Starting phenix.real_space_refine on Wed Sep 17 16:06:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gct_4386/09_2025/6gct_4386.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gct_4386/09_2025/6gct_4386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gct_4386/09_2025/6gct_4386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gct_4386/09_2025/6gct_4386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gct_4386/09_2025/6gct_4386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gct_4386/09_2025/6gct_4386.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 48 5.16 5 C 6324 2.51 5 N 1605 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9672 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3214 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 16, 'TRANS': 415} Chain breaks: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: B, C Time building chain proxies: 2.30, per 1000 atoms: 0.24 Number of scatterers: 9672 At special positions: 0 Unit cell: (117.392, 119.416, 82.984, 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 48 16.00 O 1695 8.00 N 1605 7.00 C 6324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 363.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 6 sheets defined 75.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.789A pdb=" N ARG A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 52 " --> pdb=" O CYS A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 52' Processing helix chain 'A' and resid 52 through 76 removed outlier: 3.913A pdb=" N VAL A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.910A pdb=" N LEU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.674A pdb=" N VAL A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 154 removed outlier: 3.618A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 removed outlier: 3.652A pdb=" N PHE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 234 through 249 removed outlier: 3.878A pdb=" N ALA A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.823A pdb=" N SER A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 290 removed outlier: 4.113A pdb=" N TRP A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.705A pdb=" N MET A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 319 removed outlier: 3.693A pdb=" N TYR A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 330 removed outlier: 3.695A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.558A pdb=" N TRP A 338 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.529A pdb=" N LEU A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 4.158A pdb=" N MET A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.551A pdb=" N CYS A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 410 through 424 removed outlier: 3.553A pdb=" N THR A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 441 removed outlier: 3.641A pdb=" N THR A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 449 through 452 removed outlier: 3.560A pdb=" N HIS A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 452' Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 459 through 487 removed outlier: 3.558A pdb=" N VAL A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 removed outlier: 3.789A pdb=" N ARG B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 52 " --> pdb=" O CYS B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 52' Processing helix chain 'B' and resid 52 through 76 removed outlier: 3.912A pdb=" N VAL B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 62 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 90 through 118 removed outlier: 3.909A pdb=" N LEU B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Proline residue: B 106 - end of helix removed outlier: 3.674A pdb=" N VAL B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 154 removed outlier: 3.617A pdb=" N LEU B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 192 removed outlier: 3.651A pdb=" N PHE B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 Processing helix chain 'B' and resid 234 through 249 removed outlier: 3.878A pdb=" N ALA B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.823A pdb=" N SER B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 290 removed outlier: 4.114A pdb=" N TRP B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.705A pdb=" N MET B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 319 removed outlier: 3.692A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 removed outlier: 3.695A pdb=" N PHE B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.558A pdb=" N TRP B 338 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.530A pdb=" N LEU B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 368 removed outlier: 4.157A pdb=" N MET B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.551A pdb=" N CYS B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 Processing helix chain 'B' and resid 410 through 