.8943 (mp) REVERT: D 84 PHE cc_start: 0.9040 (m-10) cc_final: 0.8590 (m-80) REVERT: D 121 HIS cc_start: 0.9169 (t70) cc_final: 0.8628 (t-170) REVERT: D 126 LYS cc_start: 0.9323 (tmmt) cc_final: 0.9073 (tmtt) REVERT: D 153 LYS cc_start: 0.8948 (tmmt) cc_final: 0.7935 (pttt) REVERT: D 168 GLU cc_start: 0.9007 (pm20) cc_final: 0.8515 (pm20) REVERT: D 210 PHE cc_start: 0.9337 (m-80) cc_final: 0.8944 (m-80) REVERT: D 217 LYS cc_start: 0.9555 (ptpp) cc_final: 0.8907 (pttt) REVERT: D 229 CYS cc_start: 0.7581 (p) cc_final: 0.7058 (p) REVERT: D 231 TYR cc_start: 0.8922 (t80) cc_final: 0.8398 (t80) REVERT: D 234 TYR cc_start: 0.9084 (m-80) cc_final: 0.8623 (m-80) REVERT: D 242 TYR cc_start: 0.8311 (m-10) cc_final: 0.8050 (m-10) REVERT: D 255 MET cc_start: 0.8901 (ptm) cc_final: 0.8204 (ppp) REVERT: D 306 LEU cc_start: 0.9681 (mm) cc_final: 0.9301 (mm) REVERT: D 320 ASN cc_start: 0.9124 (t0) cc_final: 0.8910 (t0) REVERT: D 321 ASN cc_start: 0.9557 (t0) cc_final: 0.9238 (t0) REVERT: D 342 MET cc_start: 0.9107 (mmt) cc_final: 0.8156 (mmt) REVERT: D 367 GLU cc_start: 0.8194 (tp30) cc_final: 0.7990 (tp30) REVERT: D 369 TYR cc_start: 0.9067 (m-80) cc_final: 0.8776 (m-10) REVERT: D 401 TRP cc_start: 0.9549 (m-10) cc_final: 0.9338 (m-10) REVERT: D 417 TYR cc_start: 0.8867 (m-80) cc_final: 0.8630 (m-80) REVERT: D 443 TYR cc_start: 0.9353 (m-80) cc_final: 0.9069 (m-80) REVERT: D 470 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8569 (tt0) REVERT: E 21 VAL cc_start: 0.9492 (t) cc_final: 0.9208 (p) REVERT: E 107 GLU cc_start: 0.8799 (tp30) cc_final: 0.8276 (tp30) REVERT: E 110 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.8254 (mmm-85) REVERT: E 127 PHE cc_start: 0.8731 (t80) cc_final: 0.7693 (t80) REVERT: E 200 MET cc_start: 0.9384 (mmm) cc_final: 0.8410 (tpp) REVERT: E 208 MET cc_start: 0.8738 (ppp) cc_final: 0.8172 (ppp) REVERT: E 224 ILE cc_start: 0.9772 (pt) cc_final: 0.9142 (mm) REVERT: E 234 TYR cc_start: 0.9361 (m-80) cc_final: 0.9012 (m-10) REVERT: E 246 LEU cc_start: 0.9607 (mm) cc_final: 0.9404 (mm) REVERT: E 251 ARG cc_start: 0.8928 (ptt-90) cc_final: 0.8473 (ptt90) REVERT: E 254 GLN cc_start: 0.9143 (pt0) cc_final: 0.8847 (pm20) REVERT: E 314 GLN cc_start: 0.9344 (mt0) cc_final: 0.8760 (pm20) REVERT: E 324 CYS cc_start: 0.9254 (p) cc_final: 0.8734 (p) REVERT: E 335 ASP cc_start: 0.8496 (t0) cc_final: 0.8275 (t0) REVERT: E 338 ARG cc_start: 0.9376 (mtt-85) cc_final: 0.8846 (mmt90) REVERT: E 354 TYR cc_start: 0.8352 (t80) cc_final: 0.8079 (t80) REVERT: E 399 GLU cc_start: 0.9581 (tm-30) cc_final: 0.9364 (tm-30) REVERT: E 400 ASP cc_start: 0.8832 (p0) cc_final: 0.8513 (p0) REVERT: E 451 LYS cc_start: 0.9338 (mttm) cc_final: 0.8889 (mtpp) outliers start: 1 outliers final: 0 residues processed: 616 average time/residue: 0.1337 time to fit residues: 132.1388 Evaluate side-chains 484 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 73 optimal weight: 0.0570 chunk 201 optimal weight: 8.9990 chunk 42 optimal weight: 50.0000 chunk 232 optimal weight: 10.0000 overall best weight: 3.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN A 319 HIS A 358 ASN C 192 ASN ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 372 GLN E 97 GLN E 156 GLN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 ASN E 365 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.138462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093966 restraints weight = 54923.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.097041 restraints weight = 28050.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099081 restraints weight = 17982.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100350 restraints weight = 13221.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101194 restraints weight = 10813.200| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22436 Z= 0.158 Angle : 0.641 9.784 30525 Z= 0.324 Chirality : 0.046 0.191 3307 Planarity : 0.005 0.073 3973 Dihedral : 5.528 60.029 2998 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.15), residues: 2755 helix: -1.23 (0.35), residues: 206 sheet: -1.32 (0.19), residues: 697 loop : -2.42 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 98 TYR 0.022 0.001 TYR B 71 PHE 0.020 0.001 PHE A 291 TRP 0.020 0.001 TRP B 312 HIS 0.013 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00357 (22431) covalent geometry : angle 0.64117 (30515) SS BOND : bond 0.00180 ( 5) SS BOND : angle 0.85170 ( 10) hydrogen bonds : bond 0.03328 ( 404) hydrogen bonds : angle 6.59493 ( 1074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 628 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 MET cc_start: 0.5918 (mmm) cc_final: 0.5494 (mtt) REVERT: H 36 VAL cc_start: 0.6133 (m) cc_final: 0.5587 (t) REVERT: B 20 LYS cc_start: 0.9347 (pttp) cc_final: 0.9075 (ptpp) REVERT: B 25 ASP cc_start: 0.7978 (t70) cc_final: 0.7774 (t70) REVERT: B 36 TYR cc_start: 0.9402 (t80) cc_final: 0.9177 (t80) REVERT: B 80 ASP cc_start: 0.9312 (t0) cc_final: 0.9090 (t0) REVERT: B 84 PHE cc_start: 0.8621 (t80) cc_final: 0.8335 (t80) REVERT: B 128 ASP cc_start: 0.9177 (m-30) cc_final: 0.8899 (m-30) REVERT: B 163 LYS cc_start: 0.9469 (tppp) cc_final: 0.9234 (tppp) REVERT: B 237 MET cc_start: 0.9002 (mtt) cc_final: 0.8785 (mtt) REVERT: B 242 TYR cc_start: 0.9125 (m-10) cc_final: 0.8853 (m-10) REVERT: B 248 PHE cc_start: 0.8241 (t80) cc_final: 0.7583 (t80) REVERT: B 255 MET cc_start: 0.8578 (tmm) cc_final: 0.8356 (tmm) REVERT: B 262 ASN cc_start: 0.9335 (p0) cc_final: 0.9135 (p0) REVERT: B 266 LYS cc_start: 0.9108 (ptpt) cc_final: 0.8753 (ptpt) REVERT: B 347 GLU cc_start: 0.8960 (pp20) cc_final: 0.8484 (pp20) REVERT: B 387 MET cc_start: 0.9576 (mtp) cc_final: 0.9177 (mtt) REVERT: B 393 MET cc_start: 0.9042 (ttm) cc_final: 0.8770 (ttm) REVERT: B 452 GLU cc_start: 0.9222 (pm20) cc_final: 0.8819 (pm20) REVERT: A 67 SER cc_start: 0.9362 (t) cc_final: 0.8963 (m) REVERT: A 127 PHE cc_start: 0.9274 (t80) cc_final: 0.8417 (t80) REVERT: A 128 ASP cc_start: 0.9214 (m-30) cc_final: 0.8230 (m-30) REVERT: A 148 LEU cc_start: 0.8717 (tp) cc_final: 0.8486 (tp) REVERT: A 153 LYS cc_start: 0.9317 (ptmm) cc_final: 0.8553 (ttpp) REVERT: A 166 THR cc_start: 0.9279 (p) cc_final: 0.8702 (p) REVERT: A 222 ILE cc_start: 0.9373 (tp) cc_final: 0.9156 (tp) REVERT: A 244 ASP cc_start: 0.8038 (m-30) cc_final: 0.7724 (m-30) REVERT: A 255 MET cc_start: 0.8652 (ptt) cc_final: 0.8099 (ptt) REVERT: A 262 ASN cc_start: 0.8682 (p0) cc_final: 0.8070 (p0) REVERT: A 309 LYS cc_start: 0.9491 (mttp) cc_final: 0.9140 (mmmm) REVERT: A 320 ASN cc_start: 0.8316 (t0) cc_final: 0.7738 (t0) REVERT: A 387 MET cc_start: 0.9188 (ptp) cc_final: 0.8971 (ptp) REVERT: A 402 GLN cc_start: 0.8910 (tp40) cc_final: 0.7905 (pp30) REVERT: A 451 LYS cc_start: 0.8589 (mttt) cc_final: 0.8335 (mtpt) REVERT: C 29 SER cc_start: 0.9073 (m) cc_final: 0.8436 (p) REVERT: C 107 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7744 (tp30) REVERT: C 128 ASP cc_start: 0.9212 (m-30) cc_final: 0.8989 (m-30) REVERT: C 148 LEU cc_start: 0.9189 (tp) cc_final: 0.8915 (tp) REVERT: C 151 ASP cc_start: 0.7769 (p0) cc_final: 0.7385 (p0) REVERT: C 154 GLN cc_start: 0.9121 (mm110) cc_final: 0.8784 (mt0) REVERT: C 156 GLN cc_start: 0.8503 (mt0) cc_final: 0.8104 (mt0) REVERT: C 159 LEU cc_start: 0.9335 (mm) cc_final: 0.9132 (mm) REVERT: C 160 ILE cc_start: 0.9259 (mp) cc_final: 0.9052 (mp) REVERT: C 208 MET cc_start: 0.9072 (ptp) cc_final: 0.7138 (ptp) REVERT: C 209 ASP cc_start: 0.9063 (m-30) cc_final: 0.8701 (m-30) REVERT: C 229 CYS cc_start: 0.8276 (p) cc_final: 0.7942 (p) REVERT: C 236 LYS cc_start: 0.9384 (tttt) cc_final: 0.8886 (mmtt) REVERT: C 248 PHE cc_start: 0.7357 (t80) cc_final: 0.7143 (t80) REVERT: C 296 SER cc_start: 0.7324 (p) cc_final: 0.6768 (t) REVERT: C 342 MET cc_start: 0.6906 (mmm) cc_final: 0.6588 (mmm) REVERT: C 347 GLU cc_start: 0.9316 (pm20) cc_final: 0.8710 (pp20) REVERT: C 368 GLU cc_start: 0.7976 (tt0) cc_final: 0.7501 (tt0) REVERT: C 387 MET cc_start: 0.9406 (mtm) cc_final: 0.9196 (mtt) REVERT: C 394 ASP cc_start: 0.9296 (t0) cc_final: 0.8971 (t70) REVERT: C 402 GLN cc_start: 0.9505 (mt0) cc_final: 0.9205 (mp10) REVERT: C 451 LYS cc_start: 0.9199 (mttt) cc_final: 0.8484 (mptp) REVERT: D 34 TYR cc_start: 0.9369 (m-80) cc_final: 0.9035 (m-10) REVERT: D 65 LYS cc_start: 0.9448 (ttpt) cc_final: 0.9083 (tptm) REVERT: D 84 PHE cc_start: 0.8965 (m-10) cc_final: 0.8516 (m-80) REVERT: D 99 LEU cc_start: 0.8769 (mt) cc_final: 0.8567 (mt) REVERT: D 121 HIS cc_start: 0.9186 (t70) cc_final: 0.8637 (t-170) REVERT: D 126 LYS cc_start: 0.9306 (tmmt) cc_final: 0.9067 (tmtt) REVERT: D 150 MET cc_start: 0.8977 (pmm) cc_final: 0.8704 (pmm) REVERT: D 153 LYS cc_start: 0.9064 (tmmt) cc_final: 0.8146 (pttt) REVERT: D 168 GLU cc_start: 0.8987 (pm20) cc_final: 0.8415 (pm20) REVERT: D 210 PHE cc_start: 0.9333 (m-80) cc_final: 0.8993 (m-80) REVERT: D 231 TYR cc_start: 0.9046 (t80) cc_final: 0.8187 (t80) REVERT: D 234 TYR cc_start: 0.9113 (m-80) cc_final: 0.8617 (m-80) REVERT: D 240 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8732 (tm-30) REVERT: D 242 TYR cc_start: 0.8315 (m-10) cc_final: 0.8040 (m-10) REVERT: D 255 MET cc_start: 0.8828 (ptm) cc_final: 0.8140 (ppp) REVERT: D 306 LEU cc_start: 0.9625 (mm) cc_final: 0.9310 (mm) REVERT: D 315 ARG cc_start: 0.9021 (mtp-110) cc_final: 0.8682 (mtp85) REVERT: D 321 ASN cc_start: 0.9558 (t0) cc_final: 0.9230 (t0) REVERT: D 342 MET cc_start: 0.9076 (mmt) cc_final: 0.7977 (mmt) REVERT: D 367 GLU cc_start: 0.8269 (tp30) cc_final: 0.8052 (tp30) REVERT: D 369 TYR cc_start: 0.9164 (m-80) cc_final: 0.8816 (m-10) REVERT: D 401 TRP cc_start: 0.9543 (m-10) cc_final: 0.9284 (m-10) REVERT: D 443 TYR cc_start: 0.9449 (m-80) cc_final: 0.9050 (m-80) REVERT: D 470 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8668 (tt0) REVERT: E 21 VAL cc_start: 0.9529 (t) cc_final: 0.9241 (p) REVERT: E 69 LEU cc_start: 0.9654 (mp) cc_final: 0.9437 (mt) REVERT: E 172 LYS cc_start: 0.8716 (tptt) cc_final: 0.8436 (tppt) REVERT: E 200 MET cc_start: 0.9317 (mmm) cc_final: 0.8368 (tpp) REVERT: E 208 MET cc_start: 0.8615 (ppp) cc_final: 0.7969 (ppp) REVERT: E 224 ILE cc_start: 0.9761 (pt) cc_final: 0.9143 (mm) REVERT: E 234 TYR cc_start: 0.9330 (m-80) cc_final: 0.8947 (m-10) REVERT: E 254 GLN cc_start: 0.9038 (pt0) cc_final: 0.8731 (pm20) REVERT: E 338 ARG cc_start: 0.9272 (mtt-85) cc_final: 0.8787 (mtp85) REVERT: E 368 GLU cc_start: 0.8899 (pt0) cc_final: 0.8542 (pm20) REVERT: E 399 GLU cc_start: 0.9580 (tm-30) cc_final: 0.9377 (tm-30) REVERT: E 400 ASP cc_start: 0.8779 (p0) cc_final: 0.8490 (p0) REVERT: E 417 TYR cc_start: 0.8832 (m-80) cc_final: 0.8604 (m-80) REVERT: E 451 LYS cc_start: 0.9305 (mttm) cc_final: 0.8864 (mtpp) outliers start: 1 outliers final: 0 residues processed: 629 average time/residue: 0.1315 time to fit residues: 133.5112 Evaluate side-chains 523 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 237 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 249 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 238 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 341 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 414 GLN ** C 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN E 341 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.137766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093527 restraints weight = 54988.