Starting phenix.real_space_refine on Wed Mar 4 14:54:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oxl_20220/03_2026/6oxl_20220.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oxl_20220/03_2026/6oxl_20220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oxl_20220/03_2026/6oxl_20220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oxl_20220/03_2026/6oxl_20220.map" model { file = "/net/cci-nas-00/data/ceres_data/6oxl_20220/03_2026/6oxl_20220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oxl_20220/03_2026/6oxl_20220.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.173 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 74 5.16 5 C 9236 2.51 5 N 2435 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14413 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4629 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 567} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 4465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4465 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 24, 'TRANS': 539} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "M" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3118 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 372} Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 3, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1190 Classifications: {'peptide': 141} Link IDs: {'TRANS': 140} Chain: "N" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 975 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "n" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 2.96, per 1000 atoms: 0.21 Number of scatterers: 14413 At special positions: 0 Unit cell: (100.92, 107.88, 124.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 1 15.00 O 2667 8.00 N 2435 7.00 C 9236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 448.0 milliseconds 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 11 sheets defined 57.9% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.654A pdb=" N VAL A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 45 Processing helix chain 'A' and resid 52 through 68 Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.787A pdb=" N LEU A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.598A pdb=" N ILE A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.925A pdb=" N ARG A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 139 removed outlier: 4.011A pdb=" N LEU A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 4.173A pdb=" N ALA A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 161 through 179 removed outlier: 3.530A pdb=" N LYS A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.693A pdb=" N VAL A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.669A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.678A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 removed outlier: 4.021A pdb=" N LEU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.591A pdb=" N TYR A 268 " --> pdb=" O LEU A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 273 through 291 removed outlier: 4.047A pdb=" N GLU A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 287 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 304 through 321 removed outlier: 3.814A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.655A pdb=" N LEU A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.779A pdb=" N HIS A 340 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.686A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.864A pdb=" N LYS A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.536A pdb=" N VAL A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.830A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.579A pdb=" N VAL A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 removed outlier: 3.528A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.500A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 removed outlier: 4.427A pdb=" N TYR A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.742A pdb=" N VAL A 497 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.512A pdb=" N ASN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.522A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.872A pdb=" N ASP A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 589 removed outlier: 3.571A pdb=" N GLN A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'B' and resid 13 through 23 removed outlier: 3.587A pdb=" N GLU B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 removed outlier: 3.585A pdb=" N ARG B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.641A pdb=" N VAL B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 removed