Starting phenix.real_space_refine on Thu Jul 31 22:09:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ji1_9832/07_2025/6ji1_9832.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ji1_9832/07_2025/6ji1_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_9832/07_2025/6ji1_9832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ji1_9832/07_2025/6ji1_9832.map" model { file = "/net/cci-nas-00/data/ceres_data/6ji1_9832/07_2025/6ji1_9832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ji1_9832/07_2025/6ji1_9832.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Restraints were copied for chains: C, B, D Time building chain proxies: 7.42, per 1000 atoms: 0.53 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: 3.47 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.24 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: 3.52 Time building geometry restraints manager: 4.09 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.180 Find NCS groups from input model: 0.260 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- 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 : 7.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.036 0.005 TRP C 54 HIS 0.009 0.002 HIS B 179 PHE 0.044 0.004 PHE D 38 TYR 0.026 0.004 TYR A 240 ARG 0.017 0.002 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.30919 ( 576) hydrogen bonds : angle 10.03494 ( 1692) covalent geometry : bond 0.00963 (14344) covalent geometry : angle 1.25669 (19552) *********************** 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 : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.9089 (pp) cc_final: 0.8747 (tp) REVERT: A 138 LYS cc_start: 0.7949 (ptpt) cc_final: 0.7713 (ptpt) REVERT: A 158 MET cc_start: 0.6662 (mtm) cc_final: 0.6365 (mtm) REVERT: A 303 LEU cc_start: 0.8114 (tp) cc_final: 0.7287 (tp) REVERT: A 304 ARG cc_start: 0.6305 (pmm-80) cc_final: 0.5493 (ttm-80) REVERT: A 462 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7945 (p) REVERT: B 127 LEU cc_start: 0.9104 (pp) cc_final: 0.8745 (tp) REVERT: B 138 LYS cc_start: 0.7953 (ptpt) cc_final: 0.7728 (ptpt) REVERT: B 158 MET cc_start: 0.6660 (mtm) cc_final: 0.6367 (mtm) REVERT: B 303 LEU cc_start: 0.8123 (tp) cc_final: 0.7276 (tp) REVERT: B 304 ARG cc_start: 0.6250 (pmm-80) cc_final: 0.5530 (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: 0.8735 (tp) REVERT: C 138 LYS cc_start: 0.7965 (ptpt) cc_final: 0.7733 (ptpt) REVERT: C 158 MET cc_start: 0.6644 (mtm) cc_final: 0.6371 (mtm) REVERT: C 303 LEU cc_start: 0.8124 (tp) cc_final: 0.7276 (tp) REVERT: C 304 ARG cc_start: 0.6230 (pmm-80) cc_final: 0.5528 (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: 0.8771 (tp) REVERT: D 138 LYS cc_start: 0.7953 (ptpt) cc_final: 0.7730 (ptpt) REVERT: D 158 MET cc_start: 0.6644 (mtm) cc_final: 0.6355 (mtm) REVERT: D 303 LEU cc_start: 0.8125 (tp) cc_final: 0.7267 (tp) REVERT: D 304 ARG cc_start: 0.6248 (pmm-80) cc_final: 0.5545 (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: 0.2354 time to fit residues: 179.4981 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 : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 324 GLN B 329 ASN C 151 ASN C 324 GLN D 151 ASN D 324 GLN D 329 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123939 restraints weight = 25677.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.127304 restraints weight = 15548.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129654 restraints weight = 10708.882| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14344 Z= 0.159 Angle : 0.757 8.462 19552 Z= 0.397 Chirality : 0.043 0.192 2288 Planarity : 0.007 0.101 2388 Dihedral : 7.503 43.015 1956 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 1.11 % Allowed : 8.30 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.17), residues: 1808 helix: -2.33 (0.12), residues: 1136 sheet: None (None), residues: 0 loop : -2.57 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 389 HIS 0.009 0.002 HIS C 200 PHE 0.016 0.002 PHE A 287 TYR 0.014 0.002 TYR C 62 ARG 0.006 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.05009 ( 576) hydrogen bonds : angle 5.11557 ( 1692) covalent geometry : bond 0.00330 (14344) covalent geometry : angle 0.75745 (19552) *********************** 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 480 