424 removed outlier: 3.552A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 removed outlier: 3.642A pdb=" N THR B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 Processing helix chain 'B' and resid 449 through 452 removed outlier: 3.562A pdb=" N HIS B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 452' Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 459 through 487 removed outlier: 3.558A pdb=" N VAL B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 removed outlier: 3.790A pdb=" N ARG C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN C 52 " --> pdb=" O CYS C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 52' Processing helix chain 'C' and resid 52 through 76 removed outlier: 3.912A pdb=" N VAL C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 62 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 90 through 118 removed outlier: 3.910A pdb=" N LEU C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 97 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Proline residue: C 106 - end of helix removed outlier: 3.675A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY C 115 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 154 removed outlier: 3.617A pdb=" N LEU C 132 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.651A pdb=" N PHE C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 234 through 249 removed outlier: 3.878A pdb=" N ALA C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.824A pdb=" N SER C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 290 removed outlier: 4.114A pdb=" N TRP C 272 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.706A pdb=" N MET C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE C 283 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 319 removed outlier: 3.693A pdb=" N TYR C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 307 " --> pdb=" O GLY C 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 319 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 330 removed outlier: 3.695A pdb=" N PHE C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 removed outlier: 3.558A pdb=" N TRP C 338 " --> pdb=" O TYR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.530A pdb=" N LEU C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 368 removed outlier: 4.158A pdb=" N MET C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU C 366 " --> pdb=" O LYS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 378 through 383 Processing helix chain 'C' and resid 387 through 398 removed outlier: 3.551A pdb=" N CYS C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 Processing helix chain 'C' and resid 410 through 424 removed outlier: 3.552A pdb=" N THR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 441 removed outlier: 3.641A pdb=" N THR C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 449 through 452 removed outlier: 3.562A pdb=" N HIS C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 452' Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 459 through 487 removed outlier: 3.557A pdb=" N VAL C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG C 465 " --> pdb=" O TRP C 461 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 484 " --> pdb=" O GLY C 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 203 Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 209 Processing sheet with id=AA3, first strand: chain 'B' and resid 202 through 203 Processing sheet with id=AA4, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AA5, first strand: chain 'C' and resid 202 through 203 Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 209 501 hydrogen bonds defined for protein. 1440 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: 1.25 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2698 1.33 - 1.45: 1748 1.45 - 1.57: 5319 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 9840 Sorted by residual: bond pdb=" CA MET C 387 " pdb=" CB MET C 387 " ideal model delta sigma weight residual 1.539 1.399 0.140 4.88e-02 4.20e+02 8.26e+00 bond pdb=" CA MET B 387 " pdb=" CB MET B 387 " ideal model delta sigma weight residual 1.539 1.399 0.140 4.88e-02 4.20e+02 8.25e+00 bond pdb=" CA MET A 387 " pdb=" CB MET A 387 " ideal model delta sigma weight residual 1.539 1.400 0.140 4.88e-02 4.20e+02 8.20e+00 bond pdb=" CB ASN C 190 " pdb=" CG ASN C 190 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.42e+00 bond pdb=" CB ASN A 190 " pdb=" CG ASN A 190 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.41e+00 ... (remaining 9835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 12746 2.83 - 5.66: 522 5.66 - 8.50: 115 8.50 - 11.33: 9 11.33 - 14.16: 9 Bond angle restraints: 13401 Sorted by residual: angle pdb=" C LEU A 409 " pdb=" N ASP A 410 " pdb=" CA ASP A 410 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C LEU C 409 " pdb=" N ASP C 410 " pdb=" CA ASP C 410 