Starting phenix.real_space_refine on Wed Mar 4 13:14:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ji1_9832/03_2026/6ji1_9832.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ji1_9832/03_2026/6ji1_9832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ji1_9832/03_2026/6ji1_9832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ji1_9832/03_2026/6ji1_9832.map" model { file = "/net/cci-nas-00/data/ceres_data/6ji1_9832/03_2026/6ji1_9832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ji1_9832/03_2026/6ji1_9832.cif" } resolution = 4.1 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= 0.004 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 80 5.16 5 C 9284 2.51 5 N 2232 2.21 5 O 2396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13992 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3498 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 448} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 44 Restraints were copied for chains: B, C, D Time building chain proxies: 2.65, per 1000 atoms: 0.19 Number of scatterers: 13992 At special positions: 0 Unit cell: (127.89, 127.89, 77.43, 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 80 16.00 O 2396 8.00 N 2232 7.00 C 9284 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: 1.08 Conformation dependent library (CDL) restraints added in 693.4 milliseconds 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3368 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 0 sheets defined 73.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.752A pdb=" N MET A 15 " --> pdb=" O THR A 11 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR A 16 " --> pdb=" O HIS A 12 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.582A pdb=" N MET A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 72 removed outlier: 3.970A pdb=" N LEU A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 61 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 3.736A pdb=" N GLY A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.710A pdb=" N VAL A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.930A pdb=" N LEU A 110 " --> pdb=" O MET A 106 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 4.257A pdb=" N GLY A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 159 removed outlier: 4.619A pdb=" N ILE A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.586A pdb=" N VAL A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 198 removed outlier: 3.678A pdb=" N PHE A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 200 No H-bonds generated for 'chain 'A' and resid 199 through 200' Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.576A pdb=" N ALA A 204 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 236 removed outlier: 4.803A pdb=" N ILE A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.879A pdb=" N ARG A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.713A pdb=" N HIS A 261 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 292 removed outlier: 3.657A pdb=" N PHE A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 324 through 327 Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.637A pdb=" N ILE A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 334 " --> pdb=" O PRO A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 381 removed outlier: 3.628A pdb=" N LEU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 364 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 378 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 380 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.829A pdb=" N GLY A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 397 " --> pdb=" O TRP A 393 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 399 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 439 removed outlier: 4.296A pdb=" N TYR A 429 " --> pdb=" O MET A 425 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 459 through 484 removed outlier: 3.820A pdb=" N ASN A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 467 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A 481 " --> pdb=" O CYS A 477 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.936A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 492' Processing helix chain 'B' and resid 9 through 32 removed outlier: 3.752A pdb=" N MET B 15 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR B 16 " --> pdb=" O HIS B 12 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 29 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.583A pdb=" N MET B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN B 41 " --> pdb=" O TYR B 37 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 72 removed outlier: 3.970A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 61 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Proline residue: B 65 - end of helix removed outlier: 3.736A pdb=" N GLY B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 87 through 95 removed outlier: 3.711A pdb=" N VAL B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.930A pdb=" N LEU B 110 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 129 removed outlier: 4.258A pdb=" N GLY B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 159 removed outlier: 4.619A pdb=" N ILE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 159 " --> pdb=" O THR B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 removed outlier: 3.585A pdb=" N VAL B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 198 removed outlier: 3.678A pdb=" N PHE B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 200 No H-bonds generated for 'chain 'B' and resid 199 through 200' Processing helix chain 'B' and resid 201 through 206 removed outlier: 3.575A pdb=" N ALA B 204 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN B 205 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 236 removed outlier: 4.803A pdb=" N ILE B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.878A pdb=" N ARG B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.713A pdb=" N HIS B 261 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 292 removed outlier: 3.657A pdb=" N PHE B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 287 " --> pdb=" O GLN B 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 324 through 327 Processing helix chain 'B' and resid 328 through 336 removed outlier: 3.635A pdb=" N ILE B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET B 334 " --> pdb=" O PRO B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 381 removed outlier: 3.628A pdb=" N LEU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR B 374 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY B 375 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 378 " --> pdb=" O TYR B 374 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 380 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.829A pdb=" N GLY B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B 397 " --> pdb=" O TRP B 393 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 399 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 removed outlier: 4.295A pdb=" N TYR B 429 