outlier: 3.705A pdb=" N GLN B 59 " --> pdb=" O ASN B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 62 through 79 removed outlier: 3.532A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.752A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 85 " --> pdb=" O PRO B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 85' Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 100 through 113 removed outlier: 3.546A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 130 removed outlier: 5.118A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.532A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 151 removed outlier: 3.671A pdb=" N THR B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 170 removed outlier: 3.764A pdb=" N ASP B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 187 removed outlier: 4.051A pdb=" N ASN B 179 " --> pdb=" O MET B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 202 through 212 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 235 through 245 removed outlier: 3.631A pdb=" N SER B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 removed outlier: 4.005A pdb=" N SER B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 252 through 264 removed outlier: 4.131A pdb=" N VAL B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.695A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.583A pdb=" N TYR B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 4.119A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.665A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 357 " --> pdb=" O GLN B 353 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 removed outlier: 4.116A pdb=" N LYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 382 removed outlier: 3.627A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 399 removed outlier: 3.534A pdb=" N ASP B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 406 through 421 removed outlier: 4.853A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 434 through 436 No H-bonds generated for 'chain 'B' and resid 434 through 436' Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.638A pdb=" N TRP B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.600A pdb=" N VAL B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.889A pdb=" N GLN B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 531 removed outlier: 3.784A pdb=" N ARG B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.752A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 564 removed outlier: 3.615A pdb=" N GLU B 562 " --> pdb=" O THR B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.854A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 569 through 574' Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 27 through 36 removed outlier: 3.520A pdb=" N PHE M 32 " --> pdb=" O ALA M 28 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.766A pdb=" N CYS M 86 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA M 91 " --> pdb=" O ASP M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 103 removed outlier: 3.540A pdb=" N LYS M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN M 103 " --> pdb=" O GLU M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 112 removed outlier: 3.580A pdb=" N TYR M 109 " --> pdb=" O PHE M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 130 removed outlier: 4.007A pdb=" N LYS M 130 " --> pdb=" O THR M 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 36 removed outlier: 3.640A pdb=" N GLN S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS S 36 " --> pdb=" O ILE S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 96 removed outlier: 3.576A pdb=" N GLU S 82 " --> pdb=" O LEU S 78 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL S 90 " --> pdb=" O ASN S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 104 removed outlier: 3.500A pdb=" N ASP S 102 " --> pdb=" O CYS S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 117 removed outlier: 3.526A pdb=" N TYR S 111 " --> pdb=" O PHE S 107 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR S 112 " --> pdb=" O TYR S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 140 removed outlier: 3.666A pdb=" N MET S 137 " --> pdb=" O LYS S 133 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER S 140 " --> pdb=" O LEU S 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 35 removed outlier: 3.564A pdb=" N GLU N 34 " --> pdb=" O ARG N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 138 removed outlier: 3.745A pdb=" N PHE N 118 " --> pdb=" O ASP N 114 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS N 125 " --> pdb=" O ALA N 121 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE N 126 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS N 137 " --> pdb=" O CYS N 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 17 removed outlier: 3.567A pdb=" N PHE M 56 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'M' and resid 245 through 248 removed outlier: 6.301A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU M 183 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR M 431 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N MET M 185 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR M 433 " --> pdb=" O MET M 185 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE M 390 " --> pdb=" O SER M 428 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE M 430 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N MET M 388 " --> pdb=" O ILE M 430 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU M 432 " --> pdb=" O ILE M 386 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE M 386 " --> pdb=" O GLU M 432 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU M 316 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA M 359 " --> pdb=" O LEU M 316 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA M 350 " --> pdb=" O LYS M 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 245 through 248 removed outlier: 6.301A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 262 through 265 removed outlier: 3.828A pdb=" N LYS M 405 " --> pdb=" O LYS M 213 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR M 403 " --> pdb=" O GLY M 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 287 through 296 removed outlier: 3.879A pdb=" N VAL M 296 " --> pdb=" O LYS M 300 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M 300 " --> pdb=" O VAL M 296 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN M 334 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.483A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.483A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'N' and resid 67 through 72 removed outlier: 6.763A pdb=" N LEU N 59 " --> pdb=" O PHE N 68 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN N 70 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE N 57 " --> pdb=" O GLN N 70 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA N 55 " --> pdb=" O PRO N 72 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP N 42 " --> pdb=" O HIS N 17 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS N 17 " --> pdb=" O TRP N 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY N 44 " --> pdb=" O GLU N 15 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS N 11 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA N 50 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL N 9 " --> pdb=" O ALA N 50 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1953 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4365 1.33 - 1.45: 2041 1.45 - 1.57: 8147 1.57 - 1.69: 3 1.69 - 1.81: 113 Bond restraints: 14669 Sorted by residual: bond pdb=" OG1 TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.717 1.629 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" O1P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O2P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.528 1.612 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C GLU B 544 " pdb=" N LYS B 545 " ideal model delta sigma weight residual 1.329 1.267 0.061 1.60e-02 3.91e+03 1.47e+01 bond pdb=" C THR S 14 " pdb=" N ARG S 15 " ideal model delta sigma weight residual 1.332 1.297 0.034 1.29e-02 6.01e+03 7.10e+00 ... (remaining 14664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 19385 2.84 - 5.68: 416 5.68 - 8.51: 51 8.51 - 11.35: 8 11.35 - 14.19: 4 Bond angle restraints: 19864 Sorted by residual: angle pdb=" N ALA B 254 " pdb=" CA ALA B 254 " pdb=" C ALA B 254 " ideal model delta sigma weight residual 111.28 119.34 -8.06 1.09e+00 8.42e-01 5.47e+01 angle pdb=" N LEU A 447 " pdb=" CA LEU A 447 " pdb=" C LEU A 447 " ideal model delta sigma weight residual 111.28 106.29 4.99 1.09e+00 8.42e-01 2.10e+01 angle pdb=" C PHE S 52 " pdb=" N ARG S 53 " pdb=" CA ARG S 53 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C THR B 8 " pdb=" N THR B 9 " pdb=" CA THR B 9 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CA LEU A 532 " pdb=" CB LEU A 532 " pdb=" CG LEU A 532 " ideal model delta sigma weight residual 116.30 130.49 -14.19 3.50e+00 8.16e-02 1.64e+01 ... (remaining 19859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.34: 8538 15.34 - 30.69: 336 30.69 - 46.03: 78 46.03 - 61.37: 3 61.37 - 76.72: 2 Dihedral angle restraints: 8957 sinusoidal: 3592 harmonic: 5365 Sorted by residual: dihedral pdb=" CA