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C LEU B 409 " pdb=" N ASP B 410 " pdb=" CA ASP B 410 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" CA LEU A 321 " pdb=" CB LEU A 321 " pdb=" CG LEU A 321 " ideal model delta sigma weight residual 116.30 130.46 -14.16 3.50e+00 8.16e-02 1.64e+01 angle pdb=" CA LEU B 321 " pdb=" CB LEU B 321 " pdb=" CG LEU B 321 " ideal model delta sigma weight residual 116.30 130.46 -14.16 3.50e+00 8.16e-02 1.64e+01 ... (remaining 13396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 5141 15.74 - 31.49: 454 31.49 - 47.23: 165 47.23 - 62.97: 21 62.97 - 78.71: 9 Dihedral angle restraints: 5790 sinusoidal: 2127 harmonic: 3663 Sorted by residual: dihedral pdb=" CA ALA C 123 " pdb=" C ALA C 123 " pdb=" N LEU C 124 " pdb=" CA LEU C 124 " ideal model delta harmonic sigma weight residual 180.00 -148.26 -31.74 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CA ALA B 123 " pdb=" C ALA B 123 " pdb=" N LEU B 124 " pdb=" CA LEU B 124 " ideal model delta harmonic sigma weight residual -180.00 -148.26 -31.74 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CA ALA A 123 " pdb=" C ALA A 123 " pdb=" N LEU A 124 " pdb=" CA LEU A 124 " ideal model delta harmonic sigma weight residual 180.00 -148.28 -31.72 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 5787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1209 0.071 - 0.143: 392 0.143 - 0.214: 60 0.214 - 0.286: 10 0.286 - 0.357: 6 Chirality restraints: 1677 Sorted by residual: chirality pdb=" CA ASP B 410 " pdb=" N ASP B 410 " pdb=" C ASP B 410 " pdb=" CB ASP B 410 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASP C 410 " pdb=" N ASP C 410 " pdb=" C ASP C 410 " pdb=" CB ASP C 410 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA ASP A 410 " pdb=" N ASP A 410 " pdb=" C ASP A 410 " pdb=" CB ASP A 410 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 1674 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 321 " 0.044 5.00e-02 4.00e+02 6.55e-02 6.85e+00 pdb=" N PRO A 322 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 379 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO C 380 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 380 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 380 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 321 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO C 322 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.037 5.00e-02 4.00e+02 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3288 2.84 - 3.36: 10139 3.36 - 3.87: 15988 3.87 - 4.39: 18808 4.39 - 4.90: 29440 Nonbonded interactions: 77663 Sorted by model distance: nonbonded pdb=" OE1 GLU A 227 " pdb=" NH2 ARG C 202 " model vdw 2.330 3.120 nonbonded pdb=" O LEU C 119 " pdb=" NH1 ARG C 246 " model vdw 2.334 3.120 nonbonded pdb=" O LEU B 119 " pdb=" NH1 ARG B 246 " model vdw 2.334 3.120 nonbonded pdb=" O LEU A 119 " pdb=" NH1 ARG A 246 " model vdw 2.334 3.120 nonbonded pdb=" O LYS A 372 " pdb=" OG SER A 375 " model vdw 2.335 3.040 ... (remaining 77658 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.850 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.012 0.140 9840 Z= 0.509 Angle : 1.401 14.161 13401 Z= 0.698 Chirality : 0.072 0.357 1677 Planarity : 0.008 0.065 1665 Dihedral : 14.504 78.713 3438 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.93 % Rotamer: Outliers : 5.57 % Allowed : 16.42 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.53 (0.15), residues: 1284 helix: -4.40 (0.08), residues: 879 sheet: -3.60 (0.50), residues: 60 loop : -3.38 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 330 TYR 0.023 0.004 TYR C 485 PHE 0.023 0.003 PHE B 201 TRP 0.008 0.002 TRP C 275 HIS 0.006 0.002 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.01175 ( 9840) covalent geometry : angle 1.40114 (13401) hydrogen bonds : bond 0.30330 ( 501) hydrogen bonds : angle 11.54622 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 130 TRP cc_start: 0.7754 (m100) cc_final: 0.7465 (m100) REVERT: A 248 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9065 (tt) REVERT: A 473 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 130 TRP cc_start: 0.7843 (m100) cc_final: 0.7607 (m100) REVERT: B 181 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7869 (mp) REVERT: B 263 ASN cc_start: 0.8929 (p0) cc_final: 0.8709 (p0) REVERT: B 483 GLN cc_start: 0.7767 (pp30) cc_final: 0.6904 (pp30) REVERT: C 130 TRP cc_start: 0.7865 (m100) cc_final: 0.7505 (m100) REVERT: C 186 ASP cc_start: 0.8724 (t70) cc_final: 0.8496 (t0) REVERT: C 275 TRP cc_start: 0.8221 (m100) cc_final: 0.7533 (m-10) REVERT: C 483 GLN cc_start: 0.7831 (pp30) cc_final: 0.7278 (pp30) outliers start: 57 outliers final: 18 residues processed: 324 average time/residue: 0.0873 time to fit residues: 41.0570 Evaluate side-chains 235 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 320 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 316 HIS A 367 ASN A 373 HIS A 386 ASN A 403 GLN A 484 ASN B 154 GLN B 260 ASN B 316 HIS B 367 ASN B 373 HIS B 403 GLN B 484 ASN C 154 GLN C 316 HIS C 367 ASN C 386 ASN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.087172 restraints weight = 20512.