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 430 " --> pdb=" O MET B 426 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 459 through 484 removed outlier: 3.820A pdb=" N ASN B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 479 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA B 481 " --> pdb=" O CYS B 477 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.936A pdb=" N LEU B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 492' Processing helix chain 'C' and resid 9 through 32 removed outlier: 3.753A pdb=" N MET C 15 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR C 16 " --> pdb=" O HIS C 12 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL C 17 " --> pdb=" O SER C 13 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY C 30 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.582A pdb=" N MET C 39 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN C 41 " --> pdb=" O TYR C 37 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.970A pdb=" N LEU C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 61 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Proline residue: C 65 - end of helix removed outlier: 3.736A pdb=" N GLY C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 Processing helix chain 'C' and resid 87 through 95 removed outlier: 3.711A pdb=" N VAL C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.930A pdb=" N LEU C 110 " --> pdb=" O MET C 106 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 129 removed outlier: 4.257A pdb=" N GLY C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU C 127 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 159 removed outlier: 4.620A pdb=" N ILE C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU C 159 " --> pdb=" O THR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.586A pdb=" N VAL C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 198 removed outlier: 3.677A pdb=" N PHE C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS C 186 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 200 No H-bonds generated for 'chain 'C' and resid 199 through 200' Processing helix chain 'C' and resid 201 through 206 removed outlier: 3.575A pdb=" N ALA C 204 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN C 205 " --> pdb=" O SER C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 236 removed outlier: 4.803A pdb=" N ILE C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.878A pdb=" N ARG C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.712A pdb=" N HIS C 261 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 292 removed outlier: 3.657A pdb=" N PHE C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 287 " --> pdb=" O GLN C 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 324 through 327 Processing helix chain 'C' and resid 328 through 336 removed outlier: 3.635A pdb=" N ILE C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 372 removed outlier: 3.627A pdb=" N LEU C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE C 364 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.823A pdb=" N GLY C 378 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 380 " --> pdb=" O PHE C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 403 removed outlier: 3.830A pdb=" N GLY C 394 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 397 " --> pdb=" O TRP C 393 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 399 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 439 removed outlier: 4.296A pdb=" N TYR C 429 " --> pdb=" O MET C 425 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE C 430 " --> pdb=" O MET C 426 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 459 through 484 removed outlier: 3.820A pdb=" N ASN C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 466 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 467 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN C 468 " --> pdb=" O THR C 464 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE C 480 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 481 " --> pdb=" O CYS C 477 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 3.937A pdb=" N LEU C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 492' Processing helix chain 'D' and resid 9 through 32 removed outlier: 3.752A pdb=" N MET D 15 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR D 16 " --> pdb=" O HIS D 12 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR D 29 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY D 30 " --> pdb=" O PHE D 26 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.584A pdb=" N MET D 39 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 72 removed outlier: 3.970A pdb=" N LEU D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 61 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Proline residue: D 65 - end of helix removed outlier: 3.736A pdb=" N GLY D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'D' and resid 87 through 95 removed outlier: 3.710A pdb=" N VAL D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.930A pdb=" N LEU D 110 " --> pdb=" O MET D 106 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 129 removed outlier: 4.257A pdb=" N GLY D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 159 removed outlier: 4.619A pdb=" N ILE D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE D 156 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU D 159 " --> pdb=" O THR D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 169 removed outlier: 3.585A pdb=" N VAL D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 198 removed outlier: 3.677A pdb=" N PHE D 182 " --> pdb=" O TRP D 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 200 No H-bonds generated for 'chain 'D' and resid 199 through 200' Processing helix chain 'D' and resid 201 through 206 removed outlier: 3.575A pdb=" N ALA D 204 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN D 205 " --> pdb=" O SER D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 236 removed outlier: 4.802A pdb=" N ILE D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.879A pdb=" N ARG D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.712A pdb=" N HIS D 261 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 292 removed outlier: 3.657A pdb=" N PHE D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 287 " --> pdb=" O GLN D 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE D 290 " --> pdb=" O PHE D 286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 302 Processing helix chain 'D' and resid 324 through 327 Processing helix chain 'D' and resid 328 through 336 removed outlier: 3.636A pdb=" N ILE D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET D 334 " --> pdb=" O PRO D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 381 removed outlier: 3.628A pdb=" N LEU D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE D 364 " --> pdb=" O PHE D 360 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE D 373 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR D 374 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY D 375 