GLN B 154 " pdb=" C GLN B 154 " pdb=" N MET B 155 " pdb=" CA MET B 155 " ideal model delta harmonic sigma weight residual 180.00 150.87 29.13 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA CYS S 70 " pdb=" C CYS S 70 " pdb=" N VAL S 71 " pdb=" CA VAL S 71 " ideal model delta harmonic sigma weight residual 180.00 -153.22 -26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA TRP M 421 " pdb=" C TRP M 421 " pdb=" N VAL M 422 " pdb=" CA VAL M 422 " ideal model delta harmonic sigma weight residual 180.00 156.12 23.88 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 8954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1667 0.059 - 0.117: 530 0.117 - 0.176: 104 0.176 - 0.234: 11 0.234 - 0.293: 2 Chirality restraints: 2314 Sorted by residual: chirality pdb=" CB ILE M 355 " pdb=" CA ILE M 355 " pdb=" CG1 ILE M 355 " pdb=" CG2 ILE M 355 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ALA B 254 " pdb=" N ALA B 254 " pdb=" C ALA B 254 " pdb=" CB ALA B 254 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASP M 282 " pdb=" N ASP M 282 " pdb=" C ASP M 282 " pdb=" CB ASP M 282 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2311 not shown) Planarity restraints: 2522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO N 22 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO N 23 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO N 23 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO N 23 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 245 " -0.049 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO B 246 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 246 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 246 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 421 " -0.023 2.00e-02 2.50e+03 1.64e-02 6.72e+00 pdb=" CG TRP M 421 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP M 421 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP M 421 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 421 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP M 421 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP M 421 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 421 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 421 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP M 421 " -0.001 2.00e-02 2.50e+03 ... (remaining 2519 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3324 2.77 - 3.30: 12895 3.30 - 3.83: 23047 3.83 - 4.37: 28410 4.37 - 4.90: 47768 Nonbonded interactions: 115444 Sorted by model distance: nonbonded pdb=" OE2 GLU M 179 " pdb=" OH TYR M 277 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU A 494 " pdb=" OG1 THR A 537 " model vdw 2.240 3.040 nonbonded pdb=" O PHE M 287 " pdb=" OH TYR M 431 " model vdw 2.255 3.040 nonbonded pdb=" NE2 GLN B 348 " pdb=" OE1 GLN B 386 " model vdw 2.271 3.120 nonbonded pdb=" OH TYR B 328 " pdb=" OD1 ASP N 117 " model vdw 2.273 3.040 ... (remaining 115439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.010 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 0.094 14669 Z= 0.413 Angle : 1.086 14.188 19864 Z= 0.611 Chirality : 0.058 0.293 2314 Planarity : 0.007 0.073 2522 Dihedral : 9.339 76.719 5457 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.06 % Allowed : 0.95 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.46 (0.14), residues: 1772 helix: -4.63 (0.06), residues: 965 sheet: -1.75 (0.36), residues: 193 loop : -1.99 (0.21), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 579 TYR 0.036 0.004 TYR B 455 PHE 0.040 0.004 PHE S 67 TRP 0.045 0.005 TRP M 421 HIS 0.014 0.002 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.01008 (14669) covalent geometry : angle 1.08622 (19864) hydrogen bonds : bond 0.29972 ( 651) hydrogen bonds : angle 10.82116 ( 1953) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8389 (mmmt) REVERT: A 77 MET cc_start: 0.8564 (tpp) cc_final: 0.8305 (tpp) REVERT: A 114 ASN cc_start: 0.8569 (t0) cc_final: 0.8247 (t0) REVERT: A 128 MET cc_start: 0.8407 (mtm) cc_final: 0.8159 (mtp) REVERT: B 205 ASN cc_start: 0.8699 (t0) cc_final: 0.8463 (m-40) REVERT: B 340 ASP cc_start: 0.9122 (t0) cc_final: 0.8690 (t0) REVERT: B 344 ARG cc_start: 0.8523 (mtt90) cc_final: 0.8303 (mtt-85) REVERT: B 384 VAL cc_start: 0.8929 (t) cc_final: 0.8621 (m) REVERT: B 408 GLN cc_start: 0.8502 (mt0) cc_final: 0.8217 (mt0) REVERT: B 565 CYS cc_start: 0.9052 (m) cc_final: 0.8632 (t) REVERT: M 218 ASP cc_start: 0.8217 (m-30) cc_final: 0.7809 (p0) REVERT: M 282 ASP cc_start: 0.8869 (p0) cc_final: 0.8626 (p0) REVERT: M 298 ARG cc_start: 0.8095 (ptp90) cc_final: 0.7588 (mtt180) REVERT: S 1 MET cc_start: 0.8369 (ptm) cc_final: 