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 2.258 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: A 32 GLN cc_start: 0.8727 (tt0) cc_final: 0.8148 (tt0) REVERT: A 79 LYS cc_start: 0.8223 (mppt) cc_final: 0.7777 (mmtp) REVERT: A 138 LYS cc_start: 0.8016 (ptpt) cc_final: 0.7694 (ptpt) REVERT: A 159 LEU cc_start: 0.8142 (mt) cc_final: 0.7832 (mt) REVERT: A 293 GLN cc_start: 0.7903 (mp10) cc_final: 0.7428 (mp10) REVERT: A 303 LEU cc_start: 0.8205 (tp) cc_final: 0.7342 (tp) REVERT: B 32 GLN cc_start: 0.8658 (tt0) cc_final: 0.8404 (tt0) REVERT: B 79 LYS cc_start: 0.8221 (mppt) cc_final: 0.7790 (mmtp) REVERT: B 138 LYS cc_start: 0.8004 (ptpt) cc_final: 0.7700 (ptpt) REVERT: B 159 LEU cc_start: 0.8153 (mt) cc_final: 0.7831 (mt) REVERT: B 293 GLN cc_start: 0.7885 (mp10) cc_final: 0.7404 (mp10) REVERT: B 303 LEU cc_start: 0.8227 (tp) cc_final: 0.7387 (tp) REVERT: C 32 GLN cc_start: 0.8649 (tt0) cc_final: 0.8367 (tt0) REVERT: C 79 LYS cc_start: 0.8227 (mppt) cc_final: 0.7772 (mptt) REVERT: C 138 LYS cc_start: 0.8034 (ptpt) cc_final: 0.7720 (ptpt) REVERT: C 159 LEU cc_start: 0.8154 (mt) cc_final: 0.7825 (mt) REVERT: C 293 GLN cc_start: 0.7901 (mp10) cc_final: 0.7500 (mp10) REVERT: C 303 LEU cc_start: 0.8228 (tp) cc_final: 0.7383 (tp) REVERT: D 32 GLN cc_start: 0.8621 (tt0) cc_final: 0.8404 (tt0) REVERT: D 79 LYS cc_start: 0.8212 (mppt) cc_final: 0.7793 (mmtp) REVERT: D 138 LYS cc_start: 0.8004 (ptpt) cc_final: 0.7697 (ptpt) REVERT: D 159 LEU cc_start: 0.8148 (mt) cc_final: 0.7828 (mt) REVERT: D 293 GLN cc_start: 0.7901 (mp10) cc_final: 0.7421 (mp10) REVERT: D 303 LEU cc_start: 0.8226 (tp) cc_final: 0.7382 (tp) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.2990 time to fit residues: 211.4983 Evaluate side-chains 351 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 158 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 124 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.0060 chunk 152 optimal weight: 0.2980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.130957 restraints weight = 26011.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134521 restraints weight = 15588.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136971 restraints weight = 10589.901| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14344 Z= 0.119 Angle : 0.673 7.876 19552 Z= 0.343 Chirality : 0.042 0.213 2288 Planarity : 0.006 0.095 2388 Dihedral : 6.397 42.218 1956 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.47 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.19), residues: 1808 helix: -1.40 (0.14), residues: 1104 sheet: None (None), residues: 0 loop : -1.84 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 389 HIS 0.006 0.001 HIS A 200 PHE 0.017 0.002 PHE D 360 TYR 0.011 0.001 TYR A 240 ARG 0.002 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 576) hydrogen bonds : angle 4.44910 ( 1692) covalent geometry : bond 0.00253 (14344) covalent geometry : angle 0.67270 (19552) *********************** 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 469 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7579 (m) cc_final: 0.6995 (m) REVERT: A 79 LYS cc_start: 0.8253 (mppt) cc_final: 0.7807 (mptt) REVERT: A 113 ILE cc_start: 0.9098 (mt) cc_final: 0.8664 (mt) REVERT: A 138 LYS cc_start: 0.7618 (ptpt) cc_final: 0.7346 (ptpt) REVERT: A 303 LEU cc_start: 0.7904 (tp) cc_final: 0.7231 (tp) REVERT: A 326 GLN cc_start: 0.7397 (mt0) cc_final: 0.6486 (tm-30) REVERT: B 11 THR cc_start: 0.7611 (m) cc_final: 0.7015 (m) REVERT: B 79 LYS cc_start: 0.8258 (mppt) cc_final: 0.7847 (mmtp) REVERT: B 113 ILE cc_start: 0.9103 (mt) cc_final: 0.8614 (mt) REVERT: B 138 LYS cc_start: 0.7648 (ptpt) cc_final: 0.7385 (ptpt) REVERT: B 303 LEU cc_start: 0.7904 (tp) cc_final: 0.7233 (tp) REVERT: B 326 GLN cc_start: 0.7132 (mt0) cc_final: 0.6398 (tm-30) REVERT: B 329 ASN cc_start: 0.7576 (m-40) cc_final: 0.7308 (m-40) REVERT: C 11 THR cc_start: 0.7558 (m) cc_final: 0.6973 (m) REVERT: C 79 LYS cc_start: 0.8261 (mppt) cc_final: 0.7802 (mptt) REVERT: C 138 LYS cc_start: 0.7616 (ptpt) cc_final: 0.7354 (ptpt) REVERT: C 293 GLN cc_start: 0.7819 (mp10) cc_final: 0.7583 (mp10) REVERT: C 303 LEU cc_start: 0.7856 (tp) cc_final: 0.7192 (tp) REVERT: C 326 GLN cc_start: 0.7350 (mt0) cc_final: 0.6480 (tm-30) REVERT: D 11 THR cc_start: 0.7598 (m) cc_final: 0.7005 (m) REVERT: D 79 LYS cc_start: 0.8264 (mppt) cc_final: 0.7819 (mmtp) REVERT: D 138 LYS cc_start: 0.7617 (ptpt) cc_final: 0.7337 (ptpt) REVERT: D 303 LEU cc_start: 0.7867 (tp) cc_final: 0.7209 (tp) REVERT: D 326 GLN cc_start: 0.7121 (mt0) cc_final: 0.6413 (tm-30) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.3228 time to fit residues: 225.6346 Evaluate side-chains 381 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 96 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 GLN B 324 GLN B 379 GLN C 379 GLN D 324 GLN D 379 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.152275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130326 restraints weight = 26112.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133815 restraints weight = 15751.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136215 restraints weight = 10711.870| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4864 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= 0.116 Angle : 0.639 7.088 19552 Z= 0.327 Chirality : 0.041 0.218 2288 Planarity : 0.006 0.092 2388 Dihedral : 5.976 41.758 1956 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.88 % Allowed : 5.81 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.19), residues: 1808 helix: -1.04 (0.14), residues: 1148 sheet: None (None), residues: 0 loop : -1.65 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 389 HIS 0.006 0.001 HIS A 200 PHE 0.015 0.001 PHE D 38 TYR 0.015 0.002 TYR D 28 ARG 0.002 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 576) hydrogen bonds : angle 4.35468 ( 1692) covalent geometry : bond 0.00259 (14344) covalent geometry : angle 0.63905 (19552) *********************** 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 456 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.661 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 79 LYS cc_start: 0.8409 (mppt) cc_final: 0.7933 (mmtp) REVERT: A 121 LYS cc_start: 0.9301 (tmmt) cc_final: 0.9058 (mmtm) REVERT: A 158 MET cc_start: 0.7499 (tpt) cc_final: 0.6961 (tpt) REVERT: A 303 LEU cc_start: 0.7804 (tp) cc_final: 0.7174 (tp) REVERT: A 326 GLN cc_start: 0.7578 (mt0) cc_final: 0.6510 (tm-30) REVERT: B 79 LYS cc_start: 0.8411 (mppt) cc_final: 0.7948 (mmtp) REVERT: B 303 LEU cc_start: 0.7837 (tp) cc_final: 0.7246 (tp) REVERT: B 379 GLN cc_start: 0.8396 (mt0) cc_final: 0.8152 (mt0) REVERT: C 24 GLU cc_start: 0.8421 (tp30) cc_final: 0.8180 (tp30) REVERT: C 79 LYS cc_start: 0.8351 (mppt) cc_final: 0.7882 (mmtp) REVERT: C 303 LEU cc_start: 0.7833 (tp) cc_final: 0.7240 (tp) REVERT: C 326 GLN cc_start: 0.7593 (mt0) cc_final: 0.6519 (tm-30) REVERT: C 379 GLN cc_start: 0.8436 (mt0) cc_final: 0.8179 (mt0) REVERT: D 79 LYS cc_start: 0.8403 (mppt) cc_final: 0.7963 (mmtp) REVERT: D 113 ILE cc_start: 0.9087 (mt) cc_final: 0.8480 (mt) REVERT: D 303 LEU cc_start: 0.7832 (tp) cc_final: 0.7247 (tp) REVERT: D 326 GLN cc_start: 0.7665 (mt0) cc_final: 0.6504 (tm-30) REVERT: D 379 GLN cc_start: 0.8416 (mt0) cc_final: 0.8124 (mt0) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.3940 time to fit residues: 281.2077 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 : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 72 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 177 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 101 optimal weight: 0.0060 chunk 100 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 176 optimal weight: 0.0010 chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN B 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133469 restraints weight = 25665.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136935 restraints weight = 15591.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.139380 restraints weight = 10678.194| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 14344 Z= 0.104 Angle : 0.624 8.432 19552 Z= 0.312 Chirality : 0.041 0.224 2288 Planarity : 0.006 0.091 2388 Dihedral : 5.522 39.747 1956 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.70 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 1808 helix: -0.48 (0.15), residues: 1108 sheet: None (None), residues: 0 loop : -1.66 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 389 HIS 0.005 0.001 HIS C 200 PHE 0.012 0.001 PHE C 360 TYR 0.019 0.001 TYR D 146 ARG 0.003 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.02941 ( 576) hydrogen bonds : angle 4.02545 ( 1692) covalent geometry : bond 0.00232 (14344) covalent geometry : angle 0.62434 (19552) *********************** 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 473 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7575 (m) cc_final: 0.7178 (m) REVERT: A 79 LYS cc_start: 0.8475 (mppt) cc_final: 0.8164 (mptt) REVERT: A 158 MET cc_start: 0.7459 (tpt) cc_final: 0.6896 (tpt) REVERT: A 175 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7163 (mm-30) REVERT: A 199 MET cc_start: 0.7377 (mtt) cc_final: 0.7176 (mtm) REVERT: A 303 LEU cc_start: 0.7767 (tp) cc_final: 0.7118 (tp) REVERT: A 326 GLN cc_start: 0.7453 (mt0) cc_final: 0.6545 (tm-30) REVERT: A 477 CYS cc_start: 0.6387 (m) cc_final: 0.6049 (p) REVERT: B 11 THR cc_start: 0.7580 (m) cc_final: 0.7214 (m) REVERT: B 79 LYS cc_start: 0.8446 (mppt) cc_final: 0.8147 (mptt) REVERT: B 175 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7230 (mm-30) REVERT: B 178 TRP cc_start: 0.7155 (m100) cc_final: 0.6784 (m100) REVERT: B 303 LEU cc_start: 0.7733 (tp) cc_final: 0.7126 (tp) REVERT: B 329 ASN cc_start: 0.7603 (m-40) cc_final: 0.7370 (m-40) REVERT: B 379 GLN cc_start: 0.8289 (mt0) cc_final: 0.7921 (mt0) REVERT: B 477 CYS cc_start: 0.6497 (m) cc_final: 0.6122 (p) REVERT: C 11 THR cc_start: 0.7577 (m) cc_final: 0.7189 (m) REVERT: C 79 LYS cc_start: 0.8389 (mppt) cc_final: 0.8122 (mmtp) REVERT: C 113 ILE cc_start: 0.9002 (mt) cc_final: 0.8251 (mt) REVERT: C 158 MET cc_start: 0.7465 (tpt) cc_final: 0.6933 (tpt) REVERT: C 175 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7168 (mm-30) REVERT: C 193 LEU cc_start: 0.8661 (mt) cc_final: 0.8452 (pp) REVERT: C 303 LEU cc_start: 0.7732 (tp) cc_final: 0.7107 (tp) REVERT: C 326 GLN cc_start: 0.7390 (mt0) cc_final: 0.6475 (tm-30) REVERT: C 477 CYS cc_start: 0.6501 (m) cc_final: 0.6130 (p) REVERT: D 11 THR cc_start: 0.7562 (m) cc_final: 0.7167 (m) REVERT: D 79 LYS cc_start: 0.8500 (mppt) cc_final: 0.8201 (mptt) REVERT: D 158 MET cc_start: 0.7658 (tpt) cc_final: 0.7084 (tpt) REVERT: D 175 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7237 (mm-30) REVERT: D 178 TRP cc_start: 0.7113 (m100) cc_final: 0.6749 (m100) REVERT: D 303 LEU cc_start: 0.7756 (tp) cc_final: 0.7151 (tp) REVERT: D 477 CYS cc_start: 0.6580 (m) cc_final: 0.6092 (p) outliers start: 0 outliers final: 0 residues processed: 473 average time/residue: 0.2548 time to fit residues: 182.2903 Evaluate side-chains 373 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 61 optimal weight: 2.9990 chunk 182 optimal weight: 0.0270 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 468 ASN B 117 ASN B 195 ASN B 305 ASN C 305 ASN D 305 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.154597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132114 restraints weight = 25836.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135565 restraints weight = 15584.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.138098 restraints weight = 10624.062| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14344 Z= 0.109 Angle : 0.629 6.882 19552 Z= 0.315 Chirality : 0.041 0.244 2288 Planarity : 0.006 0.089 2388 Dihedral : 5.347 39.908 1956 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.88 % Allowed : 5.31 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1808 helix: -0.49 (0.15), residues: 1172 sheet: None (None), residues: 0 loop : -1.56 (0.28), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 389 HIS 0.005 0.001 HIS C 200 PHE 0.012 0.001 PHE C 360 TYR 0.021 0.001 TYR C 240 ARG 0.001 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.02875 ( 576) hydrogen bonds : angle 3.94995 ( 1692) covalent geometry : bond 0.00247 (14344) covalent geometry : angle 0.62862 (19552) *********************** 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 463 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7486 (m) cc_final: 0.7068 (m) REVERT: A 79 LYS cc_start: 0.8582 (mppt) cc_final: 0.8286 (mptt) REVERT: A 158 MET cc_start: 0.7514 (tpt) cc_final: 0.7041 (tpt) REVERT: A 175 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7112 (mm-30) REVERT: A 199 MET cc_start: 0.7379 (mtt) cc_final: 0.7047 (mtp) REVERT: A 240 TYR cc_start: 0.5153 (m-80) cc_final: 0.4390 (m-10) REVERT: A 303 LEU cc_start: 0.7814 (tp) cc_final: 