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY D 378 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 380 " --> pdb=" O PHE D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 403 removed outlier: 3.829A pdb=" N GLY D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA D 396 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER D 397 " --> pdb=" O TRP D 393 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 399 " --> pdb=" O TYR D 395 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 removed outlier: 4.295A pdb=" N TYR D 429 " --> pdb=" O MET D 425 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE D 430 " --> pdb=" O MET D 426 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 459 through 484 removed outlier: 3.820A pdb=" N ASN D 465 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU D 466 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE D 467 " --> pdb=" O TYR D 463 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN D 468 " --> pdb=" O THR D 464 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 476 " --> pdb=" O VAL D 472 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 479 " --> pdb=" O VAL D 475 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE D 480 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA D 481 " --> pdb=" O CYS D 477 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.937A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 487 through 492' 576 hydrogen bonds defined for protein. 1692 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: 1.79 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4083 1.34 - 1.46: 3418 1.46 - 1.58: 6699 1.58 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 14344 Sorted by residual: bond pdb=" CB ASN D 468 " pdb=" CG ASN D 468 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.82e+00 bond pdb=" CB ASN B 468 " pdb=" CG ASN B 468 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.73e+00 bond pdb=" CB ASN C 468 " pdb=" CG ASN C 468 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.65e+00 bond pdb=" CB ASN A 468 " pdb=" CG ASN A 468 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.56e+00 bond pdb=" C GLY D 118 " pdb=" N LEU D 119 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.73e-02 3.34e+03 4.58e+00 ... (remaining 14339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 17695 1.93 - 3.87: 1478 3.87 - 5.80: 282 5.80 - 7.74: 81 7.74 - 9.67: 16 Bond angle restraints: 19552 Sorted by residual: angle pdb=" N THR C 161 " pdb=" CA THR C 161 " pdb=" C THR C 161 " ideal model delta sigma weight residual 109.81 119.00 -9.19 2.21e+00 2.05e-01 1.73e+01 angle pdb=" N THR B 161 " pdb=" CA THR B 161 " pdb=" C THR B 161 " ideal model delta sigma weight residual 109.81 118.96 -9.15 2.21e+00 2.05e-01 1.72e+01 angle pdb=" N THR D 161 " pdb=" CA THR D 161 " pdb=" C THR D 161 " ideal model delta sigma weight residual 109.81 118.93 -9.12 2.21e+00 2.05e-01 1.70e+01 angle pdb=" N THR A 161 " pdb=" CA THR A 161 " pdb=" C THR A 161 " ideal model delta sigma weight residual 109.81 118.93 -9.12 2.21e+00 2.05e-01 1.70e+01 angle pdb=" C ASP B 46 " pdb=" N ASP B 47 " pdb=" CA ASP B 47 " ideal model delta sigma weight residual 121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01 ... (remaining 19547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 7199 14.02 - 28.03: 785 28.03 - 42.05: 108 42.05 - 56.06: 12 56.06 - 70.07: 8 Dihedral angle restraints: 8112 sinusoidal: 2832 harmonic: 5280 Sorted by residual: dihedral pdb=" CA LYS A 359 " pdb=" C LYS A 359 " pdb=" N PHE A 360 " pdb=" CA PHE A 360 " ideal model delta harmonic sigma weight residual 180.00 143.52 36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA LYS B 359 " pdb=" C LYS B 359 " pdb=" N PHE B 360 " pdb=" CA PHE B 360 " ideal model delta harmonic sigma weight residual 180.00 143.53 36.47 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA LYS D 359 " pdb=" C LYS D 359 " pdb=" N PHE D 360 " pdb=" CA PHE D 360 " ideal model delta harmonic sigma weight residual 180.00 143.56 36.44 0 5.00e+00 4.00e-02 5.31e+01 ... (remaining 8109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1589 0.060 - 0.120: 585 0.120 - 0.180: 94 0.180 - 0.240: 16 0.240 - 0.299: 4 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CB VAL C 484 " pdb=" CA VAL C 484 " pdb=" CG1 VAL C 484 " pdb=" CG2 VAL C 484 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB VAL A 484 " pdb=" CA VAL A 484 " pdb=" CG1 VAL A 484 " pdb=" CG2 VAL A 484 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB VAL B 484 " pdb=" CA VAL B 484 " pdb=" CG1 VAL B 484 " pdb=" CG2 VAL B 484 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 2285 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 161 " 0.091 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO B 162 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 161 " -0.091 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO D 162 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO D 162 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO D 162 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 161 " -0.091 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO C 162 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO C 162 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO C 162 " -0.074 5.00e-02 4.00e+02 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3615 2.78 - 3.31: 14332 3.31 - 3.84: 21481 3.84 - 4.37: 26880 4.37 - 4.90: 40916 Nonbonded interactions: 107224 Sorted by model distance: nonbonded pdb=" O ASN B 51 " pdb=" OG SER B 55 " model vdw 2.250 3.040 nonbonded pdb=" O ASN D 51 " pdb=" OG SER D 55 " model vdw 2.250 3.040 nonbonded pdb=" O ASN C 51 " pdb=" OG SER C 55 " model vdw 2.250 3.040 nonbonded pdb=" O ASN A 51 " pdb=" OG SER A 55 " model vdw 2.250 3.040 nonbonded pdb=" O SER B 433 " pdb=" OG SER B 436 " model vdw 2.254 3.040 ... (remaining 107219 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.170 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.010 0.084 14344 Z= 0.436 Angle : 1.257 9.674 19552 Z= 0.683 Chirality : 0.061 0.299 2288 Planarity : 0.011 0.138 2388 Dihedral : 11.774 70.075 4744 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 5.31 % Allowed : 11.17 % Favored : 83.52 % Rotamer: Outliers : 0.57 % Allowed : 5.41 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.16), residues: 1808 helix: -3.53 (0.10), residues: 960 sheet: None (None), residues: 0 loop : -2.61 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 304 TYR 0.026 0.004 TYR A 240 PHE 0.044 0.004 PHE D 38 TRP 0.036 0.005 TRP C 54 HIS 0.009 0.002 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00963 (14344) covalent geometry : angle 1.25669 (19552) hydrogen bonds : bond 0.30919 ( 576) hydrogen bonds : angle 10.03494 ( 1692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 512 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.9089 (pp) cc_final: 0.8743 (tp) REVERT: A 138 LYS cc_start: 0.7949 (ptpt) cc_final: 0.7715 (ptpt) REVERT: A 158 MET cc_start: 0.6662 (mtm) cc_final: 0.6367 (mtm) REVERT: A 303 LEU cc_start: 0.8114 (tp) cc_final: 0.7293 (tp) REVERT: A 