0.8065 (ptt) REVERT: S 21 MET cc_start: 0.8305 (mtp) cc_final: 0.8080 (mtp) REVERT: N 53 LYS cc_start: 0.8746 (mttt) cc_final: 0.8431 (mmtt) REVERT: N 61 ASP cc_start: 0.8215 (t0) cc_final: 0.7824 (m-30) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.1492 time to fit residues: 55.2401 Evaluate side-chains 155 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 76 HIS A 81 ASN A 92 GLN A 200 HIS A 216 GLN A 218 ASN ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 ASN A 568 GLN B 56 ASN B 75 ASN B 200 ASN B 203 ASN B 250 HIS B 386 GLN M 27 ASN M 135 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 125 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114351 restraints weight = 23544.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117916 restraints weight = 12698.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.120275 restraints weight = 8091.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121860 restraints weight = 5721.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122989 restraints weight = 4353.453| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14669 Z= 0.150 Angle : 0.642 12.662 19864 Z= 0.336 Chirality : 0.043 0.161 2314 Planarity : 0.005 0.065 2522 Dihedral : 5.567 27.835 1956 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.32 % Allowed : 5.93 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.17), residues: 1772 helix: -2.92 (0.12), residues: 983 sheet: -1.74 (0.32), residues: 225 loop : -1.37 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 388 TYR 0.015 0.002 TYR A 412 PHE 0.017 0.002 PHE M 81 TRP 0.018 0.002 TRP M 353 HIS 0.008 0.001 HIS M 416 Details of bonding type rmsd covalent geometry : bond 0.00338 (14669) covalent geometry : angle 0.64152 (19864) hydrogen bonds : bond 0.04837 ( 651) hydrogen bonds : angle 5.73407 ( 1953) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.547 Fit side-chains REVERT: A 118 ASN cc_start: 0.7772 (m-40) cc_final: 0.7381 (t0) REVERT: A 128 MET cc_start: 0.8076 (mtm) cc_final: 0.7814 (mtp) REVERT: B 29 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8302 (mppt) REVERT: M 410 LYS cc_start: 0.7046 (mmtt) cc_final: 0.6064 (ptmt) REVERT: N 53 LYS cc_start: 0.8465 (mttt) cc_final: 0.8238 (mmtt) REVERT: N 54 VAL cc_start: 0.8865 (t) cc_final: 0.8627 (p) REVERT: N 70 GLN cc_start: 0.8094 (tt0) cc_final: 0.7761 (tt0) REVERT: N 76 PHE cc_start: 0.7417 (t80) cc_final: 0.7203 (t80) REVERT: N 138 GLN cc_start: 0.7003 (mm110) cc_final: 0.6735 (tp40) outliers start: 21 outliers final: 9 residues processed: 185 average time/residue: 0.1284 time to fit residues: 34.0978 Evaluate side-chains 146 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 188 TRP Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 23 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS S 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115254 restraints weight = 23386.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118851 restraints weight = 12668.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121211 restraints weight = 8096.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122812 restraints weight = 5740.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123904 restraints weight = 4374.807| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14669 Z= 0.124 Angle : 0.565 11.306 19864 Z= 0.290 Chirality : 0.042 0.204 2314 Planarity : 0.004 0.063 2522 Dihedral : 4.970 26.378 1956 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 1.32 % Allowed : 7.31 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.18), residues: 1772 helix: -1.76 (0.14), residues: 995 sheet: -1.48 (0.31), residues: 234 loop : -0.88 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 344 TYR 0.014 0.001 TYR N 56 PHE 0.019 0.001 PHE N 135 TRP 0.011 0.001 TRP M 421 HIS 0.006 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00289 (14669) covalent geometry : angle 0.56502 (19864) hydrogen bonds : bond 0.03593 ( 651) hydrogen bonds : angle 5.00166 ( 1953) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.8103 (mtm) cc_final: 0.7899 (mtt) REVERT: B 29 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8389 (mppt) REVERT: B 83 MET cc_start: 0.7223 (ttp) cc_final: 0.6889 (ttp) REVERT: B 448 MET cc_start: 0.8058 (tpp) cc_final: 0.7500 (tpt) REVERT: M 282 ASP cc_start: 0.8773 (p0) cc_final: 0.8522 (p0) REVERT: M 410 LYS cc_start: 0.7012 (mmtt) cc_final: 0.6151 (ptmt) REVERT: N 53 LYS cc_start: 0.8469 (mttt) cc_final: 0.8185 (mmtt) outliers start: 21 outliers final: 12 residues processed: 176 average time/residue: 0.1169 time to fit residues: 30.6204 Evaluate side-chains 147 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 74 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112289 restraints weight = 22929.