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087219 restraints weight = 19044.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087650 restraints weight = 15488.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.087733 restraints weight = 14494.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.087924 restraints weight = 12779.685| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9840 Z= 0.150 Angle : 0.840 14.596 13401 Z= 0.403 Chirality : 0.045 0.205 1677 Planarity : 0.006 0.046 1665 Dihedral : 7.444 58.951 1403 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 7.62 % Allowed : 19.06 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.73 (0.18), residues: 1284 helix: -3.00 (0.12), residues: 903 sheet: -3.56 (0.52), residues: 60 loop : -2.63 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 189 TYR 0.020 0.002 TYR A 276 PHE 0.031 0.002 PHE B 400 TRP 0.021 0.001 TRP C 461 HIS 0.004 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9840) covalent geometry : angle 0.84013 (13401) hydrogen bonds : bond 0.04024 ( 501) hydrogen bonds : angle 5.93114 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 282 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8208 (tm) REVERT: A 91 PHE cc_start: 0.8851 (t80) cc_final: 0.8608 (t80) REVERT: A 132 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8572 (tt) REVERT: A 246 ARG cc_start: 0.8215 (tmm-80) cc_final: 0.7917 (tmm-80) REVERT: A 248 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9105 (tt) REVERT: A 311 LEU cc_start: 0.9403 (tp) cc_final: 0.9153 (tt) REVERT: A 331 LYS cc_start: 0.8884 (mmtt) cc_final: 0.8623 (mmmt) REVERT: B 130 TRP cc_start: 0.7781 (m100) cc_final: 0.7524 (m100) REVERT: B 149 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8687 (tp) REVERT: B 247 LYS cc_start: 0.8174 (tttt) cc_final: 0.7857 (ttmt) REVERT: B 292 MET cc_start: 0.6909 (mmt) cc_final: 0.6657 (mmt) REVERT: C 275 TRP cc_start: 0.8129 (m100) cc_final: 0.7436 (m-10) REVERT: C 305 TYR cc_start: 0.8918 (t80) cc_final: 0.8715 (t80) REVERT: C 361 MET cc_start: 0.6858 (mpp) cc_final: 0.6547 (mpp) REVERT: C 387 MET cc_start: 0.8359 (mtp) cc_final: 0.8046 (mtp) REVERT: C 388 ASP cc_start: 0.8771 (m-30) cc_final: 0.8533 (m-30) REVERT: C 482 LEU cc_start: 0.8911 (mm) cc_final: 0.8699 (mm) REVERT: B 601 GLN cc_start: 0.8388 (pm20) cc_final: 0.8062 (pm20) outliers start: 78 outliers final: 25 residues processed: 336 average time/residue: 0.0790 time to fit residues: 39.8923 Evaluate side-chains 263 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 392 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN B 260 ASN B 316 HIS B 403 GLN C 386 ASN C 394 GLN C 484 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089592 restraints weight = 20830.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.089241 restraints weight = 21784.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.089684 restraints weight = 18517.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089852 restraints weight = 15621.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090125 restraints weight = 14247.761| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9840 Z= 0.141 Angle : 0.843 14.188 13401 Z= 0.388 Chirality : 0.044 0.191 1677 Planarity : 0.005 0.043 1665 Dihedral : 6.494 57.261 1384 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 6.94 % Allowed : 22.78 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.21), residues: 1284 helix: -2.23 (0.15), residues: 864 sheet: -3.41 (0.56), residues: 60 loop : -2.06 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 246 TYR 0.007 0.001 TYR C 305 PHE 0.031 0.002 PHE B 400 TRP 0.025 0.001 TRP C 461 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9840) covalent geometry : angle 0.84342 (13401) hydrogen bonds : bond 0.03435 ( 501) hydrogen bonds : angle 5.31831 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 258 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8169 (tm) REVERT: A 132 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8631 (tt) REVERT: A 246 ARG cc_start: 0.8251 (tmm-80) cc_final: 0.8011 (tmm-80) REVERT: A 482 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8764 (tp) REVERT: B 119 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7492 (tt) REVERT: B 149 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8331 (tp) REVERT: B 247 LYS cc_start: 0.8128 (tttt) cc_final: 0.7850 (ttmt) REVERT: C 232 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9169 (tp) REVERT: C 275 TRP cc_start: 0.8073 (m100) cc_final: 0.7712 (m-10) REVERT: C 305 TYR cc_start: 0.8901 (t80) cc_final: 0.8620 (t80) REVERT: C 325 TYR cc_start: 0.8294 (t80) cc_final: 0.8031 (t80) REVERT: C 441 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8251 (mt) outliers start: 71 outliers final: 28 residues processed: 308 average time/residue: 0.0762 time to fit residues: 35.2060 Evaluate side-chains 259 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 114 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 386 ASN C 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.088884 restraints weight = 21045.