304 ARG cc_start: 0.6305 (pmm-80) cc_final: 0.5496 (ttm-80) REVERT: A 462 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7944 (p) REVERT: B 127 LEU cc_start: 0.9104 (pp) cc_final: 0.8742 (tp) REVERT: B 138 LYS cc_start: 0.7953 (ptpt) cc_final: 0.7729 (ptpt) REVERT: B 158 MET cc_start: 0.6660 (mtm) cc_final: 0.6369 (mtm) REVERT: B 303 LEU cc_start: 0.8123 (tp) cc_final: 0.7282 (tp) REVERT: B 304 ARG cc_start: 0.6251 (pmm-80) cc_final: 0.5533 (ttm-80) REVERT: B 462 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7959 (p) REVERT: C 127 LEU cc_start: 0.9113 (pp) cc_final: 0.8732 (tp) REVERT: C 138 LYS cc_start: 0.7965 (ptpt) cc_final: 0.7734 (ptpt) REVERT: C 158 MET cc_start: 0.6644 (mtm) cc_final: 0.6373 (mtm) REVERT: C 303 LEU cc_start: 0.8124 (tp) cc_final: 0.7281 (tp) REVERT: C 304 ARG cc_start: 0.6231 (pmm-80) cc_final: 0.5531 (ttm-80) REVERT: C 462 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7942 (p) REVERT: D 127 LEU cc_start: 0.9122 (pp) cc_final: 0.8766 (tp) REVERT: D 138 LYS cc_start: 0.7953 (ptpt) cc_final: 0.7732 (ptpt) REVERT: D 158 MET cc_start: 0.6644 (mtm) cc_final: 0.6359 (mtm) REVERT: D 303 LEU cc_start: 0.8125 (tp) cc_final: 0.7274 (tp) REVERT: D 304 ARG cc_start: 0.6249 (pmm-80) cc_final: 0.5548 (ttm-80) REVERT: D 462 VAL cc_start: 0.8194 (OUTLIER) cc_final: 0.7962 (p) outliers start: 8 outliers final: 0 residues processed: 516 average time/residue: 0.0979 time to fit residues: 76.1777 Evaluate side-chains 338 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 334 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0020 chunk 149 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 324 GLN B 151 ASN B 195 ASN B 324 GLN B 329 ASN B 379 GLN C 151 ASN C 324 GLN D 151 ASN D 195 ASN D 324 GLN D 329 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.147074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124505 restraints weight = 25364.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127923 restraints weight = 15207.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.130287 restraints weight = 10379.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.132018 restraints weight = 7768.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133112 restraints weight = 6247.555| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14344 Z= 0.142 Angle : 0.752 8.641 19552 Z= 0.391 Chirality : 0.043 0.207 2288 Planarity : 0.007 0.100 2388 Dihedral : 7.462 42.936 1956 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 1.11 % Allowed : 7.91 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.17), residues: 1808 helix: -2.32 (0.12), residues: 1140 sheet: None (None), residues: 0 loop : -2.55 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 80 TYR 0.012 0.002 TYR C 62 PHE 0.016 0.002 PHE A 287 TRP 0.020 0.002 TRP D 389 HIS 0.009 0.002 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00305 (14344) covalent geometry : angle 0.75192 (19552) hydrogen bonds : bond 0.04926 ( 576) hydrogen bonds : angle 5.10154 ( 1692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8205 (mppt) cc_final: 0.7764 (mptt) REVERT: A 117 ASN cc_start: 0.8222 (t0) cc_final: 0.8008 (t0) REVERT: A 138 LYS cc_start: 0.7929 (ptpt) cc_final: 0.7618 (ptpt) REVERT: A 159 LEU cc_start: 0.8123 (mt) cc_final: 0.7831 (mt) REVERT: A 293 GLN cc_start: 0.7755 (mp10) cc_final: 0.7392 (mp10) REVERT: A 303 LEU cc_start: 0.8216 (tp) cc_final: 0.7392 (tp) REVERT: B 79 LYS cc_start: 0.8203 (mppt) cc_final: 0.7762 (mptt) REVERT: B 138 LYS cc_start: 0.7932 (ptpt) cc_final: 0.7624 (ptpt) REVERT: B 159 LEU cc_start: 0.8130 (mt) cc_final: 0.7838 (mt) REVERT: B 293 GLN cc_start: 0.7792 (mp10) cc_final: 0.7425 (mp10) REVERT: B 303 LEU cc_start: 0.8225 (tp) cc_final: 0.7399 (tp) REVERT: C 11 THR cc_start: 0.7424 (m) cc_final: 0.6843 (m) REVERT: C 79 LYS cc_start: 0.8218 (mppt) cc_final: 0.7793 (mptt) REVERT: C 138 LYS cc_start: 0.7970 (ptpt) cc_final: 0.7648 (ptpt) REVERT: C 159 LEU cc_start: 0.8132 (mt) cc_final: 0.7829 (mt) REVERT: C 293 GLN cc_start: 0.7807 (mp10) cc_final: 0.7418 (mp10) REVERT: C 303 LEU cc_start: 0.8228 (tp) cc_final: 0.7394 (tp) REVERT: D 79 LYS cc_start: 0.8191 (mppt) cc_final: 0.7763 (mptt) REVERT: D 138 LYS cc_start: 0.7925 (ptpt) cc_final: 0.7621 (ptpt) REVERT: D 159 LEU cc_start: 0.8127 (mt) cc_final: 0.7839 (mt) REVERT: D 293 GLN cc_start: 0.7836 (mp10) cc_final: 0.7446 (mp10) REVERT: D 303 LEU cc_start: 0.8222 (tp) cc_final: 0.7393 (tp) outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.1028 time to fit residues: 74.3950 Evaluate side-chains 364 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 44 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 103 optimal weight: 0.0070 chunk 170 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127992 restraints weight = 26324.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.131375 restraints weight = 15941.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.133822 restraints weight = 10980.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135490 restraints weight = 8242.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.136580 restraints weight = 6658.172| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14344 Z= 0.126 Angle : 0.684 7.818 19552 Z= 0.350 Chirality : 0.043 0.211 2288 Planarity : 0.006 0.096 2388 Dihedral : 6.512 42.296 1956 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.29 % Favored : 89.82 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.19), residues: 1808 helix: -1.47 (0.14), residues: 1144 sheet: None (None), residues: 0 loop : -1.89 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 25 TYR 0.013 0.002 TYR C 62 PHE 0.016 0.002 PHE A 38 TRP 0.027 0.002 TRP B 389 HIS 0.006 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00274 (14344) covalent geometry : angle 0.68351 (19552) hydrogen bonds : bond 0.03995 ( 576) hydrogen bonds : angle 4.60254 ( 1692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7392 (m) cc_final: 0.6840 (m) REVERT: A 79 LYS cc_start: 0.8252 (mppt) cc_final: 0.7837 (mmtp) REVERT: A 303 LEU cc_start: 0.7951 (tp) cc_final: 0.7247 (tp) REVERT: A 326 GLN cc_start: 0.7523 (mt0) cc_final: 0.6514 (tm-30) REVERT: B 11 THR cc_start: 0.7377 (m) cc_final: 0.6836 (m) REVERT: B 32 GLN cc_start: 0.8749 (tt0) cc_final: 0.8305 (tm-30) REVERT: B 79 LYS cc_start: 0.8285 (mppt) cc_final: 0.7861 (mmtp) REVERT: B 138 LYS cc_start: 0.7525 (ptpt) cc_final: 0.7271 (ptpt) REVERT: B 303 LEU cc_start: 0.7949 (tp) cc_final: 0.7261 (tp) REVERT: B 326 GLN cc_start: 0.7356 (mt0) cc_final: 0.6445 (tm-30) REVERT: B 329 ASN cc_start: 0.7669 (m-40) cc_final: 0.7387 (m-40) REVERT: C 11 THR cc_start: 0.7392 (m) cc_final: 0.6857 (m) REVERT: C 79 LYS cc_start: 0.8272 (mppt) cc_final: 0.7835 (mmtp) REVERT: C 138 LYS cc_start: 0.7546 (ptpt) cc_final: 0.7289 (ptpt) REVERT: C 303 LEU cc_start: 0.7944 (tp) cc_final: 0.7237 (tp) REVERT: C 326 GLN cc_start: 0.7286 (mt0) cc_final: 0.6551 (tm-30) REVERT: D 11 THR cc_start: 0.7386 (m) cc_final: 0.6838 (m) REVERT: D 79 LYS cc_start: 0.8316 (mppt) cc_final: 0.7884 (mmtp) REVERT: D 303 LEU cc_start: 0.7958 (tp) cc_final: 0.7252 (tp) REVERT: D 326 GLN cc_start: 0.7347 (mt0) cc_final: 0.6568 (tm-30) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.1049 time to fit residues: 72.2458 Evaluate side-chains 338 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 36 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 151 optimal weight: 0.2980 chunk 166 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 379 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.151432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.128909 restraints weight = 26423.