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096578 restraints weight = 28021.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098632 restraints weight = 17860.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099910 restraints weight = 13128.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.100833 restraints weight = 10701.782| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22436 Z= 0.184 Angle : 0.648 8.385 30525 Z= 0.329 Chirality : 0.046 0.184 3307 Planarity : 0.005 0.106 3973 Dihedral : 5.514 66.912 2998 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.15), residues: 2755 helix: -1.04 (0.36), residues: 200 sheet: -1.34 (0.19), residues: 702 loop : -2.31 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 251 TYR 0.022 0.001 TYR A 36 PHE 0.020 0.001 PHE A 291 TRP 0.045 0.001 TRP B 312 HIS 0.013 0.002 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00410 (22431) covalent geometry : angle 0.64782 (30515) SS BOND : bond 0.00253 ( 5) SS BOND : angle 1.21918 ( 10) hydrogen bonds : bond 0.03311 ( 404) hydrogen bonds : angle 6.51548 ( 1074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 VAL cc_start: 0.6378 (m) cc_final: 0.5810 (t) REVERT: B 20 LYS cc_start: 0.9355 (pttp) cc_final: 0.9077 (ptpp) REVERT: B 36 TYR cc_start: 0.9443 (t80) cc_final: 0.9206 (t80) REVERT: B 78 LEU cc_start: 0.9518 (mm) cc_final: 0.9313 (mm) REVERT: B 80 ASP cc_start: 0.9305 (t0) cc_final: 0.9032 (t0) REVERT: B 84 PHE cc_start: 0.8622 (t80) cc_final: 0.8303 (t80) REVERT: B 163 LYS cc_start: 0.9471 (tppp) cc_final: 0.9237 (tppp) REVERT: B 242 TYR cc_start: 0.9145 (m-10) cc_final: 0.8875 (m-10) REVERT: B 248 PHE cc_start: 0.8228 (t80) cc_final: 0.7584 (t80) REVERT: B 255 MET cc_start: 0.8625 (tmm) cc_final: 0.8230 (tmm) REVERT: B 266 LYS cc_start: 0.9098 (ptpt) cc_final: 0.8780 (ptpt) REVERT: B 347 GLU cc_start: 0.8930 (pp20) cc_final: 0.8493 (pp20) REVERT: B 387 MET cc_start: 0.9582 (mtp) cc_final: 0.9244 (mtp) REVERT: B 393 MET cc_start: 0.9034 (ttm) cc_final: 0.8786 (ttm) REVERT: B 452 GLU cc_start: 0.9223 (pm20) cc_final: 0.8769 (pm20) REVERT: A 67 SER cc_start: 0.9323 (t) cc_final: 0.8942 (m) REVERT: A 127 PHE cc_start: 0.9263 (t80) cc_final: 0.8391 (t80) REVERT: A 128 ASP cc_start: 0.9199 (m-30) cc_final: 0.8211 (m-30) REVERT: A 222 ILE cc_start: 0.9387 (tp) cc_final: 0.9172 (tp) REVERT: A 229 CYS cc_start: 0.8493 (p) cc_final: 0.8274 (p) REVERT: A 244 ASP cc_start: 0.8066 (m-30) cc_final: 0.7822 (m-30) REVERT: A 255 MET cc_start: 0.8700 (ptt) cc_final: 0.8282 (ptt) REVERT: A 262 ASN cc_start: 0.8682 (p0) cc_final: 0.8108 (p0) REVERT: A 291 PHE cc_start: 0.8901 (m-10) cc_final: 0.8697 (m-10) REVERT: A 309 LYS cc_start: 0.9488 (mttp) cc_final: 0.9154 (mmmm) REVERT: A 320 ASN cc_start: 0.8374 (t0) cc_final: 0.7794 (t0) REVERT: A 331 VAL cc_start: 0.9841 (t) cc_final: 0.9621 (p) REVERT: A 359 PHE cc_start: 0.9004 (m-80) cc_final: 0.8337 (m-10) REVERT: A 387 MET cc_start: 0.9181 (ptp) cc_final: 0.8940 (ptp) REVERT: A 402 GLN cc_start: 0.8933 (tp40) cc_final: 0.7940 (pp30) REVERT: A 418 ARG cc_start: 0.4847 (mpp-170) cc_final: 0.3620 (mpt-90) REVERT: A 451 LYS cc_start: 0.8625 (mttt) cc_final: 0.8366 (mtpt) REVERT: C 29 SER cc_start: 0.9066 (m) cc_final: 0.8423 (p) REVERT: C 107 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7775 (tp30) REVERT: C 128 ASP cc_start: 0.9226 (m-30) cc_final: 0.9006 (m-30) REVERT: C 151 ASP cc_start: 0.7565 (p0) cc_final: 0.7004 (p0) REVERT: C 156 GLN cc_start: 0.8564 (mt0) cc_final: 0.8083 (mt0) REVERT: C 159 LEU cc_start: 0.9365 (mm) cc_final: 0.9151 (mm) REVERT: C 160 ILE cc_start: 0.9203 (mp) cc_final: 0.8975 (mp) REVERT: C 208 MET cc_start: 0.9063 (ptp) cc_final: 0.7017 (ptp) REVERT: C 209 ASP cc_start: 0.9021 (m-30) cc_final: 0.8708 (m-30) REVERT: C 229 CYS cc_start: 0.8260 (p) cc_final: 0.7941 (p) REVERT: C 236 LYS cc_start: 0.9431 (tttt) cc_final: 0.9048 (mmtt) REVERT: C 246 LEU cc_start: 0.9440 (tp) cc_final: 0.9222 (tp) REVERT: C 296 SER cc_start: 0.7494 (p) cc_final: 0.6895 (t) REVERT: C 342 MET cc_start: 0.6964 (mmm) cc_final: 0.6659 (mmm) REVERT: C 347 GLU cc_start: 0.9311 (pm20) cc_final: 0.8717 (pp20) REVERT: C 394 ASP cc_start: 0.9287 (t0) cc_final: 0.8981 (t70) REVERT: C 402 GLN cc_start: 0.9503 (mt0) cc_final: 0.9189 (mp10) REVERT: C 451 LYS cc_start: 0.9214 (mttt) cc_final: 0.8849 (mttm) REVERT: D 34 TYR cc_start: 0.9354 (m-80) cc_final: 0.8996 (m-10) REVERT: D 65 LYS cc_start: 0.9397 (ttpt) cc_final: 0.9062 (tptm) REVERT: D 84 PHE cc_start: 0.9026 (m-10) cc_final: 0.8571 (m-80) REVERT: D 126 LYS cc_start: 0.9283 (tmmt) cc_final: 0.9017 (tmtt) REVERT: D 150 MET cc_start: 0.8927 (pmm) cc_final: 0.8641 (pmm) REVERT: D 153 LYS cc_start: 0.9101 (tmmt) cc_final: 0.8219 (pttm) REVERT: D 168 GLU cc_start: 0.9029 (pm20) cc_final: 0.8472 (pm20) REVERT: D 210 PHE cc_start: 0.9318 (m-80) cc_final: 0.9010 (m-80) REVERT: D 222 ILE cc_start: 0.9455 (pt) cc_final: 0.9252 (pt) REVERT: D 231 TYR cc_start: 0.9058 (t80) cc_final: 0.8081 (t80) REVERT: D 234 TYR cc_start: 0.9042 (m-80) cc_final: 0.8508 (m-80) REVERT: D 242 TYR cc_start: 0.8322 (m-10) cc_final: 0.8079 (m-10) REVERT: D 255 MET cc_start: 0.8908 (ptm) cc_final: 0.8150 (ppp) REVERT: D 306 LEU cc_start: 0.9637 (mm) cc_final: 0.9330 (mm) REVERT: D 320 ASN cc_start: 0.8995 (t0) cc_final: 0.8770 (t0) REVERT: D 321 