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.088496 restraints weight = 20939.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.088956 restraints weight = 18200.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.089121 restraints weight = 15239.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089525 restraints weight = 14078.761| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9840 Z= 0.147 Angle : 0.837 14.610 13401 Z= 0.385 Chirality : 0.045 0.256 1677 Planarity : 0.004 0.041 1665 Dihedral : 5.901 59.402 1380 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.74 % Allowed : 25.90 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.22), residues: 1284 helix: -1.98 (0.16), residues: 882 sheet: -3.31 (0.57), residues: 60 loop : -1.55 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 301 TYR 0.011 0.001 TYR B 325 PHE 0.031 0.002 PHE B 400 TRP 0.014 0.001 TRP C 461 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9840) covalent geometry : angle 0.83688 (13401) hydrogen bonds : bond 0.03217 ( 501) hydrogen bonds : angle 5.12217 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 242 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8180 (tm) REVERT: A 119 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7930 (tt) REVERT: A 132 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8683 (tt) REVERT: A 246 ARG cc_start: 0.8401 (tmm-80) cc_final: 0.8084 (tmm-80) REVERT: A 268 VAL cc_start: 0.9104 (p) cc_final: 0.8744 (t) REVERT: A 323 LEU cc_start: 0.8940 (tt) cc_final: 0.8726 (tt) REVERT: A 473 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8446 (tm-30) REVERT: B 149 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8532 (tp) REVERT: B 247 LYS cc_start: 0.8324 (tttt) cc_final: 0.7935 (ttmt) REVERT: B 455 LEU cc_start: 0.8627 (pt) cc_final: 0.8425 (pt) REVERT: C 283 PHE cc_start: 0.8420 (m-80) cc_final: 0.8202 (m-80) REVERT: C 305 TYR cc_start: 0.9041 (t80) cc_final: 0.8681 (t80) REVERT: C 413 LYS cc_start: 0.9037 (ttmp) cc_final: 0.8773 (ttpt) outliers start: 69 outliers final: 34 residues processed: 293 average time/residue: 0.0765 time to fit residues: 33.4762 Evaluate side-chains 261 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 79 optimal weight: 0.7980 chunk 126 optimal weight: 0.0670 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 93 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 65 optimal weight: 0.0470 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS C 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.090211 restraints weight = 20820.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090568 restraints weight = 14578.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.090865 restraints weight = 11686.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.091144 restraints weight = 11161.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091225 restraints weight = 10470.070| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9840 Z= 0.132 Angle : 0.849 14.774 13401 Z= 0.380 Chirality : 0.045 0.216 1677 Planarity : 0.004 0.039 1665 Dihedral : 5.375 31.247 1376 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.55 % Allowed : 26.49 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.22), residues: 1284 helix: -1.78 (0.16), residues: 894 sheet: -3.10 (0.59), residues: 60 loop : -1.52 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.011 0.001 TYR C 325 PHE 0.027 0.001 PHE B 400 TRP 0.010 0.001 TRP A 461 HIS 0.003 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9840) covalent geometry : angle 0.84907 (13401) hydrogen bonds : bond 0.03158 ( 501) hydrogen bonds : angle 4.97542 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.7272 (m-80) cc_final: 0.6156 (m-80) REVERT: A 119 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7880 (tt) REVERT: A 132 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8693 (tt) REVERT: A 246 ARG cc_start: 0.8365 (tmm-80) cc_final: 0.8024 (tmm-80) REVERT: A 323 LEU cc_start: 0.8923 (tt) cc_final: 0.8706 (tt) REVERT: A 334 TYR cc_start: 0.6753 (m-80) cc_final: 0.6361 (m-10) REVERT: A 341 VAL cc_start: 0.8492 (t) cc_final: 0.8265 (p) REVERT: A 473 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8309 (tm-30) REVERT: B 90 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.8974 (t) REVERT: B 149 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8584 (tp) REVERT: B 247 LYS cc_start: 0.8313 (tttt) cc_final: 0.7941 (ttmt) REVERT: B 341 VAL cc_start: 0.8527 (t) cc_final: 0.8278 (p) REVERT: C 112 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8933 (tt) REVERT: C 305 TYR cc_start: 0.9127 (t80) cc_final: 0.8792 (t80) REVERT: C 320 VAL cc_start: 0.8751 (m) cc_final: 0.8544 (p) REVERT: C 388 ASP cc_start: 0.8615 (m-30) cc_final: 0.8175 (m-30) outliers start: 67 outliers final: 34 residues processed: 305 average time/residue: 0.0759 time to fit residues: 34.6766 Evaluate side-chains 261 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 121 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 0.0020 chunk 71 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.086235 restraints weight = 20713.