0.7129 (tp) REVERT: A 326 GLN cc_start: 0.7513 (mt0) cc_final: 0.6430 (tm-30) REVERT: A 376 PHE cc_start: 0.8334 (t80) cc_final: 0.8057 (t80) REVERT: A 379 GLN cc_start: 0.8363 (mt0) cc_final: 0.8077 (mt0) REVERT: A 477 CYS cc_start: 0.6397 (m) cc_final: 0.5892 (p) REVERT: B 11 THR cc_start: 0.7507 (m) cc_final: 0.7068 (m) REVERT: B 79 LYS cc_start: 0.8512 (mppt) cc_final: 0.8237 (mptt) REVERT: B 175 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7121 (mm-30) REVERT: B 199 MET cc_start: 0.7418 (mtt) cc_final: 0.7079 (mtp) REVERT: B 240 TYR cc_start: 0.5097 (m-80) cc_final: 0.4368 (m-10) REVERT: B 303 LEU cc_start: 0.7748 (tp) cc_final: 0.7101 (tp) REVERT: B 376 PHE cc_start: 0.8350 (t80) cc_final: 0.8050 (t80) REVERT: B 379 GLN cc_start: 0.8322 (mt0) cc_final: 0.8033 (mt0) REVERT: B 477 CYS cc_start: 0.6472 (m) cc_final: 0.6005 (p) REVERT: C 11 THR cc_start: 0.7502 (m) cc_final: 0.7067 (m) REVERT: C 16 THR cc_start: 0.8064 (p) cc_final: 0.7800 (p) REVERT: C 79 LYS cc_start: 0.8478 (mppt) cc_final: 0.7913 (mmmt) REVERT: C 158 MET cc_start: 0.7474 (tpt) cc_final: 0.7002 (tpt) REVERT: C 175 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7116 (mm-30) REVERT: C 199 MET cc_start: 0.7401 (mtt) cc_final: 0.7009 (mtp) REVERT: C 240 TYR cc_start: 0.5114 (m-80) cc_final: 0.4460 (m-10) REVERT: C 303 LEU cc_start: 0.7774 (tp) cc_final: 0.7121 (tp) REVERT: C 326 GLN cc_start: 0.7462 (mt0) cc_final: 0.6440 (tm-30) REVERT: C 477 CYS cc_start: 0.6418 (m) cc_final: 0.5966 (p) REVERT: D 11 THR cc_start: 0.7471 (m) cc_final: 0.7018 (m) REVERT: D 79 LYS cc_start: 0.8537 (mppt) cc_final: 0.8229 (mptt) REVERT: D 121 LYS cc_start: 0.9319 (tmmt) cc_final: 0.8948 (mmtm) REVERT: D 158 MET cc_start: 0.7741 (tpt) cc_final: 0.7157 (tpt) REVERT: D 175 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7123 (mm-30) REVERT: D 199 MET cc_start: 0.7421 (mtt) cc_final: 0.7075 (mtp) REVERT: D 240 TYR cc_start: 0.5109 (m-80) cc_final: 0.4396 (m-10) REVERT: D 303 LEU cc_start: 0.7831 (tp) cc_final: 0.7181 (tp) REVERT: D 477 CYS cc_start: 0.6534 (m) cc_final: 0.6049 (p) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.2510 time to fit residues: 176.3538 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 : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 0 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN D 195 ASN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.152742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130151 restraints weight = 26148.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.133625 restraints weight = 15759.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136001 restraints weight = 10716.530| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14344 Z= 0.126 Angle : 0.647 6.827 19552 Z= 0.325 Chirality : 0.042 0.251 2288 Planarity : 0.006 0.094 2388 Dihedral : 5.460 40.126 1956 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.14 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.20), residues: 1808 helix: -0.44 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.18 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 389 HIS 0.006 0.001 HIS C 200 PHE 0.015 0.001 PHE B 38 TYR 0.022 0.002 TYR B 28 ARG 0.004 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 576) hydrogen bonds : angle 4.04442 ( 1692) covalent geometry : bond 0.00293 (14344) covalent geometry : angle 0.64713 (19552) *********************** 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 446 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7345 (m) cc_final: 0.6899 (m) REVERT: A 74 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8632 (mtmt) REVERT: A 158 MET cc_start: 0.7700 (tpt) cc_final: 0.7152 (tpt) REVERT: A 175 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7162 (mm-30) REVERT: A 199 MET cc_start: 0.7445 (mtt) cc_final: 0.7038 (mtp) REVERT: A 240 TYR cc_start: 0.5205 (m-80) cc_final: 0.4333 (m-10) REVERT: A 303 LEU cc_start: 0.7935 (tp) cc_final: 0.7563 (tp) REVERT: A 376 PHE cc_start: 0.8477 (t80) cc_final: 0.8173 (t80) REVERT: A 379 GLN cc_start: 0.8417 (mt0) cc_final: 0.8047 (mt0) REVERT: A 477 CYS cc_start: 0.6436 (m) cc_final: 0.6000 (p) REVERT: B 11 THR cc_start: 0.7410 (m) cc_final: 0.6949 (m) REVERT: B 79 LYS cc_start: 0.8573 (mppt) cc_final: 0.8288 (mptt) REVERT: B 175 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7175 (mm-30) REVERT: B 199 MET cc_start: 0.7449 (mtt) cc_final: 0.7081 (mtp) REVERT: B 240 TYR cc_start: 0.5097 (m-80) cc_final: 0.4268 (m-10) REVERT: B 303 LEU cc_start: 0.7981 (tp) cc_final: 0.7601 (tp) REVERT: B 376 PHE cc_start: 0.8492 (t80) cc_final: 0.8185 (t80) REVERT: B 379 GLN cc_start: 0.8401 (mt0) cc_final: 0.8066 (mt0) REVERT: B 408 LEU cc_start: 0.7290 (mt) cc_final: 0.6947 (mp) REVERT: B 477 CYS cc_start: 0.6481 (m) cc_final: 0.6057 (p) REVERT: C 11 THR cc_start: 0.7376 (m) cc_final: 0.6952 (m) REVERT: C 21 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 74 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8681 (mtmt) REVERT: C 79 LYS cc_start: 0.8256 (mppt) cc_final: 0.7755 (mmmt) REVERT: C 113 ILE cc_start: 0.9133 (pt) cc_final: 0.8919 (tt) REVERT: C 158 MET cc_start: 0.7660 (tpt) cc_final: 0.7180 (tpt) REVERT: C 175 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7155 (mm-30) REVERT: C 199 MET cc_start: 0.7455 (mtt) cc_final: 0.7127 (mtp) REVERT: C 240 TYR cc_start: 0.5201 (m-80) cc_final: 0.4362 (m-10) REVERT: C 303 LEU cc_start: 0.7939 (tp) cc_final: 0.7563 (tp) REVERT: C 477 CYS cc_start: 0.6480 (m) cc_final: 0.6048 (p) REVERT: D 11 THR cc_start: 0.7415 (m) cc_final: 0.6981 (m) REVERT: D 74 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8423 (mtmm) REVERT: D 79 LYS cc_start: 0.8603 (mppt) cc_final: 0.8323 (mptt) REVERT: D 121 LYS cc_start: 0.9297 (tmmt) cc_final: 0.8948 (mmtm) REVERT: D 175 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7177 (mm-30) REVERT: D 199 MET cc_start: 0.7425 (mtt) cc_final: 0.7035 (mtp) REVERT: D 240 TYR cc_start: 0.5084 (m-80) cc_final: 0.4294 (m-10) REVERT: D 303 LEU cc_start: 0.7944 (tp) cc_final: 0.7576 (tp) REVERT: D 477 CYS cc_start: 0.6455 (m) cc_final: 0.5988 (p) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.2178 time to fit residues: 146.3897 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 : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 65 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 195 ASN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN D 195 ASN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.153932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131849 restraints weight = 26468.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134789 restraints weight = 16838.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136811 restraints weight = 12002.622| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14344 Z= 0.155 Angle : 0.679 7.469 19552 Z= 0.345 Chirality : 0.044 0.256 2288 Planarity : 0.006 0.091 2388 Dihedral : 5.675 42.494 1956 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.19 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1808 helix: -0.42 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -1.46 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 389 HIS 0.006 0.002 HIS B 179 PHE 0.027 0.002 PHE C 120 TYR 0.018 0.002 TYR C 146 ARG 0.002 0.000 ARG D 25 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 576) hydrogen bonds : angle 4.26800 ( 1692) covalent geometry : bond 0.00359 (14344) covalent geometry : angle 0.67858 (19552) *********************** 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 438 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7419 (m) cc_final: 0.6959 (m) REVERT: A 199 MET cc_start: 0.7561 (mtt) cc_final: 0.7123 (mtp) REVERT: A 303 LEU cc_start: 0.7932 (tp) cc_final: 0.7425 (tp) REVERT: A 379 GLN cc_start: 0.8462 (mt0) cc_final: 0.7755 (mt0) REVERT: A 477 CYS cc_start: 0.6346 (m) cc_final: 0.6045 (p) REVERT: B 11 THR cc_start: 0.7458 (m) cc_final: 0.6998 (m) REVERT: B 79 LYS cc_start: 0.8621 (mppt) cc_final: 0.8325 (mptt) REVERT: B 199 MET cc_start: 0.7421 (mtt) cc_final: 0.7008 (mtp) REVERT: B 303 LEU cc_start: 0.7901 (tp) cc_final: 0.7396 (tp) REVERT: B 379 GLN cc_start: 0.8474 (mt0) cc_final: 0.7747 (mt0) REVERT: B 475 VAL cc_start: 0.7581 (t) cc_final: 0.7367 (t) REVERT: C 11 THR cc_start: 0.7418 (m) cc_final: 0.6998 (m) REVERT: C 79 LYS cc_start: 0.8153 (mppt) cc_final: 0.7604 (mmmt) REVERT: C 113 ILE cc_start: 0.9091 (pt) cc_final: 0.8790 (tt) REVERT: C 199 MET cc_start: 0.7541 (mtt) cc_final: 0.7114 (mtp) REVERT: C 303 LEU cc_start: 0.7914 (tp) cc_final: 0.7438 (tp) REVERT: C 477 CYS cc_start: 0.6367 (m) cc_final: 0.6094 (p) REVERT: D 11 THR cc_start: 0.7488 (m) cc_final: 0.7037 (m) REVERT: D 79 LYS cc_start: 0.8640 (mppt) cc_final: 0.8348 (mptt) REVERT: D 199 MET cc_start: 0.7454 (mtt) cc_final: 0.7024 (mtp) REVERT: D 240 TYR cc_start: 0.5098 (m-80) cc_final: 0.4241 (m-10) REVERT: D 303 LEU cc_start: 0.7907 (tp) cc_final: 0.7404 (tp) REVERT: D 477 CYS cc_start: 0.6412 (m) cc_final: 0.6059 (p) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.2357 time to fit residues: 154.0160 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 : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 180 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 141 optimal weight: 0.0060 chunk 66 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.152924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.129949 restraints weight = 25463.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133345 restraints weight = 15468.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135628 restraints weight = 10642.400| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14344 Z= 0.122 Angle : 0.659 7.761 19552 Z= 0.331 Chirality : 0.043 0.262 2288 Planarity : 0.006 0.093 2388 Dihedral : 5.475 41.127 1956 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.13 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1808 helix: -0.31 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 389 HIS 0.005 0.001 HIS D 200 PHE 0.031 0.002 PHE C 120 TYR 0.019 0.002 TYR C 146 ARG 0.002 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 576) hydrogen bonds : angle 4.07724 ( 1692) covalent geometry : bond 0.00280 (14344) covalent geometry : angle 0.65934 (19552) *********************** 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 457 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 1.457 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.7391 (m) cc_final: 0.6957 (m) REVERT: A 158 MET cc_start: 0.7684 (tpt) cc_final: 0.7109 (tpt) REVERT: A 199 MET cc_start: 0.7610 (mtt) cc_final: 0.7150 (mtp) REVERT: A 303 LEU cc_start: 0.7885 (tp) cc_final: 0.7414 (tp) REVERT: A 376 PHE cc_start: 0.8474 (t80) cc_final: 0.8189 (t80) REVERT: A 379 GLN cc_start: 0.8497 (mt0) cc_final: 0.8126 (mt0) REVERT: A 477 CYS cc_start: 0.6329 (m) cc_final: 0.6013 (p) REVERT: B 11 THR cc_start: 0.7414 (m) cc_final: 0.6965 (m) REVERT: B 79 LYS cc_start: 0.8585 (mppt) cc_final: 0.7828 (mmmt) REVERT: B 138 LYS cc_start: 0.7695 (ptpt) cc_final: 0.7404 (ptpt) REVERT: B 199 MET cc_start: 0.7343 (mtt) cc_final: 0.6956 (mtp) REVERT: B 303 LEU cc_start: 0.7894 (tp) cc_final: 0.7419 (tp) REVERT: B 376 PHE cc_start: 0.8499 (t80) cc_final: 0.8202 (t80) REVERT: B 379 GLN cc_start: 0.8493 (mt0) cc_final: 0.8111 (mt0) REVERT: C 11 THR cc_start: 0.7392 (m) cc_final: 0.6990 (m) REVERT: C 16 THR cc_start: 0.7960 (p) cc_final: 0.7711 (p) REVERT: C 79 LYS cc_start: 0.8250 (mppt) cc_final: 0.7805 (mmmt) REVERT: C 158 MET cc_start: 0.7745 (tpt) cc_final: 0.7173 (tpt) REVERT: C 199 MET cc_start: 0.7417 (mtt) cc_final: 0.6940 (mtp) REVERT: C 303 LEU cc_start: 0.7909 (tp) cc_final: 0.7440 (tp) REVERT: C 477 CYS cc_start: 0.6276 (m) cc_final: 0.5849 (p) REVERT: D 11 THR cc_start: 0.7413 (m) cc_final: 0.6973 (m) REVERT: D 79 LYS cc_start: 0.8553 (mppt) cc_final: 0.7833 (mmmt) REVERT: D 138 LYS cc_start: 0.7513 (ptpt) cc_final: 0.7300 (ptpt) REVERT: D 158 MET cc_start: 0.7729 (tpt) cc_final: 0.7085 (tpt) REVERT: D 199 MET cc_start: 0.7429 (mtt) cc_final: 0.7025 (mtp) REVERT: D 240 TYR cc_start: 0.5115 (m-80) cc_final: 0.4271 (m-10) REVERT: D 303 LEU cc_start: 0.7832 (tp) cc_final: 0.7381 (tp) REVERT: D 326 GLN cc_start: 0.7710 (mt0) cc_final: 0.6697 (tm-30) REVERT: D 477 CYS cc_start: 0.6356 (m) cc_final: 0.5957 (p) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.2189 time to fit residues: 151.0726 Evaluate side-chains 392 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 141 optimal weight: 0.0870 chunk 176 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 0.0070 chunk 97 optimal weight: 0.5980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN C 195 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134859 restraints weight = 25174.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138367 restraints weight = 15472.