ASN cc_start: 0.9566 (t0) cc_final: 0.9234 (t0) REVERT: D 342 MET cc_start: 0.9114 (mmt) cc_final: 0.8013 (mmt) REVERT: D 367 GLU cc_start: 0.8242 (tp30) cc_final: 0.7990 (tp30) REVERT: D 369 TYR cc_start: 0.9169 (m-80) cc_final: 0.8864 (m-10) REVERT: D 417 TYR cc_start: 0.8887 (m-80) cc_final: 0.8612 (m-80) REVERT: D 443 TYR cc_start: 0.9467 (m-80) cc_final: 0.9078 (m-80) REVERT: D 470 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8694 (tt0) REVERT: E 172 LYS cc_start: 0.8501 (tptt) cc_final: 0.8181 (tppt) REVERT: E 200 MET cc_start: 0.9307 (mmm) cc_final: 0.8398 (tpp) REVERT: E 208 MET cc_start: 0.8572 (ppp) cc_final: 0.7903 (ppp) REVERT: E 224 ILE cc_start: 0.9761 (pt) cc_final: 0.9094 (mm) REVERT: E 234 TYR cc_start: 0.9458 (m-80) cc_final: 0.8954 (m-80) REVERT: E 254 GLN cc_start: 0.8936 (pt0) cc_final: 0.8627 (pm20) REVERT: E 324 CYS cc_start: 0.9233 (p) cc_final: 0.8927 (p) REVERT: E 338 ARG cc_start: 0.9341 (mtt-85) cc_final: 0.8761 (mtp85) REVERT: E 368 GLU cc_start: 0.8958 (pt0) cc_final: 0.8550 (pm20) REVERT: E 400 ASP cc_start: 0.8751 (p0) cc_final: 0.8434 (p0) REVERT: E 417 TYR cc_start: 0.8813 (m-80) cc_final: 0.8553 (m-80) REVERT: E 451 LYS cc_start: 0.9337 (mttm) cc_final: 0.8873 (mtpp) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.1301 time to fit residues: 127.7685 Evaluate side-chains 492 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 109 optimal weight: 9.9990 chunk 214 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 76 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 165 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 139 GLN B 214 GLN B 254 GLN A 93 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 319 HIS C 321 ASN C 341 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 214 GLN E 156 GLN E 259 HIS E 341 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.143110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100146 restraints weight = 54536.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.103661 restraints weight = 27221.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105977 restraints weight = 16911.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107521 restraints weight = 12053.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108454 restraints weight = 9537.889| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22436 Z= 0.111 Angle : 0.629 9.177 30525 Z= 0.313 Chirality : 0.045 0.183 3307 Planarity : 0.005 0.074 3973 Dihedral : 5.155 65.628 2998 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.12 % Allowed : 1.06 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -2.58 (0.15), residues: 2755 helix: -1.22 (0.34), residues: 212 sheet: -1.07 (0.19), residues: 712 loop : -2.16 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 98 TYR 0.018 0.001 TYR B 71 PHE 0.016 0.001 PHE A 291 TRP 0.036 0.001 TRP D 401 HIS 0.012 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00252 (22431) covalent geometry : angle 0.62842 (30515) SS BOND : bond 0.00333 ( 5) SS BOND : angle 1.11446 ( 10) hydrogen bonds : bond 0.03021 ( 404) hydrogen bonds : angle 6.22094 ( 1074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 656 time to evaluate : 0.814 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: L 21 MET cc_start: 0.6295 (mmp) cc_final: 0.5187 (mtt) REVERT: H 36 VAL cc_start: 0.6899 (m) cc_final: 0.6350 (t) REVERT: B 70 GLN cc_start: 0.9084 (mt0) cc_final: 0.8698 (mt0) REVERT: B 78 LEU cc_start: 0.9472 (mm) cc_final: 0.9236 (mm) REVERT: B 80 ASP cc_start: 0.9314 (t0) cc_final: 0.8938 (t0) REVERT: B 84 PHE cc_start: 0.8501 (t80) cc_final: 0.8145 (t80) REVERT: B 156 GLN cc_start: 0.9262 (mt0) cc_final: 0.7949 (tt0) REVERT: B 163 LYS cc_start: 0.9397 (tppp) cc_final: 0.9134 (tppp) REVERT: B 233 ASP cc_start: 0.8028 (t0) cc_final: 0.7734 (t0) REVERT: B 242 TYR cc_start: 0.9090 (m-10) cc_final: 0.8772 (m-80) REVERT: B 248 PHE cc_start: 0.8180 (t80) cc_final: 0.7478 (t80) REVERT: B 255 MET cc_start: 0.8638 (tmm) cc_final: 0.8355 (tmm) REVERT: B 266 LYS cc_start: 0.9110 (ptpt) cc_final: 0.8774 (ptpt) REVERT: B 306 LEU cc_start: 0.9774 (mm) cc_final: 0.9546 (mm) REVERT: B 347 GLU cc_start: 0.8924 (pp20) cc_final: 0.8477 (pp20) REVERT: B 387 MET cc_start: 0.9577 (mtp) cc_final: 0.8942 (mtt) REVERT: B 393 MET cc_start: 0.8985 (ttm) cc_final: 0.8635 (ttm) REVERT: B 452 GLU cc_start: 0.9239 (pm20) cc_final: 0.8844 (pm20) REVERT: A 67 SER cc_start: 0.9359 (t) cc_final: 0.8897 (m) REVERT: A 127 PHE cc_start: 0.9199 (t80) cc_final: 0.8955 (t80) REVERT: A 128 ASP cc_start: 0.9087 (m-30) cc_final: 0.8875 (m-30) REVERT: A 148 LEU cc_start: 0.8666 (tp) cc_final: 0.8349 (tp) REVERT: A 153 LYS cc_start: 0.9243 (ptmm) cc_final: 0.8608 (ttpp) REVERT: A 222 ILE cc_start: 0.9400 (tp) cc_final: 0.9170 (tp) REVERT: A 229 CYS cc_start: 0.8574 (p) cc_final: 0.8367 (p) REVERT: A 244 ASP cc_start: 0.7976 (m-30) cc_final: 0.7693 (m-30) REVERT: A 255 MET cc_start: 0.8577 (ptt) cc_final: 0.8122 (ptt) REVERT: A 309 LYS cc_start: 0.9374 (mttp) cc_final: 0.9141 (mmmm) REVERT: A 320 ASN cc_start: 0.8241 (t0) cc_final: 0.7607 (t0) REVERT: A 359 PHE cc_start: 0.9063 (m-80) cc_final: 0.8299 (m-10) REVERT: A 387 MET cc_start: 0.9211 (ptp) cc_final: 0.9004 (ptp) REVERT: A 402 GLN cc_start: 0.8874 (tp40) cc_final: 0.7845 (pp30) REVERT: A 451 LYS cc_start: 0.8502 (mttt) cc_final: 0.8255 (mtpt) REVERT: C 29 SER cc_start: 0.8957 (m) cc_final: 0.8244 (p) REVERT: C 107 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7835 (tp30) REVERT: C 148 LEU cc_start: 0.9141 (tp) cc_final: 0.8648 (tp) REVERT: C 151 ASP cc_start: 0.7367 (p0) cc_final: 0.6979 (p0) REVERT: C 159 LEU cc_start: 0.9388 (mm) cc_final: 0.9187 (mm) REVERT: C 163 LYS cc_start: 0.9140 (ttmt) cc_final: 0.8850 (ttpt) REVERT: C 208 MET cc_start: 0.8977 (ptp) cc_final: 0.7022 (ptp) REVERT: C 209 ASP cc_start: 0.9042 (m-30) cc_final: 0.8707 (m-30) REVERT: C 236 LYS cc_start: 0.9352 (tttt) cc_final: 0.9075 (mmtt) REVERT: C 242 TYR cc_start: 0.9048 (m-80) cc_final: 0.8789 (m-80) REVERT: C 296 SER cc_start: 0.7434 (p) cc_final: 0.6817 (t) REVERT: C 330 PHE cc_start: 0.9087 (m-80) cc_final: 0.7397 (m-80) REVERT: C 342 MET cc_start: 0.6783 (mmm) cc_final: 0.6475 (mmm) REVERT: C 347 GLU cc_start: 0.9280 (pm20) cc_final: 0.8630 (pp20) REVERT: C 389 TYR cc_start: 0.9564 (t80) cc_final: 0.9349 (t80) REVERT: C 394 ASP cc_start: 0.9276 (t0) cc_final: 0.8939 (t70) REVERT: C 400 ASP cc_start: 0.9249 (p0) cc_final: 0.8986 (p0) REVERT: C 402 GLN cc_start: 0.9435 (mt0) cc_final: 0.9113 (mp10) REVERT: C 451 LYS cc_start: 0.9169 (mttt) cc_final: 0.8485 (mptp) REVERT: D 34 TYR cc_start: 0.9379 (m-80) cc_final: 0.9050 (m-10) REVERT: D 65 LYS cc_start: 0.9467 (ttpt) cc_final: 0.9108 (tptm) REVERT: D 84 PHE cc_start: 0.8956 (m-10) cc_final: 0.8583 (m-80) REVERT: D 101 TRP cc_start: 0.8399 (m100) cc_final: 0.7955 (m100) REVERT: D 121 HIS cc_start: 0.9221 (t70) cc_final: 0.8891 (t-170) REVERT: D 123 TYR cc_start: 0.9095 (m-80) cc_final: 0.8883 (m-80) REVERT: D 126 LYS cc_start: 0.9262 (tmmt) cc_final: 0.8998 (tmtt) REVERT: D 150 MET cc_start: 0.8992 (pmm) cc_final: 0.8649 (pmm) REVERT: D 153 LYS cc_start: 0.9095 (tmmt) cc_final: 0.8200 (pttt) REVERT: D 168 GLU cc_start: 0.9048 (pm20) cc_final: 0.8358 (pm20) REVERT: D 189 GLU cc_start: 0.8984 (tp30) cc_final: 0.8534 (mp0) REVERT: D 210 PHE cc_start: 0.9321 (m-80) cc_final: 0.8764 (m-80) REVERT: D 222 ILE cc_start: 0.9343 (pt) cc_final: 0.8475 (mp) REVERT: D 229 CYS cc_start: 0.6815 (p) cc_final: 0.6381 (p) REVERT: D 231 TYR cc_start: 0.8975 (t80) cc_final: 0.8105 (t80) REVERT: D 234 TYR cc_start: 0.9030 (m-80) cc_final: 0.8544 (m-80) REVERT: D 240 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8560 (tm-30) REVERT: D 242 TYR cc_start: 0.8348 (m-10) cc_final: 0.8107 (m-80) REVERT: D 247 PHE cc_start: 0.8966 (m-10) cc_final: 0.8299 (m-80) REVERT: D 255 MET cc_start: 0.8809 (ptm) cc_final: 0.8180 (ppp) REVERT: D 306 LEU cc_start: 0.9593 (mm) cc_final: 0.9275 (mm) REVERT: D 321 ASN cc_start: 0.9554 (t0) cc_final: 0.9207 (t0) REVERT: D 342 MET cc_start: 0.9097 (mmt) cc_final: 0.7891 (mmt) REVERT: D 351 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9119 (tp30) REVERT: D 362 TYR cc_start: 0.9183 (m-10) cc_final: 0.8927 (m-10) REVERT: D 369 TYR cc_start: 0.9135 (m-80) cc_final: 0.8723 (m-10) REVERT: D 372 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7727 (mm110) REVERT: D 378 CYS cc_start: 0.9056 (m) cc_final: 0.8365 (t) REVERT: D 393 MET cc_start: 0.9388 (tpp) cc_final: 0.8873 (tpp) REVERT: D 417 TYR cc_start: 0.8856 (m-80) cc_final: 0.8607 (m-80) REVERT: D 470 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8757 (tt0) REVERT: E 97 GLN cc_start: 0.9149 (mt0) cc_final: 0.8783 (mp10) REVERT: E 112 GLN cc_start: 0.9696 (mm-40) cc_final: 0.9424 (mm110) REVERT: E 114 LEU cc_start: 0.9245 (mm) cc_final: 0.8993 (mm) REVERT: E 172 LYS cc_start: 0.8498 (tptt) cc_final: 0.8158 (tppt) REVERT: E 200 MET cc_start: 0.9200 (mmm) cc_final: 0.8327 (tpp) REVERT: E 208 MET cc_start: 0.8660 (ppp) cc_final: 0.7918 (ppp) REVERT: E 224 ILE cc_start: 0.9752 (pt) cc_final: 0.9116 (mm) REVERT: E 234 TYR cc_start: 0.9442 (m-80) cc_final: 0.8972 (m-10) REVERT: E 254 GLN cc_start: 0.8870 (pt0) cc_final: 0.8505 (pt0) REVERT: E 299 ILE cc_start: 0.9054 (pt) cc_final: 0.8849 (pt) REVERT: E 324 CYS cc_start: 0.9269 (p) cc_final: 0.9022 (p) REVERT: E 338 ARG cc_start: 0.9208 (mtt-85) cc_final: 0.8795 (mtp85) REVERT: E 400 ASP cc_start: 0.8714 (p0) cc_final: 0.8471 (p0) REVERT: E 417 TYR cc_start: 0.8758 (m-80) cc_final: 0.8449 (m-80) REVERT: E 451 LYS cc_start: 0.9289 (mttm) cc_final: 0.8862 (mtpp) outliers start: 3 outliers final: 1 residues processed: 659 average time/residue: 0.1329 time to fit residues: 140.9708 Evaluate side-chains 521 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 520 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 265 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 48 optimal weight: 0.0040 chunk 9 optimal weight: 40.0000 chunk 178 optimal weight: 9.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 139 GLN B 254 GLN B 259 HIS ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN C 319 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN ** E 441 ASN ** 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 = 0.3889 r_free = 0.3889 target = 0.139126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095090 restraints weight = 55002.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098203 restraints weight = 27927.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.100322 restraints weight = 17761.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101659 restraints weight = 12952.