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132327 restraints weight = 16117.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134617 restraints weight = 11078.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136267 restraints weight = 8371.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137301 restraints weight = 6781.256| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14344 Z= 0.117 Angle : 0.649 8.099 19552 Z= 0.331 Chirality : 0.042 0.216 2288 Planarity : 0.006 0.093 2388 Dihedral : 6.055 42.145 1956 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.88 % Allowed : 5.48 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.19), residues: 1808 helix: -1.16 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -1.77 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.012 0.002 TYR D 29 PHE 0.010 0.001 PHE D 38 TRP 0.023 0.001 TRP B 389 HIS 0.006 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00257 (14344) covalent geometry : angle 0.64887 (19552) hydrogen bonds : bond 0.03396 ( 576) hydrogen bonds : angle 4.35621 ( 1692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8361 (mppt) cc_final: 0.7879 (mmtp) REVERT: A 158 MET cc_start: 0.7634 (tpt) cc_final: 0.7037 (tpt) REVERT: A 303 LEU cc_start: 0.7887 (tp) cc_final: 0.7284 (tp) REVERT: A 326 GLN cc_start: 0.7632 (mt0) cc_final: 0.6561 (tm-30) REVERT: A 379 GLN cc_start: 0.8326 (mt0) cc_final: 0.8046 (mt0) REVERT: B 32 GLN cc_start: 0.8695 (tt0) cc_final: 0.8261 (tm-30) REVERT: B 57 CYS cc_start: 0.7412 (t) cc_final: 0.7205 (t) REVERT: B 79 LYS cc_start: 0.8393 (mppt) cc_final: 0.7911 (mmtp) REVERT: B 178 TRP cc_start: 0.7255 (m100) cc_final: 0.6712 (m100) REVERT: B 303 LEU cc_start: 0.7906 (tp) cc_final: 0.7294 (tp) REVERT: B 326 GLN cc_start: 0.7669 (mt0) cc_final: 0.6522 (tm-30) REVERT: B 329 ASN cc_start: 0.7324 (m-40) cc_final: 0.7109 (m-40) REVERT: B 379 GLN cc_start: 0.8471 (mt0) cc_final: 0.8005 (mt0) REVERT: C 79 LYS cc_start: 0.8397 (mppt) cc_final: 0.7858 (mmtp) REVERT: C 199 MET cc_start: 0.7374 (mtt) cc_final: 0.7149 (mtm) REVERT: C 303 LEU cc_start: 0.7883 (tp) cc_final: 0.7259 (tp) REVERT: C 326 GLN cc_start: 0.7745 (mt0) cc_final: 0.6666 (tm-30) REVERT: C 379 GLN cc_start: 0.8358 (mt0) cc_final: 0.8076 (mt0) REVERT: D 57 CYS cc_start: 0.7544 (t) cc_final: 0.7342 (t) REVERT: D 79 LYS cc_start: 0.8398 (mppt) cc_final: 0.7931 (mmtp) REVERT: D 178 TRP cc_start: 0.7341 (m100) cc_final: 0.6745 (m100) REVERT: D 199 MET cc_start: 0.7395 (mtt) cc_final: 0.7179 (mtm) REVERT: D 303 LEU cc_start: 0.7890 (tp) cc_final: 0.7271 (tp) REVERT: D 326 GLN cc_start: 0.7737 (mt0) cc_final: 0.6648 (tm-30) REVERT: D 379 GLN cc_start: 0.8372 (mt0) cc_final: 0.8056 (mt0) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.0958 time to fit residues: 69.3552 Evaluate side-chains 365 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 24 optimal weight: 0.1980 chunk 103 optimal weight: 8.9990 chunk 160 optimal weight: 0.0770 chunk 95 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 324 GLN B 324 GLN C 195 ASN C 324 GLN D 324 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.130749 restraints weight = 26152.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.134164 restraints weight = 15865.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.136588 restraints weight = 10913.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.138248 restraints weight = 8186.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.139295 restraints weight = 6631.751| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14344 Z= 0.106 Angle : 0.616 6.766 19552 Z= 0.311 Chirality : 0.041 0.224 2288 Planarity : 0.006 0.091 2388 Dihedral : 5.694 40.454 1956 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.08 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.20), residues: 1808 helix: -0.73 (0.14), residues: 1140 sheet: None (None), residues: 0 loop : -1.87 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.010 0.001 TYR B 438 PHE 0.011 0.001 PHE C 360 TRP 0.021 0.001 TRP B 389 HIS 0.006 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00237 (14344) covalent geometry : angle 0.61638 (19552) hydrogen bonds : bond 0.02954 ( 576) hydrogen bonds : angle 4.02348 ( 1692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7560 (m) cc_final: 0.7162 (m) REVERT: A 79 LYS cc_start: 0.8516 (mppt) cc_final: 0.8229 (mmtp) REVERT: A 199 MET cc_start: 0.7354 (mtt) cc_final: 0.7013 (mtp) REVERT: A 303 LEU cc_start: 0.7825 (tp) cc_final: 0.7153 (tp) REVERT: A 326 GLN cc_start: 0.7428 (mt0) cc_final: 0.6451 (tm-30) REVERT: A 477 CYS cc_start: 0.6409 (m) cc_final: 0.5964 (p) REVERT: B 11 THR cc_start: 0.7527 (m) cc_final: 0.7127 (m) REVERT: B 32 GLN cc_start: 0.8687 (tt0) cc_final: 0.7949 (tm-30) REVERT: B 79 LYS cc_start: 0.8547 (mppt) cc_final: 0.8272 (mmtp) REVERT: B 178 TRP cc_start: 0.7087 (m100) cc_final: 0.6621 (m100) REVERT: B 199 MET cc_start: 0.7335 (mtt) cc_final: 0.7026 (mtp) REVERT: B 303 LEU cc_start: 0.7859 (tp) cc_final: 0.7282 (tp) REVERT: B 376 PHE cc_start: 0.8599 (t80) cc_final: 0.7840 (t80) REVERT: B 379 GLN cc_start: 0.8346 (mt0) cc_final: 0.7602 (mt0) REVERT: B 477 CYS cc_start: 0.6488 (m) cc_final: 0.6073 (p) REVERT: C 11 THR cc_start: 0.7544 (m) cc_final: 0.7142 (m) REVERT: C 32 GLN cc_start: 0.8846 (tt0) cc_final: 0.7927 (tm-30) REVERT: C 79 LYS cc_start: 0.8476 (mppt) cc_final: 0.7962 (mptt) REVERT: C 158 MET cc_start: 0.7622 (tpt) cc_final: 0.6870 (tpt) REVERT: C 199 MET cc_start: 0.7340 (mtt) cc_final: 0.7003 (mtp) REVERT: C 303 LEU cc_start: 0.7859 (tp) cc_final: 0.7254 (tp) REVERT: C 326 GLN cc_start: 0.7724 (mt0) cc_final: 0.6552 (tm-30) REVERT: C 477 CYS cc_start: 0.6420 (m) cc_final: 0.6098 (p) REVERT: D 11 THR cc_start: 0.7529 (m) cc_final: 0.7125 (m) REVERT: D 32 GLN cc_start: 0.8783 (tt0) cc_final: 0.7778 (tm-30) REVERT: D 79 LYS cc_start: 0.8485 (mppt) cc_final: 0.8155 (mptt) REVERT: D 158 MET cc_start: 0.7620 (tpt) cc_final: 0.6841 (tpt) REVERT: D 178 TRP cc_start: 0.7149 (m100) cc_final: 0.6679 (m100) REVERT: D 199 MET cc_start: 0.7352 (mtt) cc_final: 0.7038 (mtp) REVERT: D 303 LEU cc_start: 0.7855 (tp) cc_final: 0.7280 (tp) REVERT: D 477 CYS cc_start: 0.6558 (m) cc_final: 0.6157 (p) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.0944 time to fit residues: 67.5211 Evaluate side-chains 368 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 133 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 114 optimal weight: 0.0870 chunk 154 optimal weight: 6.9990 chunk 22 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN B 195 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.131897 restraints weight = 25698.