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.140809 restraints weight = 10633.572| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.6242 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= 0.110 Angle : 0.639 7.993 19552 Z= 0.318 Chirality : 0.042 0.274 2288 Planarity : 0.006 0.088 2388 Dihedral : 5.196 40.581 1956 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.08 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1808 helix: -0.01 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 389 HIS 0.005 0.001 HIS D 200 PHE 0.024 0.001 PHE C 120 TYR 0.022 0.001 TYR D 93 ARG 0.001 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 576) hydrogen bonds : angle 3.90709 ( 1692) covalent geometry : bond 0.00238 (14344) covalent geometry : angle 0.63910 (19552) ********************** 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 470 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 1.666 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: 0.7478 (m) cc_final: 0.7102 (m) REVERT: A 138 LYS cc_start: 0.7507 (ptpt) cc_final: 0.7242 (ptpt) REVERT: A 158 MET cc_start: 0.7576 (tpt) cc_final: 0.6974 (tpt) REVERT: A 199 MET cc_start: 0.7477 (mtt) cc_final: 0.7063 (mtp) REVERT: A 303 LEU cc_start: 0.7793 (tp) cc_final: 0.7357 (tp) REVERT: A 376 PHE cc_start: 0.8348 (t80) cc_final: 0.8121 (t80) REVERT: A 379 GLN cc_start: 0.8395 (mt0) cc_final: 0.8024 (mt0) REVERT: A 477 CYS cc_start: 0.6254 (m) cc_final: 0.5903 (p) REVERT: B 11 THR cc_start: 0.7484 (m) cc_final: 0.7088 (m) REVERT: B 21 GLU cc_start: 0.7350 (tp30) cc_final: 0.7135 (tp30) REVERT: B 138 LYS cc_start: 0.7497 (ptpt) cc_final: 0.7231 (ptpt) REVERT: B 158 MET cc_start: 0.7662 (tpt) cc_final: 0.6961 (tpt) REVERT: B 199 MET cc_start: 0.7373 (mtt) cc_final: 0.7043 (mtp) REVERT: B 303 LEU cc_start: 0.7834 (tp) cc_final: 0.7392 (tp) REVERT: B 376 PHE cc_start: 0.8362 (t80) cc_final: 0.8104 (t80) REVERT: B 379 GLN cc_start: 0.8350 (mt0) cc_final: 0.7982 (mt0) REVERT: B 449 VAL cc_start: 0.7222 (t) cc_final: 0.6810 (p) REVERT: C 11 THR cc_start: 0.7374 (m) cc_final: 0.6983 (m) REVERT: C 138 LYS cc_start: 0.7464 (ptpt) cc_final: 0.7208 (ptpt) REVERT: C 158 MET cc_start: 0.7618 (tpt) cc_final: 0.7065 (tpt) REVERT: C 199 MET cc_start: 0.7377 (mtt) cc_final: 0.7033 (mtp) REVERT: C 286 PHE cc_start: 0.7514 (m-10) cc_final: 0.7312 (m-80) REVERT: C 303 LEU cc_start: 0.7787 (tp) cc_final: 0.7347 (tp) REVERT: C 326 GLN cc_start: 0.7372 (mt0) cc_final: 0.6435 (tm-30) REVERT: C 477 CYS cc_start: 0.6338 (m) cc_final: 0.5969 (p) REVERT: D 11 THR cc_start: 0.7502 (m) cc_final: 0.7063 (m) REVERT: D 21 GLU cc_start: 0.7338 (tp30) cc_final: 0.7121 (tp30) REVERT: D 158 MET cc_start: 0.7551 (tpt) cc_final: 0.7059 (tpt) REVERT: D 199 MET cc_start: 0.7376 (mtt) cc_final: 0.7008 (mtp) REVERT: D 303 LEU cc_start: 0.7779 (tp) cc_final: 0.7352 (tp) REVERT: D 477 CYS cc_start: 0.6371 (m) cc_final: 0.5979 (p) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.2267 time to fit residues: 161.0868 Evaluate side-chains 401 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 0.3980 chunk 103 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 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 123 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** D 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138112 restraints weight = 25499.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141281 restraints weight = 15767.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.143477 restraints weight = 10903.882| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.6254 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= 0.118 Angle : 0.659 9.572 19552 Z= 0.326 Chirality : 0.043 0.271 2288 Planarity : 0.006 0.090 2388 Dihedral : 5.190 39.967 1956 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.47 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1808 helix: -0.04 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.46 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 389 HIS 0.006 0.001 HIS B 200 PHE 0.025 0.002 PHE C 120 TYR 0.025 0.001 TYR B 28 ARG 0.004 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 576) hydrogen bonds : angle 3.98802 ( 1692) covalent geometry : bond 0.00269 (14344) covalent geometry : angle 0.65908 (19552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5394.63 seconds wall clock time: 98 minutes 29.33 seconds (5909.33 seconds total)