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102603 restraints weight = 10506.428| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22436 Z= 0.162 Angle : 0.640 7.628 30525 Z= 0.323 Chirality : 0.045 0.243 3307 Planarity : 0.005 0.075 3973 Dihedral : 5.210 64.215 2998 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.04 % Allowed : 0.90 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -2.60 (0.15), residues: 2755 helix: -1.13 (0.35), residues: 212 sheet: -1.22 (0.19), residues: 704 loop : -2.13 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 418 TYR 0.022 0.001 TYR A 36 PHE 0.021 0.001 PHE A 291 TRP 0.046 0.001 TRP D 401 HIS 0.019 0.002 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00368 (22431) covalent geometry : angle 0.63945 (30515) SS BOND : bond 0.00220 ( 5) SS BOND : angle 0.96015 ( 10) hydrogen bonds : bond 0.03241 ( 404) hydrogen bonds : angle 6.23078 ( 1074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 603 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 MET cc_start: 0.5079 (mmp) cc_final: 0.4064 (mtt) REVERT: H 36 VAL cc_start: 0.6215 (m) cc_final: 0.5633 (t) REVERT: B 20 LYS cc_start: 0.9334 (pttp) cc_final: 0.9049 (ptpp) REVERT: B 70 GLN cc_start: 0.9119 (mt0) cc_final: 0.8757 (mt0) REVERT: B 80 ASP cc_start: 0.9237 (t0) cc_final: 0.8295 (t0) REVERT: B 83 LYS cc_start: 0.9167 (mppt) cc_final: 0.8751 (mmtm) REVERT: B 84 PHE cc_start: 0.8589 (t80) cc_final: 0.8271 (t80) REVERT: B 156 GLN cc_start: 0.9279 (mt0) cc_final: 0.8862 (mt0) REVERT: B 163 LYS cc_start: 0.9437 (tppp) cc_final: 0.9192 (tppp) REVERT: B 242 TYR cc_start: 0.9162 (m-10) cc_final: 0.8902 (m-80) REVERT: B 248 PHE cc_start: 0.8109 (t80) cc_final: 0.7448 (t80) REVERT: B 254 GLN cc_start: 0.9445 (pt0) cc_final: 0.9121 (pm20) REVERT: B 255 MET cc_start: 0.8650 (tmm) cc_final: 0.8382 (tmm) REVERT: B 266 LYS cc_start: 0.9098 (ptpt) cc_final: 0.8764 (ptpt) REVERT: B 291 PHE cc_start: 0.8843 (m-80) cc_final: 0.8616 (m-10) REVERT: B 347 GLU cc_start: 0.8911 (pp20) cc_final: 0.8494 (pp20) REVERT: B 387 MET cc_start: 0.9578 (mtp) cc_final: 0.9243 (mtp) REVERT: B 393 MET cc_start: 0.9050 (ttm) cc_final: 0.8759 (ttm) REVERT: B 452 GLU cc_start: 0.9221 (pm20) cc_final: 0.8813 (pm20) REVERT: A 67 SER cc_start: 0.9306 (t) cc_final: 0.8895 (m) REVERT: A 127 PHE cc_start: 0.9129 (t80) cc_final: 0.8875 (t80) REVERT: A 128 ASP cc_start: 0.9151 (m-30) cc_final: 0.8861 (m-30) REVERT: A 148 LEU cc_start: 0.8638 (tp) cc_final: 0.8250 (tp) REVERT: A 222 ILE cc_start: 0.9364 (tp) cc_final: 0.9132 (tp) REVERT: A 244 ASP cc_start: 0.8048 (m-30) cc_final: 0.7783 (m-30) REVERT: A 255 MET cc_start: 0.8694 (ptt) cc_final: 0.8345 (ptt) REVERT: A 309 LYS cc_start: 0.9400 (mttp) cc_final: 0.9156 (mmmm) REVERT: A 320 ASN cc_start: 0.8301 (t0) cc_final: 0.7683 (t0) REVERT: A 359 PHE cc_start: 0.9065 (m-80) cc_final: 0.8357 (m-10) REVERT: A 387 MET cc_start: 0.9158 (ptp) cc_final: 0.8935 (ptp) REVERT: A 402 GLN cc_start: 0.8866 (tp40) cc_final: 0.8544 (tp-100) REVERT: A 418 ARG cc_start: 0.5286 (mpp-170) cc_final: 0.4173 (mpt-90) REVERT: A 451 LYS cc_start: 0.8607 (mttt) cc_final: 0.8339 (mtpt) REVERT: C 29 SER cc_start: 0.8990 (m) cc_final: 0.8339 (p) REVERT: C 107 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7714 (tp30) REVERT: C 148 LEU cc_start: 0.8663 (tp) cc_final: 0.8263 (tp) REVERT: C 151 ASP cc_start: 0.7430 (p0) cc_final: 0.6921 (p0) REVERT: C 156 GLN cc_start: 0.8626 (mt0) cc_final: 0.8151 (mt0) REVERT: C 160 ILE cc_start: 0.9291 (mp) cc_final: 0.9048 (mp) REVERT: C 163 LYS cc_start: 0.9175 (ttmt) cc_final: 0.8928 (ttpt) REVERT: C 208 MET cc_start: 0.9021 (ptp) cc_final: 0.7184 (ptp) REVERT: C 209 ASP cc_start: 0.9048 (m-30) cc_final: 0.8749 (m-30) REVERT: C 229 CYS cc_start: 0.7952 (p) cc_final: 0.7648 (p) REVERT: C 248 PHE cc_start: 0.7627 (t80) cc_final: 0.7400 (t80) REVERT: C 296 SER cc_start: 0.7626 (p) cc_final: 0.6993 (t) REVERT: C 330 PHE cc_start: 0.9118 (m-80) cc_final: 0.7563 (m-80) REVERT: C 342 MET cc_start: 0.6840 (mmm) cc_final: 0.6490 (mmm) REVERT: C 347 GLU cc_start: 0.9279 (pm20) cc_final: 0.8653 (pp20) REVERT: C 367 GLU cc_start: 0.7960 (tp30) cc_final: 0.7321 (tp30) REVERT: C 387 MET cc_start: 0.9402 (mtm) cc_final: 0.9184 (mtt) REVERT: C 394 ASP cc_start: 0.9327 (t0) cc_final: 0.8957 (t70) REVERT: C 402 GLN cc_start: 0.9485 (mt0) cc_final: 0.9217 (mp10) REVERT: C 451 LYS cc_start: 0.9258 (mttt) cc_final: 0.8509 (mptp) REVERT: D 34 TYR cc_start: 0.9380 (m-80) cc_final: 0.9085 (m-10) REVERT: D 65 LYS cc_start: 0.9515 (ttpt) cc_final: 0.9128 (tptm) REVERT: D 84 PHE cc_start: 0.9053 (m-10) cc_final: 0.8607 (m-80) REVERT: D 121 HIS cc_start: 0.9160 (t70) cc_final: 0.8866 (t-170) REVERT: D 126 LYS cc_start: 0.9326 (tmmt) cc_final: 0.9009 (tmtt) REVERT: D 150 MET cc_start: 0.8954 (pmm) cc_final: 0.8651 (pmm) REVERT: D 153 LYS cc_start: 0.9087 (tmmt) cc_final: 0.8101 (pttt) REVERT: D 168 GLU cc_start: 0.9056 (pm20) cc_final: 0.8444 (pm20) REVERT: D 176 CYS cc_start: 0.7736 (p) cc_final: 0.7116 (p) REVERT: D 189 GLU cc_start: 0.9081 (tp30) cc_final: 0.8551 (mp0) REVERT: D 210 PHE cc_start: 0.9330 (m-80) cc_final: 0.8798 (m-80) REVERT: D 222 ILE cc_start: 0.9381 (pt) cc_final: 0.8529 (mp) REVERT: D 229 CYS cc_start: 0.7010 (p) cc_final: 0.6596 (p) REVERT: D 231 TYR cc_start: 0.9060 (t80) cc_final: 0.8068 (t80) REVERT: D 234 TYR cc_start: 0.9013 (m-80) cc_final: 0.8473 (m-80) REVERT: D 240 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8842 (tm-30) REVERT: D 255 MET cc_start: 0.8917 (ptm) cc_final: 0.8267 (ppp) REVERT: D 306 LEU cc_start: 0.9616 (mm) cc_final: 0.9274 (mm) REVERT: D 320 ASN cc_start: 0.8929 (t0) cc_final: 0.8683 (t0) REVERT: D 321 ASN cc_start: 0.9568 (t0) cc_final: 0.9226 (t0) REVERT: D 341 ASN cc_start: 0.8928 (m-40) cc_final: 0.8638 (m-40) REVERT: D 342 MET cc_start: 0.9073 (mmt) cc_final: 0.7899 (mmt) REVERT: D 367 GLU cc_start: 0.8264 (tp30) cc_final: 0.8036 (tp30) REVERT: D 369 TYR cc_start: 0.9175 (m-80) cc_final: 0.8774 (m-10) REVERT: D 393 MET cc_start: 0.9351 (tpp) cc_final: 0.8859 (tpp) REVERT: D 417 TYR cc_start: 0.8847 (m-80) cc_final: 0.8601 (m-80) REVERT: D 470 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8753 (tt0) REVERT: E 172 LYS cc_start: 0.8518 (tptt) cc_final: 0.8243 (tppt) REVERT: E 200 MET cc_start: 0.9138 (mmm) cc_final: 0.8324 (tpp) REVERT: E 224 ILE cc_start: 0.9750 (pt) cc_final: 0.9175 (mm) REVERT: E 234 TYR cc_start: 0.9442 (m-80) cc_final: 0.9004 (m-80) REVERT: E 254 GLN cc_start: 0.8885 (pt0) cc_final: 0.8613 (pm20) REVERT: E 314 GLN cc_start: 0.9307 (mt0) cc_final: 0.8662 (pm20) REVERT: E 324 CYS cc_start: 0.9275 (p) cc_final: 0.8996 (p) REVERT: E 338 ARG cc_start: 0.9370 (mtt-85) cc_final: 0.8787 (mtp85) REVERT: E 368 GLU cc_start: 0.8965 (pt0) cc_final: 0.8576 (pm20) REVERT: E 400 ASP cc_start: 0.8735 (p0) cc_final: 0.8464 (p0) REVERT: E 417 TYR cc_start: 0.8763 (m-80) cc_final: 0.8457 (m-80) REVERT: E 451 LYS cc_start: 0.9340 (mttm) cc_final: 0.8852 (mtpp) outliers start: 1 outliers final: 0 residues processed: 604 average time/residue: 0.1307 time to fit residues: 128.1038 Evaluate side-chains 491 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 20.0000 chunk 14 optimal weight: 40.0000 chunk 133 optimal weight: 2.9990 chunk 158 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 8 optimal weight: 50.0000 chunk 94 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 221 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 139 GLN B 254 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.139000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095246 restraints weight = 55458.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098433 restraints weight = 28225.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.100440 restraints weight = 17816.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.101876 restraints weight = 13082.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.102717 restraints weight = 10536.973| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22436 Z= 0.166 Angle : 0.650 9.407 30525 Z= 0.328 Chirality : 0.046 0.231 3307 Planarity : 0.005 0.075 3973 Dihedral : 5.243 63.477 2998 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -2.56 (0.15), residues: 2755 helix: -1.09 (0.36), residues: 206 sheet: -1.13 (0.19), residues: 721 loop : -2.13 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 418 TYR 0.024 0.001 TYR A 36 PHE 0.021 0.001 PHE A 291 TRP 0.050 0.001 TRP D 401 HIS 0.015 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00374 (22431) covalent geometry : angle 0.65009 (30515) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.90933 ( 10) hydrogen bonds : bond 0.03211 ( 404) hydrogen bonds : angle 6.24282 ( 1074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 600 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 VAL cc_start: 0.6494 (m) cc_final: 0.5895 (t) REVERT: B 25 ASP cc_start: 0.7809 (t70) cc_final: 0.7600 (t70) REVERT: B 70 GLN cc_start: 0.9111 (mt0) cc_final: 0.8671 (mt0) REVERT: B 78 LEU cc_start: 0.9524 (mm) cc_final: 0.9301 (mm) REVERT: B 80 ASP cc_start: 0.9217 (t0) cc_final: 0.8188 (t0) REVERT: B 83 LYS cc_start: 0.9142 (mppt) cc_final: 0.8789 (mmtm) REVERT: B 84 PHE cc_start: 0.8590 (t80) cc_final: 0.8271 (t80) REVERT: B 156 GLN cc_start: 0.9278 (mt0) cc_final: 0.8859 (mt0) REVERT: B 163 LYS cc_start: 0.9435 (tppp) cc_final: 0.9175 (tppp) REVERT: B 242 TYR cc_start: 0.9152 (m-10) cc_final: 0.8888 (m-80) REVERT: B 248 PHE cc_start: 0.8116 (t80) cc_final: 0.7460 (t80) REVERT: B 255 MET cc_start: 0.8695 (tmm) cc_final: 0.8361 (tmm) REVERT: B 266 LYS cc_start: 0.9095 (ptpt) cc_final: 0.8749 (ptpt) REVERT: B 347 GLU cc_start: 0.8856 (pp20) cc_final: 0.8387 (pp20) REVERT: B 387 MET cc_start: 0.9582 (mtp) cc_final: 0.9250 (mtp) REVERT: B 393 MET cc_start: 0.9046 (ttm) cc_final: 0.8737 (ttm) REVERT: B 452 GLU cc_start: 0.9188 (pm20) cc_final: 0.8873 (pm20) REVERT: A 67 SER cc_start: 0.9292 (t) cc_final: 0.8899 (m) REVERT: A 148 LEU cc_start: 0.8644 (tp) cc_final: 0.8296 (tp) REVERT: A 151 ASP cc_start: 0.8887 (t0) cc_final: 0.8685 (t0) REVERT: A 153 LYS cc_start: 0.9264 (ptmm) cc_final: 0.8583 (ttpp) REVERT: A 222 ILE cc_start: 0.9386 (tp) cc_final: 0.9143 (tp) REVERT: A 229 CYS cc_start: 0.8377 (p) cc_final: 0.8110 (p) REVERT: A 244 ASP cc_start: 0.7996 (m-30) cc_final: 0.7757 (m-30) REVERT: A 255 MET cc_start: 0.8739 (ptt) cc_final: 0.8298 (ptt) REVERT: A 309 LYS cc_start: 0.9507 (mttp) cc_final: 0.9154 (mmmm) REVERT: A 320 ASN cc_start: 0.8322 (t0) cc_final: 0.7701 (t0) REVERT: A 359 PHE cc_start: 0.9014 (m-80) cc_final: 0.8282 (m-10) REVERT: A 372 GLN cc_start: 0.8622 (mt0) cc_final: 0.8339 (mt0) REVERT: A 387 MET cc_start: 0.9173 (ptp) cc_final: 0.8937 (ptp) REVERT: A 402 GLN cc_start: 0.8865 (tp40) cc_final: 0.7888 (pp30) REVERT: A 418 ARG cc_start: 0.5051 (mpp-170) cc_final: 0.3848 (mpt-90) REVERT: A 451 LYS cc_start: 0.8611 (mttt) cc_final: 0.8341 (mtpt) REVERT: C 29 SER cc_start: 0.8999 (m) cc_final: 0.8347 (p) REVERT: C 107 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7803 (tp30) REVERT: C 148 LEU cc_start: 0.8659 (tp) cc_final: 0.8442 (tp) REVERT: C 151 ASP cc_start: 0.7403 (p0) cc_final: 0.7048 (p0) REVERT: C 154 GLN cc_start: 0.8854 (mp10) cc_final: 0.8452 (mp10) REVERT: C 156 GLN cc_start: 0.8613 (mt0) cc_final: 0.8182 (mt0) REVERT: C 160 ILE cc_start: 0.9203 (mp) cc_final: 0.8935 (mp) REVERT: C 163 LYS cc_start: 0.9171 (ttmt) cc_final: 0.8942 (ttpt) REVERT: C 208 MET cc_start: 0.9056 (ptp) cc_final: 0.7276 (ptp) REVERT: C 209 ASP cc_start: 