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115821 restraints weight = 12089.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118100 restraints weight = 7561.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119630 restraints weight = 5292.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.120710 restraints weight = 3992.949| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14669 Z= 0.130 Angle : 0.545 11.147 19864 Z= 0.276 Chirality : 0.042 0.182 2314 Planarity : 0.004 0.053 2522 Dihedral : 4.748 25.142 1956 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 1.51 % Allowed : 7.76 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.19), residues: 1772 helix: -1.21 (0.15), residues: 994 sheet: -1.35 (0.31), residues: 235 loop : -0.62 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.012 0.001 TYR S 80 PHE 0.016 0.001 PHE S 4 TRP 0.010 0.001 TRP M 421 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00308 (14669) covalent geometry : angle 0.54536 (19864) hydrogen bonds : bond 0.03260 ( 651) hydrogen bonds : angle 4.70482 ( 1953) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 128 MET cc_start: 0.8135 (mtm) cc_final: 0.7923 (mtt) REVERT: B 71 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8335 (mm) REVERT: B 216 GLU cc_start: 0.7214 (pm20) cc_final: 0.6984 (pm20) REVERT: B 448 MET cc_start: 0.8090 (tpp) cc_final: 0.7510 (tpt) REVERT: M 410 LYS cc_start: 0.7051 (mmtt) cc_final: 0.6178 (ptmt) REVERT: S 33 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7788 (mm-30) REVERT: N 53 LYS cc_start: 0.8538 (mttt) cc_final: 0.8218 (mmtt) REVERT: N 61 ASP cc_start: 0.7601 (m-30) cc_final: 0.7200 (m-30) outliers start: 24 outliers final: 13 residues processed: 163 average time/residue: 0.1200 time to fit residues: 29.0650 Evaluate side-chains 155 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 60 optimal weight: 6.9990 chunk 98 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 74 optimal weight: 0.0470 chunk 48 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS ** M 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115353 restraints weight = 23180.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118913 restraints weight = 12348.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121289 restraints weight = 7823.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122801 restraints weight = 5479.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123960 restraints weight = 4171.095| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14669 Z= 0.101 Angle : 0.518 10.436 19864 Z= 0.263 Chirality : 0.041 0.152 2314 Planarity : 0.004 0.052 2522 Dihedral : 4.510 24.085 1956 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.13 % Allowed : 8.51 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.20), residues: 1772 helix: -0.68 (0.16), residues: 994 sheet: -1.14 (0.32), residues: 236 loop : -0.47 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.013 0.001 TYR S 80 PHE 0.015 0.001 PHE S 4 TRP 0.010 0.001 TRP M 64 HIS 0.006 0.001 HIS M 10 Details of bonding type rmsd covalent geometry : bond 0.00232 (14669) covalent geometry : angle 0.51826 (19864) hydrogen bonds : bond 0.02997 ( 651) hydrogen bonds : angle 4.48731 ( 1953) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.7604 (tpp) cc_final: 0.7327 (tpp) REVERT: B 264 MET cc_start: 0.8070 (mmm) cc_final: 0.7803 (mmm) REVERT: B 448 MET cc_start: 0.8121 (tpp) cc_final: 0.7530 (tpt) REVERT: M 282 ASP cc_start: 0.8752 (p0) cc_final: 0.8477 (p0) REVERT: M 410 LYS cc_start: 0.6997 (mmtt) cc_final: 0.6146 (ptmt) REVERT: S 33 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7885 (mm-30) REVERT: N 53 LYS cc_start: 0.8535 (mttt) cc_final: 0.8188 (mmtt) REVERT: N 61 ASP cc_start: 0.7603 (m-30) cc_final: 0.7241 (m-30) outliers start: 18 outliers final: 9 residues processed: 172 average time/residue: 0.1121 time to fit residues: 29.2689 Evaluate side-chains 151 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 154 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A 550 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 GLN S 8 GLN S 46 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.124052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108417 restraints weight = 23785.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111939 restraints weight = 13063.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114273 restraints weight = 8440.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115862 restraints weight = 6050.