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135309 restraints weight = 15682.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.137669 restraints weight = 10795.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139344 restraints weight = 8117.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140423 restraints weight = 6560.026| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14344 Z= 0.104 Angle : 0.621 8.517 19552 Z= 0.311 Chirality : 0.041 0.232 2288 Planarity : 0.006 0.090 2388 Dihedral : 5.368 39.834 1956 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.92 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.20), residues: 1808 helix: -0.52 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.53 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.023 0.001 TYR C 240 PHE 0.012 0.001 PHE C 360 TRP 0.018 0.001 TRP B 389 HIS 0.006 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00228 (14344) covalent geometry : angle 0.62141 (19552) hydrogen bonds : bond 0.02812 ( 576) hydrogen bonds : angle 3.84789 ( 1692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7526 (m) cc_final: 0.7089 (m) REVERT: A 79 LYS cc_start: 0.8548 (mppt) cc_final: 0.8229 (mptt) REVERT: A 158 MET cc_start: 0.7440 (tpt) cc_final: 0.7033 (tpt) REVERT: A 175 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6964 (mm-30) REVERT: A 199 MET cc_start: 0.7349 (mtt) cc_final: 0.7030 (mtp) REVERT: A 240 TYR cc_start: 0.4970 (m-80) cc_final: 0.4398 (m-10) REVERT: A 303 LEU cc_start: 0.7788 (tp) cc_final: 0.7079 (tp) REVERT: A 326 GLN cc_start: 0.7310 (mt0) cc_final: 0.6306 (tm-30) REVERT: A 376 PHE cc_start: 0.8201 (t80) cc_final: 0.7942 (t80) REVERT: A 379 GLN cc_start: 0.8333 (mt0) cc_final: 0.8013 (mt0) REVERT: A 477 CYS cc_start: 0.6322 (m) cc_final: 0.5874 (p) REVERT: B 11 THR cc_start: 0.7588 (m) cc_final: 0.7146 (m) REVERT: B 32 GLN cc_start: 0.8708 (tt0) cc_final: 0.7936 (tm-30) REVERT: B 79 LYS cc_start: 0.8544 (mppt) cc_final: 0.8236 (mptt) REVERT: B 121 LYS cc_start: 0.8901 (mptt) cc_final: 0.8651 (mmtp) REVERT: B 158 MET cc_start: 0.7544 (tpt) cc_final: 0.6921 (tpt) REVERT: B 178 TRP cc_start: 0.7006 (m100) cc_final: 0.6575 (m100) REVERT: B 199 MET cc_start: 0.7365 (mtt) cc_final: 0.7051 (mtp) REVERT: B 240 TYR cc_start: 0.5028 (m-80) cc_final: 0.4488 (m-10) REVERT: B 303 LEU cc_start: 0.7854 (tp) cc_final: 0.7240 (tp) REVERT: B 376 PHE cc_start: 0.8588 (t80) cc_final: 0.7826 (t80) REVERT: B 379 GLN cc_start: 0.8268 (mt0) cc_final: 0.7583 (mt0) REVERT: B 477 CYS cc_start: 0.6380 (m) cc_final: 0.5956 (p) REVERT: C 11 THR cc_start: 0.7499 (m) cc_final: 0.7084 (m) REVERT: C 32 GLN cc_start: 0.8811 (tt0) cc_final: 0.7556 (tm-30) REVERT: C 79 LYS cc_start: 0.8555 (mppt) cc_final: 0.8236 (mptt) REVERT: C 175 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6983 (mm-30) REVERT: C 199 MET cc_start: 0.7305 (mtt) cc_final: 0.6999 (mtp) REVERT: C 240 TYR cc_start: 0.5090 (m-80) cc_final: 0.4520 (m-10) REVERT: C 303 LEU cc_start: 0.7841 (tp) cc_final: 0.7259 (tp) REVERT: C 477 CYS cc_start: 0.6286 (m) cc_final: 0.5863 (p) REVERT: D 11 THR cc_start: 0.7521 (m) cc_final: 0.7085 (m) REVERT: D 32 GLN cc_start: 0.8777 (tt0) cc_final: 0.7719 (tm-30) REVERT: D 74 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8388 (mtmm) REVERT: D 79 LYS cc_start: 0.8567 (mppt) cc_final: 0.8298 (mmtp) REVERT: D 178 TRP cc_start: 0.7037 (m100) cc_final: 0.6523 (m100) REVERT: D 199 MET cc_start: 0.7362 (mtt) cc_final: 0.7017 (mtp) REVERT: D 240 TYR cc_start: 0.5010 (m-80) cc_final: 0.4445 (m-10) REVERT: D 303 LEU cc_start: 0.7791 (tp) cc_final: 0.7181 (tp) REVERT: D 326 GLN cc_start: 0.7675 (mt0) cc_final: 0.6571 (tm-30) REVERT: D 477 CYS cc_start: 0.6366 (m) cc_final: 0.5824 (p) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.0897 time to fit residues: 64.8402 Evaluate side-chains 370 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 112 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 125 optimal weight: 0.0970 chunk 173 optimal weight: 0.6980 chunk 133 optimal weight: 0.0770 chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 0.0000 chunk 149 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.157524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.134729 restraints weight = 25543.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138188 restraints weight = 15653.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140570 restraints weight = 10721.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.142289 restraints weight = 8045.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143480 restraints weight = 6470.826| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14344 Z= 0.103 Angle : 0.620 7.696 19552 Z= 0.304 Chirality : 0.041 0.252 2288 Planarity : 0.006 0.092 2388 Dihedral : 5.133 38.942 1956 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.70 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.20), residues: 1808 helix: -0.35 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -1.46 (0.28), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 304 TYR 0.012 0.001 TYR A 240 PHE 0.013 0.001 PHE A 360 TRP 0.022 0.001 TRP B 389 HIS 0.006 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00225 (14344) covalent geometry : angle 0.61956 (19552) hydrogen bonds : bond 0.02728 ( 576) hydrogen bonds : angle 3.69132 ( 1692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7490 (m) cc_final: 0.7142 (m) REVERT: A 79 LYS cc_start: 0.8570 (mppt) cc_final: 0.7857 (mmmt) REVERT: A 158 MET cc_start: 0.7552 (tpt) cc_final: 0.7150 (tpt) REVERT: A 175 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6947 (mm-30) REVERT: A 199 MET cc_start: 0.7372 (mtt) cc_final: 0.7042 (mtp) REVERT: A 303 LEU cc_start: 0.7845 (tp) cc_final: 0.7572 (tp) REVERT: A 322 PRO cc_start: 0.7218 (Cg_exo) cc_final: 0.6941 (Cg_endo) REVERT: A 376 PHE cc_start: 0.8259 (t80) cc_final: 0.8004 (t80) REVERT: A 379 GLN cc_start: 0.8253 (mt0) cc_final: 0.7848 (mt0) REVERT: A 477 CYS cc_start: 0.6184 (m) cc_final: 0.5745 (p) REVERT: B 11 THR cc_start: 0.7517 (m) cc_final: 0.7153 (m) REVERT: B 32 GLN cc_start: 0.8667 (tt0) cc_final: 0.7967 (tm-30) REVERT: B 79 LYS cc_start: 0.8609 (mppt) cc_final: 0.7927 (mmmt) REVERT: B 113 ILE cc_start: 0.8989 (mt) cc_final: 0.8333 (mt) REVERT: B 158 MET cc_start: 0.7738 (tpt) cc_final: 0.7126 (tpt) REVERT: B 175 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7052 (mm-30) REVERT: B 178 TRP cc_start: 0.6999 (m100) cc_final: 0.6557 (m100) REVERT: B 199 MET cc_start: 0.7365 (mtt) cc_final: 0.7061 (mtp) REVERT: B 303 LEU cc_start: 0.7810 (tp) cc_final: 0.7274 (tp) REVERT: B 326 GLN cc_start: 0.7674 (mt0) cc_final: 0.6450 (tm-30) REVERT: B 376 PHE cc_start: 0.8503 (t80) cc_final: 0.8096 (t80) REVERT: B 379 GLN cc_start: 0.8185 (mt0) cc_final: 0.7641 (mt0) REVERT: B 477 CYS cc_start: 0.6299 (m) cc_final: 0.5812 (p) REVERT: C 11 THR cc_start: 0.7491 (m) cc_final: 0.7166 (m) REVERT: C 32 GLN cc_start: 0.8769 (tt0) cc_final: 0.7665 (tm-30) REVERT: C 79 LYS