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.086227 restraints weight = 18819.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.086854 restraints weight = 17576.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.086981 restraints weight = 14081.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.087099 restraints weight = 12307.278| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9840 Z= 0.139 Angle : 0.856 14.268 13401 Z= 0.386 Chirality : 0.046 0.287 1677 Planarity : 0.004 0.037 1665 Dihedral : 5.202 30.280 1373 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.87 % Allowed : 27.86 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.22), residues: 1284 helix: -1.56 (0.16), residues: 888 sheet: -3.03 (0.60), residues: 60 loop : -1.46 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.012 0.001 TYR C 325 PHE 0.035 0.001 PHE B 400 TRP 0.023 0.001 TRP A 461 HIS 0.002 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9840) covalent geometry : angle 0.85567 (13401) hydrogen bonds : bond 0.03162 ( 501) hydrogen bonds : angle 4.96975 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 235 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.7118 (m-80) cc_final: 0.6159 (m-80) REVERT: A 90 VAL cc_start: 0.9366 (OUTLIER) cc_final: 0.9123 (t) REVERT: A 119 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7954 (tt) REVERT: A 132 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8653 (tt) REVERT: A 151 LEU cc_start: 0.9184 (pt) cc_final: 0.8692 (pp) REVERT: A 246 ARG cc_start: 0.8345 (tmm-80) cc_final: 0.7920 (tmm-80) REVERT: A 288 LYS cc_start: 0.8887 (tmmm) cc_final: 0.8555 (ttmt) REVERT: A 334 TYR cc_start: 0.6482 (m-80) cc_final: 0.6240 (m-10) REVERT: A 372 LYS cc_start: 0.8143 (tppt) cc_final: 0.7808 (tppt) REVERT: B 90 VAL cc_start: 0.9308 (OUTLIER) cc_final: 0.8899 (t) REVERT: B 149 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8469 (tp) REVERT: B 281 ILE cc_start: 0.9017 (mt) cc_final: 0.8815 (mt) REVERT: B 341 VAL cc_start: 0.8468 (t) cc_final: 0.8189 (p) REVERT: B 413 LYS cc_start: 0.8977 (ttmp) cc_final: 0.8743 (ttmt) REVERT: C 90 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9137 (t) REVERT: C 305 TYR cc_start: 0.8982 (t80) cc_final: 0.8742 (t80) REVERT: C 320 VAL cc_start: 0.8732 (m) cc_final: 0.8498 (p) REVERT: C 341 VAL cc_start: 0.8388 (t) cc_final: 0.8031 (p) outliers start: 60 outliers final: 37 residues processed: 273 average time/residue: 0.0780 time to fit residues: 31.6230 Evaluate side-chains 267 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 0.0030 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.087523 restraints weight = 20654.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.086923 restraints weight = 24542.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.087717 restraints weight = 20631.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.087808 restraints weight = 16327.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.087984 restraints weight = 15148.328| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9840 Z= 0.139 Angle : 0.858 14.428 13401 Z= 0.387 Chirality : 0.046 0.247 1677 Planarity : 0.004 0.035 1665 Dihedral : 5.140 30.546 1373 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.06 % Allowed : 28.15 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.23), residues: 1284 helix: -1.31 (0.16), residues: 891 sheet: -3.00 (0.59), residues: 60 loop : -1.36 (0.37), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.010 0.001 TYR C 325 PHE 0.039 0.001 PHE B 400 TRP 0.023 0.001 TRP C 461 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9840) covalent geometry : angle 0.85793 (13401) hydrogen bonds : bond 0.03084 ( 501) hydrogen bonds : angle 4.93370 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 237 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6983 (m-80) cc_final: 0.6104 (m-80) REVERT: A 90 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.9114 (t) REVERT: A 119 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7909 (tt) REVERT: A 132 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8631 (tt) REVERT: A 246 ARG cc_start: 0.8374 (tmm-80) cc_final: 0.7936 (tmm-80) REVERT: A 288 LYS cc_start: 0.8871 (tmmm) cc_final: 0.8551 (ttmt) REVERT: A 372 LYS cc_start: 0.8162 (tppt) cc_final: 0.7870 (tppt) REVERT: B 90 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9072 (t) REVERT: B 323 LEU cc_start: 0.9022 (mp) cc_final: 0.8781 (tt) REVERT: B 341 VAL cc_start: 0.8448 (t) cc_final: 0.8166 (p) REVERT: B 413 LYS cc_start: 0.8973 (ttmp) cc_final: 0.8678 (ttmt) REVERT: C 89 PHE cc_start: 0.7048 (m-80) cc_final: 0.6379 (m-80) REVERT: C 90 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9123 (t) REVERT: C 320 VAL cc_start: 0.8676 (m) cc_final: 0.8437 (p) REVERT: C 341 VAL cc_start: 0.8374 (t) cc_final: 0.8003 (p) outliers start: 62 outliers final: 42 residues processed: 279 average time/residue: 0.0783 time to fit residues: 32.5309 Evaluate side-chains 272 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 115 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087304 restraints weight = 20544.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.086928 restraints weight = 22421.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.087347 restraints weight = 18391.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.087379 restraints weight = 18857.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.087919 restraints weight = 14574.536| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9840 Z= 0.137 Angle : 0.858 14.331 13401 Z= 0.386 Chirality : 0.047 0.237 1677 Planarity : 0.004 0.034 1665 Dihedral : 5.059 30.485 1373 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.57 % Allowed : 28.93 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.23), residues: 1284 helix: -1.27 (0.16), residues: 897 sheet: -2.94 (0.59), residues: 60 loop : -1.48 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.009 0.001 TYR C 325 PHE 0.036 0.001 PHE B 400 TRP 0.024 0.001 TRP A 461 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9840) covalent geometry : angle 0.85840 (13401) hydrogen bonds : bond 0.03049 ( 501) hydrogen bonds : angle 4.93942 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6885 (m-80) cc_final: 0.6112 (m-80) REVERT: A 90 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.9059 (t) REVERT: A 119 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7897 (tt) REVERT: A 132 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8604 (tt) REVERT: A 246 ARG cc_start: 0.8311 (tmm-80) cc_final: 0.7881 (tmm-80) REVERT: A 288 LYS cc_start: 0.8818 (tmmm) cc_final: 0.8507 (ttmt) REVERT: A 372 LYS cc_start: 0.8100 (tppt) cc_final: 0.7813 (tppt) REVERT: B 90 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.9031 (t) REVERT: B 323 LEU cc_start: 0.9067 (mp) cc_final: 0.8840 (tt) REVERT: B 341 VAL cc_start: 0.8424 (t) cc_final: 0.8152 (p) REVERT: B 413 LYS cc_start: 0.8948 (ttmp) cc_final: 0.8721 (ttmt) REVERT: C 89 PHE cc_start: 0.6998 (m-80) cc_final: 0.6455 (m-80) REVERT: C 90 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9068 (t) REVERT: C 320 VAL cc_start: 0.8619 (m) cc_final: 0.8388 (p) REVERT: C 341 VAL cc_start: 0.8341 (t) cc_final: 0.7969 (p) outliers start: 57 outliers final: 45 residues processed: 277 average time/residue: 0.0778 time to fit residues: 32.0016 Evaluate side-chains 272 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 99 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN C 403 GLN C 484 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087530 restraints weight = 20533.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.087212 restraints weight = 20778.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.087544 restraints weight = 19163.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.087748 restraints weight = 15914.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.088250 restraints weight = 14570.921| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9840 Z= 0.144 Angle : 0.875 14.097 13401 Z= 0.395 Chirality : 0.047 0.270 1677 Planarity : 0.004 0.034 1665 Dihedral : 5.051 30.646 1373 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.18 % Allowed : 30.21 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.23), residues: 1284 helix: -1.23 (0.16), residues: 906 sheet: -2.94 (0.59), residues: 60 loop : -1.40 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.012 0.001 TYR C 325 PHE 0.041 0.002 PHE B 400 TRP 0.025 0.001 TRP A 461 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9840) covalent geometry : angle 0.87548 (13401) hydrogen bonds : bond 0.03028 ( 501) hydrogen bonds : angle 4.94952 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 229 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6852 (m-80) cc_final: 0.6128 (m-80) REVERT: A 90 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.9046 (t) REVERT: A 119 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7901 (tt) REVERT: A 132 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8608 (tt) REVERT: A 246 ARG cc_start: 0.8327 (tmm-80) cc_final: 0.7899 (tmm-80) REVERT: A 288 LYS cc_start: 0.8846 (tmmm) cc_final: 0.8539 (ttmt) REVERT: A 292 MET cc_start: 0.6167 (mmt) cc_final: 0.5914 (mmm) REVERT: A 372 LYS cc_start: 0.8141 (tppt) cc_final: 0.7875 (tppt) REVERT: B 90 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.9020 (t) REVERT: B 323 LEU cc_start: 0.9028 (mp) cc_final: 0.8782 (tt) REVERT: B 341 VAL cc_start: 0.8420 (t) cc_final: 0.8135 (p) REVERT: B 413 LYS cc_start: 0.8956 (ttmp) cc_final: 0.8711 (ttmt) REVERT: C 89 PHE cc_start: 0.6937 (m-80) cc_final: 0.6407 (m-80) REVERT: C 90 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9029 (t) REVERT: C 320 VAL cc_start: 0.8714 (m) cc_final: 0.8467 (p) REVERT: C 341 VAL cc_start: 0.8321 (t) cc_final: 0.7938 (p) outliers start: 53 outliers final: 44 residues processed: 263 average time/residue: 0.0886 time to fit residues: 34.4598 Evaluate side-chains 273 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 87 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.087830 restraints weight = 20519.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087277 restraints weight = 22815.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.088126 restraints weight = 21297.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.088095 restraints weight = 16716.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.088298 restraints weight = 16543.278| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9840 Z= 0.141 Angle : 0.882 14.098 13401 Z= 0.398 Chirality : 0.047 0.300 1677 Planarity : 0.004 0.035 1665 Dihedral : 5.035 30.582 1373 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.47 % Allowed : 29.52 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.23), residues: 1284 helix: -1.18 (0.16), residues: 906 sheet: -2.88 (0.59), residues: 60 loop : -1.38 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.010 0.001 TYR C 325 PHE 0.039 0.002 PHE B 400 TRP 0.024 0.001 TRP C 461 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9840) covalent geometry : angle 0.88171 (13401) hydrogen bonds : bond 0.03053 ( 501) hydrogen bonds : angle 4.97351 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6705 (m-80) cc_final: 0.6078 (m-80) REVERT: A 90 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.8998 (t) REVERT: A 119 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7915 (tt) REVERT: A 132 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8600 (tt) REVERT: A 151 LEU cc_start: 0.9188 (pt) cc_final: 0.8985 (pp) REVERT: A 246 ARG cc_start: 0.8294 (tmm-80) cc_final: 0.7896 (tmm-80) REVERT: A 288 LYS cc_start: 0.8792 (tmmm) cc_final: 0.8517 (ttmt) REVERT: A 292 MET cc_start: 0.6034 (mmt) cc_final: 0.5827 (mmm) REVERT: A 360 MET cc_start: 0.7673 (tpp) cc_final: 0.7453 (tpp) REVERT: A 372 LYS cc_start: 0.8156 (tppt) cc_final: 0.7882 (tppt) REVERT: B 90 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.9012 (t) REVERT: B 323 LEU cc_start: 0.9024 (mp) cc_final: 0.8774 (tt) REVERT: B 341 VAL cc_start: 0.8398 (t) cc_final: 0.8121 (p) REVERT: B 413 LYS cc_start: 0.8925 (ttmp) cc_final: 0.8698 (ttmt) REVERT: C 89 PHE cc_start: 0.6897 (m-80) cc_final: 0.6414 (m-80) REVERT: C 90 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.8983 (t) REVERT: C 320 VAL cc_start: 0.8714 (m) cc_final: 0.8452 (p) REVERT: C 341 VAL cc_start: 0.8308 (t) cc_final: 0.7926 (p) outliers start: 56 outliers final: 44 residues processed: 270 average time/residue: 0.0859 time to fit residues: 34.5114 Evaluate side-chains 268 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 TRP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 473 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.0000 chunk 121 optimal weight: 1.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.086997 restraints weight = 20528.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.086862 restraints weight = 20189.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.087199 restraints weight = 18424.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.087438 restraints weight = 15574.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.087725 restraints weight = 14161.298| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9840 Z= 0.144 Angle : 0.897 14.170 13401 Z= 0.403 Chirality : 0.048 0.318 1677 Planarity : 0.004 0.035 1665 Dihedral : 5.049 30.594 1373 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.89 % Allowed : 30.30 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.23), residues: 1284 helix: -1.13 (0.16), residues: 906 sheet: -2.77 (0.60), residues: 60 loop : -1.33 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.009 0.001 TYR C 325 PHE 0.038 0.002 PHE B 400 TRP 0.027 0.001 TRP B 461 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9840) covalent geometry : angle 0.89663 (13401) hydrogen bonds : bond 0.03025 ( 501) hydrogen bonds : angle 4.97130 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1573.28 seconds wall clock time: 27 minutes 54.79 seconds (1674.79 seconds total)