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.116919 restraints weight = 4662.755| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 14669 Z= 0.241 Angle : 0.636 10.412 19864 Z= 0.320 Chirality : 0.046 0.189 2314 Planarity : 0.004 0.050 2522 Dihedral : 4.737 23.572 1956 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.02 % Allowed : 8.32 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.20), residues: 1772 helix: -0.72 (0.16), residues: 993 sheet: -1.16 (0.33), residues: 232 loop : -0.56 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 18 TYR 0.013 0.002 TYR A 88 PHE 0.017 0.002 PHE S 49 TRP 0.017 0.002 TRP A 462 HIS 0.006 0.001 HIS M 10 Details of bonding type rmsd covalent geometry : bond 0.00589 (14669) covalent geometry : angle 0.63608 (19864) hydrogen bonds : bond 0.03468 ( 651) hydrogen bonds : angle 4.69468 ( 1953) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.518 Fit side-chains REVERT: A 77 MET cc_start: 0.7749 (tpp) cc_final: 0.7470 (tpp) REVERT: B 264 MET cc_start: 0.8054 (mmm) cc_final: 0.7793 (mmm) REVERT: B 282 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8431 (mtmm) REVERT: B 448 MET cc_start: 0.8157 (tpp) cc_final: 0.7540 (tpt) REVERT: M 410 LYS cc_start: 0.7289 (mmtt) cc_final: 0.6401 (ptmt) REVERT: N 53 LYS cc_start: 0.8521 (mttt) cc_final: 0.8197 (mmtt) REVERT: N 70 GLN cc_start: 0.8070 (tt0) cc_final: 0.7854 (tt0) outliers start: 32 outliers final: 21 residues processed: 168 average time/residue: 0.1225 time to fit residues: 30.3058 Evaluate side-chains 162 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 149 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 123 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 165 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112660 restraints weight = 23172.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116252 restraints weight = 12444.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.118612 restraints weight = 7890.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120198 restraints weight = 5571.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121266 restraints weight = 4226.842| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14669 Z= 0.110 Angle : 0.533 10.534 19864 Z= 0.271 Chirality : 0.042 0.209 2314 Planarity : 0.004 0.047 2522 Dihedral : 4.491 23.290 1956 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.32 % Allowed : 8.89 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.20), residues: 1772 helix: -0.35 (0.16), residues: 1002 sheet: -0.99 (0.32), residues: 231 loop : -0.47 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.015 0.001 TYR S 80 PHE 0.016 0.001 PHE S 4 TRP 0.010 0.001 TRP M 421 HIS 0.005 0.001 HIS M 10 Details of bonding type rmsd covalent geometry : bond 0.00260 (14669) covalent geometry : angle 0.53299 (19864) hydrogen bonds : bond 0.02957 ( 651) hydrogen bonds : angle 4.43023 ( 1953) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.553 Fit side-chains REVERT: B 264 MET cc_start: 0.7997 (mmm) cc_final: 0.7753 (mmm) REVERT: B 448 MET cc_start: 0.8124 (tpp) cc_final: 0.7526 (tpt) REVERT: M 282 ASP cc_start: 0.8744 (p0) cc_final: 0.8421 (p0) REVERT: M 410 LYS cc_start: 0.7141 (mmtt) cc_final: 0.6281 (ptmt) REVERT: S 77 ASN cc_start: 0.8879 (p0) cc_final: 0.8541 (p0) REVERT: N 53 LYS cc_start: 0.8452 (mttt) cc_final: 0.8179 (mmtt) REVERT: N 62 ARG cc_start: 0.5706 (OUTLIER) cc_final: 0.5350 (ptp-170) REVERT: N 70 GLN cc_start: 0.8054 (tt0) cc_final: 0.7830 (tt0) outliers start: 21 outliers final: 13 residues processed: 162 average time/residue: 0.1154 time to fit residues: 28.2989 Evaluate side-chains 154 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 62 ARG Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 80 optimal weight: 0.0070 chunk 97 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113677 restraints weight = 23182.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.117232 restraints weight = 12436.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119553 restraints weight = 7862.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121061 restraints weight = 5544.