cc_start: 0.8524 (mppt) cc_final: 0.7774 (mmmt) REVERT: C 113 ILE cc_start: 0.8941 (mt) cc_final: 0.8482 (mt) REVERT: C 158 MET cc_start: 0.7615 (tpt) cc_final: 0.6922 (tpt) REVERT: C 175 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6948 (mm-30) REVERT: C 199 MET cc_start: 0.7408 (mtt) cc_final: 0.7079 (mtp) REVERT: C 247 PHE cc_start: 0.7449 (t80) cc_final: 0.7160 (t80) REVERT: C 303 LEU cc_start: 0.7757 (tp) cc_final: 0.7214 (tp) REVERT: C 477 CYS cc_start: 0.6273 (m) cc_final: 0.5785 (p) REVERT: D 11 THR cc_start: 0.7502 (m) cc_final: 0.7133 (m) REVERT: D 32 GLN cc_start: 0.8737 (tt0) cc_final: 0.7799 (tm-30) REVERT: D 74 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8597 (mtmt) REVERT: D 79 LYS cc_start: 0.8553 (mppt) cc_final: 0.7875 (mmmt) REVERT: D 113 ILE cc_start: 0.8977 (mt) cc_final: 0.8390 (mt) REVERT: D 158 MET cc_start: 0.7609 (tpt) cc_final: 0.6861 (tpt) REVERT: D 175 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7321 (mm-30) REVERT: D 178 TRP cc_start: 0.6971 (m100) cc_final: 0.6577 (m100) REVERT: D 199 MET cc_start: 0.7346 (mtt) cc_final: 0.7051 (mtp) REVERT: D 303 LEU cc_start: 0.7767 (tp) cc_final: 0.7236 (tp) REVERT: D 326 GLN cc_start: 0.7695 (mt0) cc_final: 0.6759 (tm-30) REVERT: D 477 CYS cc_start: 0.6265 (m) cc_final: 0.5729 (p) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.0877 time to fit residues: 63.3908 Evaluate side-chains 380 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 157 optimal weight: 0.0670 chunk 145 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN C 195 ASN C 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.154748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131859 restraints weight = 25618.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135232 restraints weight = 15490.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137579 restraints weight = 10589.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.139184 restraints weight = 7964.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.140340 restraints weight = 6466.922| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14344 Z= 0.122 Angle : 0.651 8.025 19552 Z= 0.326 Chirality : 0.042 0.261 2288 Planarity : 0.006 0.089 2388 Dihedral : 5.268 39.958 1956 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.14 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.20), residues: 1808 helix: -0.28 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -1.52 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 25 TYR 0.013 0.002 TYR D 291 PHE 0.027 0.001 PHE D 120 TRP 0.027 0.001 TRP C 389 HIS 0.005 0.001 HIS B 200 Details of bonding type rmsd covalent geometry : bond 0.00280 (14344) covalent geometry : angle 0.65102 (19552) hydrogen bonds : bond 0.02795 ( 576) hydrogen bonds : angle 3.85500 ( 1692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7465 (m) cc_final: 0.7132 (m) REVERT: A 74 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8270 (mtmm) REVERT: A 79 LYS cc_start: 0.8344 (mppt) cc_final: 0.7776 (mmmt) REVERT: A 158 MET cc_start: 0.7726 (tpt) cc_final: 0.7257 (tpt) REVERT: A 199 MET cc_start: 0.7372 (mtt) cc_final: 0.6979 (mtp) REVERT: A 240 TYR cc_start: 0.5174 (m-80) cc_final: 0.4355 (m-10) REVERT: A 303 LEU cc_start: 0.7887 (tp) cc_final: 0.7497 (tp) REVERT: A 376 PHE cc_start: 0.8256 (t80) cc_final: 0.8038 (t80) REVERT: A 379 GLN cc_start: 0.8339 (mt0) cc_final: 0.7899 (mt0) REVERT: A 477 CYS cc_start: 0.6309 (m) cc_final: 0.5913 (p) REVERT: B 11 THR cc_start: 0.7541 (m) cc_final: 0.7217 (m) REVERT: B 79 LYS cc_start: 0.8376 (mppt) cc_final: 0.7849 (mmmt) REVERT: B 175 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7049 (mm-30) REVERT: B 178 TRP cc_start: 0.6984 (m100) cc_final: 0.6606 (m100) REVERT: B 199 MET cc_start: 0.7426 (mtt) cc_final: 0.7077 (mtp) REVERT: B 240 TYR cc_start: 0.5052 (m-80) cc_final: 0.4383 (m-10) REVERT: B 303 LEU cc_start: 0.7929 (tp) cc_final: 0.7327 (tp) REVERT: B 326 GLN cc_start: 0.7973 (mt0) cc_final: 0.6856 (tm-30) REVERT: B 329 ASN cc_start: 0.7647 (m-40) cc_final: 0.7317 (m-40) REVERT: B 376 PHE cc_start: 0.8557 (t80) cc_final: 0.7830 (t80) REVERT: B 379 GLN cc_start: 0.8274 (mt0) cc_final: 0.7608 (mt0) REVERT: B 477 CYS cc_start: 0.6318 (m) cc_final: 0.5828 (p) REVERT: C 11 THR cc_start: 0.7487 (m) cc_final: 0.7095 (m) REVERT: C 79 LYS cc_start: 0.8560 (mppt) cc_final: 0.7852 (mmmt) REVERT: C 175 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7033 (mm-30) REVERT: C 199 MET cc_start: 0.7427 (mtt) cc_final: 0.7030 (mtp) REVERT: C 240 TYR cc_start: 0.5139 (m-80) cc_final: 0.4471 (m-10) REVERT: C 303 LEU cc_start: 0.7870 (tp) cc_final: 0.7238 (tp) REVERT: C 326 GLN cc_start: 0.7800 (mt0) cc_final: 0.6791 (tm-30) REVERT: C 477 CYS cc_start: 0.6275 (m) cc_final: 0.5791 (p) REVERT: D 11 THR cc_start: 0.7503 (m) cc_final: 0.7155 (m) REVERT: D 25 ARG cc_start: 0.7177 (mmp80) cc_final: 0.6683 (mmp80) REVERT: D 28 TYR cc_start: 0.7662 (t80) cc_final: 0.7431 (t80) REVERT: D 74 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8530 (mtmm) REVERT: D 79 LYS cc_start: 0.8228 (mppt) cc_final: 0.7802 (mmmt) REVERT: D 178 TRP cc_start: 0.7034 (m100) cc_final: 0.6562 (m100) REVERT: D 199 MET cc_start: 0.7426 (mtt) cc_final: 0.7076 (mtp) REVERT: D 240 TYR cc_start: 0.5063 (m-80) cc_final: 0.4382 (m-10) REVERT: D 303 LEU cc_start: 0.7986 (tp) cc_final: 0.7332 (tp) REVERT: D 326 GLN cc_start: 0.7828 (mt0) cc_final: 0.6697 (tm-30) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.0922 time to fit residues: 64.8102 Evaluate side-chains 370 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 160 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.155357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.132126 restraints weight = 25557.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135526 restraints weight = 15426.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137869 restraints weight = 10540.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139507 restraints weight = 7932.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140556 restraints weight = 6429.310| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14344 Z= 0.117 Angle : 0.660 8.560 19552 Z= 0.327 Chirality : 0.042 0.265 2288 Planarity : 0.006 0.092 2388 Dihedral : 5.244 40.063 1956 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.64 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.20), residues: 1808 helix: -0.21 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -1.53 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.012 0.001 TYR C 291 PHE 0.028 0.001 PHE D 120 TRP 0.021 0.001 TRP C 389 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00271 (14344) covalent geometry : angle 0.65998 (19552) hydrogen bonds : bond 0.02894 ( 576) hydrogen bonds : angle 3.92723 ( 1692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7508 (m) cc_final: 0.7167 (m) REVERT: A 29 TYR cc_start: 0.7544 (m-80) cc_final: 0.7257 (m-80) REVERT: A 74 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8187 (mtmm) REVERT: A 158 MET cc_start: 0.7798 (tpt) cc_final: 0.7283 (tpt) REVERT: A 199 MET