0.9023 (m-30) cc_final: 0.8739 (m-30) REVERT: C 229 CYS cc_start: 0.8236 (p) cc_final: 0.7932 (p) REVERT: C 248 PHE cc_start: 0.7550 (t80) cc_final: 0.7339 (t80) REVERT: C 253 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9010 (mm-30) REVERT: C 296 SER cc_start: 0.7444 (p) cc_final: 0.6754 (t) REVERT: C 330 PHE cc_start: 0.9081 (m-80) cc_final: 0.7602 (m-80) REVERT: C 342 MET cc_start: 0.6795 (mmm) cc_final: 0.6500 (mmm) REVERT: C 347 GLU cc_start: 0.9267 (pm20) cc_final: 0.8643 (pp20) REVERT: C 394 ASP cc_start: 0.9325 (t0) cc_final: 0.8954 (t70) REVERT: C 402 GLN cc_start: 0.9490 (mt0) cc_final: 0.9221 (mp10) REVERT: C 451 LYS cc_start: 0.9299 (mttt) cc_final: 0.8546 (mptp) REVERT: D 34 TYR cc_start: 0.9349 (m-80) cc_final: 0.9055 (m-10) REVERT: D 65 LYS cc_start: 0.9529 (ttpt) cc_final: 0.9124 (tptm) REVERT: D 126 LYS cc_start: 0.9252 (tmmt) cc_final: 0.8895 (tmtt) REVERT: D 150 MET cc_start: 0.8972 (pmm) cc_final: 0.8624 (pmm) REVERT: D 153 LYS cc_start: 0.9067 (tmmt) cc_final: 0.8206 (pttm) REVERT: D 168 GLU cc_start: 0.9055 (pm20) cc_final: 0.8535 (pm20) REVERT: D 176 CYS cc_start: 0.7684 (p) cc_final: 0.7040 (p) REVERT: D 189 GLU cc_start: 0.9087 (tp30) cc_final: 0.8558 (mp0) REVERT: D 196 GLU cc_start: 0.8878 (tt0) cc_final: 0.8345 (tp30) REVERT: D 210 PHE cc_start: 0.9311 (m-80) cc_final: 0.8748 (m-80) REVERT: D 229 CYS cc_start: 0.6971 (p) cc_final: 0.6554 (p) REVERT: D 231 TYR cc_start: 0.8951 (t80) cc_final: 0.7931 (t80) REVERT: D 234 TYR cc_start: 0.9014 (m-80) cc_final: 0.8482 (m-80) REVERT: D 255 MET cc_start: 0.8856 (ptm) cc_final: 0.8190 (ppp) REVERT: D 306 LEU cc_start: 0.9617 (mm) cc_final: 0.9248 (mm) REVERT: D 320 ASN cc_start: 0.8945 (t0) cc_final: 0.8659 (t0) REVERT: D 321 ASN cc_start: 0.9572 (t0) cc_final: 0.9220 (t0) REVERT: D 341 ASN cc_start: 0.8926 (m-40) cc_final: 0.8640 (m-40) REVERT: D 342 MET cc_start: 0.9123 (mmt) cc_final: 0.8200 (mmt) REVERT: D 344 LEU cc_start: 0.9358 (mt) cc_final: 0.9149 (mt) REVERT: D 367 GLU cc_start: 0.8307 (tp30) cc_final: 0.8038 (tp30) REVERT: D 369 TYR cc_start: 0.9196 (m-80) cc_final: 0.8805 (m-10) REVERT: D 393 MET cc_start: 0.9361 (tpp) cc_final: 0.8975 (tpp) REVERT: D 396 ASN cc_start: 0.9095 (p0) cc_final: 0.8846 (p0) REVERT: D 417 TYR cc_start: 0.8833 (m-80) cc_final: 0.8619 (m-80) REVERT: D 470 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8765 (tt0) REVERT: E 107 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8342 (mm-30) REVERT: E 172 LYS cc_start: 0.8567 (tptt) cc_final: 0.8313 (tppt) REVERT: E 200 MET cc_start: 0.9034 (mmm) cc_final: 0.8322 (tpp) REVERT: E 208 MET cc_start: 0.8595 (ppp) cc_final: 0.8121 (ppp) REVERT: E 224 ILE cc_start: 0.9705 (pt) cc_final: 0.9162 (mm) REVERT: E 234 TYR cc_start: 0.9454 (m-80) cc_final: 0.9069 (m-10) REVERT: E 254 GLN cc_start: 0.8798 (pt0) cc_final: 0.8571 (pm20) REVERT: E 311 TYR cc_start: 0.9190 (m-80) cc_final: 0.8851 (m-80) REVERT: E 324 CYS cc_start: 0.9259 (p) cc_final: 0.8979 (p) REVERT: E 338 ARG cc_start: 0.9340 (mtt-85) cc_final: 0.8872 (mtp85) REVERT: E 342 MET cc_start: 0.9307 (mmm) cc_final: 0.8905 (mmm) REVERT: E 368 GLU cc_start: 0.8930 (pt0) cc_final: 0.8559 (pm20) REVERT: E 400 ASP cc_start: 0.8761 (p0) cc_final: 0.8503 (p0) REVERT: E 414 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8584 (tm-30) REVERT: E 417 TYR cc_start: 0.8781 (m-80) cc_final: 0.8466 (m-80) REVERT: E 451 LYS cc_start: 0.9307 (mttm) cc_final: 0.8826 (mtpp) outliers start: 1 outliers final: 0 residues processed: 601 average time/residue: 0.1296 time to fit residues: 126.5763 Evaluate side-chains 477 residues out of total 2453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 90 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 169 optimal weight: 0.0270 chunk 267 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 overall best weight: 4.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 139 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS C 321 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS E 305 GLN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.138512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.095047 restraints weight = 55544.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098183 restraints weight = 28228.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.100283 restraints weight = 17834.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101622 restraints weight = 12998.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102489 restraints weight = 10524.886| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22436 Z= 0.172 Angle : 0.653 9.115 30525 Z= 0.330 Chirality : 0.046 0.217 3307 Planarity : 0.005 0.076 3973 Dihedral : 5.241 62.866 2998 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.08 % Allowed : 0.45 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.04 % Twisted Proline : 1.10 % 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: -2.60 (0.15), residues: 2755 helix: -1.16 (0.35), residues: 208 sheet: -1.18 (0.19), residues: 715 loop : -2.14 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 418 TYR 0.026 0.002 TYR C 369 PHE 0.030 0.001 PHE A 291 TRP 0.047 0.002 TRP B 312 HIS 0.010 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00388 (22431) covalent geometry : angle 0.65258 (30515) SS BOND : bond 0.00174 ( 5) SS BOND : angle 0.89266 ( 10) hydrogen bonds : bond 0.03229 ( 404) hydrogen bonds : angle 6.23962 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4458.95 seconds wall clock time: 77 minutes 44.67 seconds (4664.67 seconds total)