cc_start: 0.7386 (mtt) cc_final: 0.7003 (mtp) REVERT: A 303 LEU cc_start: 0.7869 (tp) cc_final: 0.7453 (tp) REVERT: A 379 GLN cc_start: 0.8339 (mt0) cc_final: 0.7582 (mt0) REVERT: A 477 CYS cc_start: 0.6261 (m) cc_final: 0.5843 (p) REVERT: B 11 THR cc_start: 0.7543 (m) cc_final: 0.7209 (m) REVERT: B 79 LYS cc_start: 0.8306 (mppt) cc_final: 0.7879 (mmmt) REVERT: B 158 MET cc_start: 0.7743 (tpt) cc_final: 0.7093 (tpt) REVERT: B 178 TRP cc_start: 0.7005 (m100) cc_final: 0.6653 (m100) REVERT: B 199 MET cc_start: 0.7354 (mtt) cc_final: 0.7013 (mtp) REVERT: B 280 LEU cc_start: 0.7269 (mp) cc_final: 0.7063 (mp) REVERT: B 326 GLN cc_start: 0.7971 (mt0) cc_final: 0.6897 (tm-30) REVERT: B 329 ASN cc_start: 0.7778 (m-40) cc_final: 0.7428 (m-40) REVERT: B 376 PHE cc_start: 0.8536 (t80) cc_final: 0.8320 (t80) REVERT: B 379 GLN cc_start: 0.8276 (mt0) cc_final: 0.7910 (mt0) REVERT: B 477 CYS cc_start: 0.6374 (m) cc_final: 0.5917 (p) REVERT: C 11 THR cc_start: 0.7506 (m) cc_final: 0.7155 (m) REVERT: C 79 LYS cc_start: 0.8312 (mppt) cc_final: 0.7738 (mmmt) REVERT: C 175 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7082 (mm-30) REVERT: C 199 MET cc_start: 0.7405 (mtt) cc_final: 0.7014 (mtp) REVERT: C 286 PHE cc_start: 0.7569 (m-80) cc_final: 0.6781 (m-80) REVERT: C 303 LEU cc_start: 0.8027 (tp) cc_final: 0.7715 (tp) REVERT: C 326 GLN cc_start: 0.7868 (mt0) cc_final: 0.6827 (tm-30) REVERT: C 477 CYS cc_start: 0.6399 (m) cc_final: 0.5872 (p) REVERT: D 11 THR cc_start: 0.7494 (m) cc_final: 0.7089 (m) REVERT: D 79 LYS cc_start: 0.8273 (mppt) cc_final: 0.7838 (mmmt) REVERT: D 158 MET cc_start: 0.7733 (tpt) cc_final: 0.7074 (tpt) REVERT: D 178 TRP cc_start: 0.7024 (m100) cc_final: 0.6643 (m100) REVERT: D 199 MET cc_start: 0.7384 (mtt) cc_final: 0.7026 (mtp) REVERT: D 280 LEU cc_start: 0.7331 (mp) cc_final: 0.7114 (mp) REVERT: D 303 LEU cc_start: 0.8025 (tp) cc_final: 0.7333 (tp) REVERT: D 326 GLN cc_start: 0.7792 (mt0) cc_final: 0.6831 (tm-30) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.0902 time to fit residues: 63.8947 Evaluate side-chains 387 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 33 optimal weight: 0.0470 chunk 165 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 130 optimal weight: 0.0570 chunk 150 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.133848 restraints weight = 25126.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.137275 restraints weight = 15345.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139648 restraints weight = 10564.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141303 restraints weight = 7998.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142433 restraints weight = 6516.666| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14344 Z= 0.112 Angle : 0.655 6.925 19552 Z= 0.325 Chirality : 0.043 0.272 2288 Planarity : 0.006 0.089 2388 Dihedral : 5.100 39.658 1956 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.03 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.20), residues: 1808 helix: -0.12 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.50 (0.28), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 42 TYR 0.012 0.001 TYR C 438 PHE 0.024 0.001 PHE C 38 TRP 0.017 0.001 TRP B 389 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00250 (14344) covalent geometry : angle 0.65510 (19552) hydrogen bonds : bond 0.02944 ( 576) hydrogen bonds : angle 3.89644 ( 1692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7542 (m) cc_final: 0.7186 (m) REVERT: A 29 TYR cc_start: 0.7551 (m-80) cc_final: 0.7336 (m-80) REVERT: A 74 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8093 (mtmm) REVERT: A 79 LYS cc_start: 0.8340 (mppt) cc_final: 0.7758 (mmmt) REVERT: A 158 MET cc_start: 0.7737 (tpt) cc_final: 0.7266 (tpt) REVERT: A 199 MET cc_start: 0.7390 (mtt) cc_final: 0.7042 (mtp) REVERT: A 303 LEU cc_start: 0.7880 (tp) cc_final: 0.7467 (tp) REVERT: A 376 PHE cc_start: 0.8222 (t80) cc_final: 0.7983 (t80) REVERT: A 379 GLN cc_start: 0.8320 (mt0) cc_final: 0.7862 (mt0) REVERT: A 477 CYS cc_start: 0.6332 (m) cc_final: 0.5913 (p) REVERT: B 11 THR cc_start: 0.7539 (m) cc_final: 0.7216 (m) REVERT: B 79 LYS cc_start: 0.8209 (mppt) cc_final: 0.7808 (mmmt) REVERT: B 178 TRP cc_start: 0.6994 (m100) cc_final: 0.6603 (m100) REVERT: B 199 MET cc_start: 0.7269 (mtt) cc_final: 0.6966 (mtp) REVERT: B 303 LEU cc_start: 0.8012 (tp) cc_final: 0.7315 (tp) REVERT: B 326 GLN cc_start: 0.7834 (mt0) cc_final: 0.6989 (tm-30) REVERT: B 376 PHE cc_start: 0.8498 (t80) cc_final: 0.8049 (t80) REVERT: B 379 GLN cc_start: 0.8202 (mt0) cc_final: 0.7730 (mt0) REVERT: B 477 CYS cc_start: 0.6336 (m) cc_final: 0.5831 (p) REVERT: C 11 THR cc_start: 0.7564 (m) cc_final: 0.7214 (m) REVERT: C 79 LYS cc_start: 0.8307 (mppt) cc_final: 0.7768 (mmmt) REVERT: C 158 MET cc_start: 0.7783 (tpt) cc_final: 0.7176 (tpt) REVERT: C 199 MET cc_start: 0.7307 (mtt) cc_final: 0.6948 (mtp) REVERT: C 286 PHE cc_start: 0.7514 (m-80) cc_final: 0.6761 (m-80) REVERT: C 303 LEU cc_start: 0.8002 (tp) cc_final: 0.7647 (tp) REVERT: C 326 GLN cc_start: 0.7834 (mt0) cc_final: 0.6847 (tm-30) REVERT: C 477 CYS cc_start: 0.6290 (m) cc_final: 0.5910 (p) REVERT: D 11 THR cc_start: 0.7471 (m) cc_final: 0.7082 (m) REVERT: D 74 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8451 (mtmm) REVERT: D 158 MET cc_start: 0.7857 (tpt) cc_final: 0.7141 (tpt) REVERT: D 178 TRP cc_start: 0.7011 (m100) cc_final: 0.6561 (m100) REVERT: D 199 MET cc_start: 0.7349 (mtt) cc_final: 0.7011 (mtp) REVERT: D 326 GLN cc_start: 0.7784 (mt0) cc_final: 0.6840 (tm-30) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.0919 time to fit residues: 65.4553 Evaluate side-chains 383 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 25 optimal weight: 6.9990 chunk 115 optimal weight: 0.0980 chunk 155 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.160730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.139076 restraints weight = 25042.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141921 restraints weight = 15907.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.143951 restraints weight = 11272.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145281 restraints weight = 8664.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.146245 restraints weight = 7176.518| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14344 Z= 0.117 Angle : 0.660 8.749 19552 Z= 0.325 Chirality : 0.043 0.274 2288 Planarity : 0.006 0.089 2388 Dihedral : 5.072 39.225 1956 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.36 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.20), residues: 1808 helix: -0.06 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.43 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.011 0.001 TYR B 438 PHE 0.019 0.001 PHE C 38 TRP 0.018 0.001 TRP D 389 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00267 (14344) covalent geometry : angle 0.66039 (19552) hydrogen bonds : bond 0.02883 ( 576) hydrogen bonds : angle 3.96277 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.34 seconds wall clock time: 41 minutes 4.12 seconds (2464.12 seconds total)