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122191 restraints weight = 4230.444| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14669 Z= 0.111 Angle : 0.531 9.846 19864 Z= 0.266 Chirality : 0.042 0.210 2314 Planarity : 0.004 0.047 2522 Dihedral : 4.371 23.174 1956 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.45 % Allowed : 9.14 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.20), residues: 1772 helix: -0.11 (0.16), residues: 1001 sheet: -0.88 (0.33), residues: 231 loop : -0.43 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.014 0.001 TYR S 80 PHE 0.014 0.001 PHE S 49 TRP 0.011 0.001 TRP A 462 HIS 0.004 0.001 HIS M 10 Details of bonding type rmsd covalent geometry : bond 0.00264 (14669) covalent geometry : angle 0.53090 (19864) hydrogen bonds : bond 0.02890 ( 651) hydrogen bonds : angle 4.33205 ( 1953) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.610 Fit side-chains REVERT: A 194 HIS cc_start: 0.7820 (t70) cc_final: 0.7437 (t-90) REVERT: B 71 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7987 (mp) REVERT: B 264 MET cc_start: 0.8012 (mmm) cc_final: 0.7775 (mmm) REVERT: B 448 MET cc_start: 0.8142 (tpp) cc_final: 0.7516 (tpt) REVERT: M 410 LYS cc_start: 0.7141 (mmtt) cc_final: 0.6249 (ptmt) REVERT: N 47 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7606 (mtm-85) REVERT: N 53 LYS cc_start: 0.8470 (mttt) cc_final: 0.8152 (mmtt) REVERT: N 56 TYR cc_start: 0.7780 (m-80) cc_final: 0.7496 (m-80) outliers start: 23 outliers final: 16 residues processed: 161 average time/residue: 0.1212 time to fit residues: 29.2169 Evaluate side-chains 159 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 108 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 127 optimal weight: 0.0970 chunk 141 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 ASN M 57 HIS ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112268 restraints weight = 23397.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115793 restraints weight = 12524.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118137 restraints weight = 7918.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119677 restraints weight = 5560.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.120694 restraints weight = 4229.510| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14669 Z= 0.145 Angle : 0.553 9.610 19864 Z= 0.278 Chirality : 0.043 0.206 2314 Planarity : 0.004 0.046 2522 Dihedral : 4.395 23.451 1956 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 1.70 % Allowed : 9.21 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1772 helix: -0.08 (0.16), residues: 1002 sheet: -0.83 (0.33), residues: 231 loop : -0.40 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 62 TYR 0.013 0.001 TYR S 80 PHE 0.016 0.001 PHE S 49 TRP 0.019 0.001 TRP A 462 HIS 0.004 0.001 HIS M 10 Details of bonding type rmsd covalent geometry : bond 0.00352 (14669) covalent geometry : angle 0.55328 (19864) hydrogen bonds : bond 0.02958 ( 651) hydrogen bonds : angle 4.35142 ( 1953) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.515 Fit side-chains REVERT: A 194 HIS cc_start: 0.7820 (t70) cc_final: 0.7444 (t-90) REVERT: B 71 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7995 (mp) REVERT: B 264 MET cc_start: 0.8034 (mmm) cc_final: 0.7792 (mmm) REVERT: B 448 MET cc_start: 0.8165 (tpp) cc_final: 0.7554 (tpt) REVERT: M 282 ASP cc_start: 0.8803 (p0) cc_final: 0.8459 (p0) REVERT: M 410 LYS cc_start: 0.7178 (mmtt) cc_final: 0.6280 (ptmt) REVERT: N 53 LYS cc_start: 0.8474 (mttt) cc_final: 0.8144 (mmtt) outliers start: 27 outliers final: 20 residues processed: 163 average time/residue: 0.1160 time to fit residues: 28.3864 Evaluate side-chains 163 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 140 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 134 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 0.0670 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113344 restraints weight = 23062.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116937 restraints weight = 12426.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119325 restraints weight = 7855.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120899 restraints weight = 5515.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.122039 restraints weight = 4192.229| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14669 Z= 0.114 Angle : 0.530 9.489 19864 Z= 0.268 Chirality : 0.042 0.211 2314 Planarity : 0.003 0.046 2522 Dihedral : 4.304 23.131 1956 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 1.13 % Allowed : 9.71 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1772 helix: 0.12 (0.16), residues: 1001 sheet: -0.69 (0.34), residues: 231 loop : -0.34 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 62 TYR 0.015 0.001 TYR S 80 PHE 0.017 0.001 PHE S 4 TRP 0.018 0.001 TRP A 462 HIS 0.006 0.001 HIS M 10 Details of bonding type rmsd covalent geometry : bond 0.00272 (14669) covalent geometry : angle 0.52972 (19864) hydrogen bonds : bond 0.02847 ( 651) hydrogen bonds : angle 4.28524 ( 1953) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3544 Ramachandran restraints generated. 1772 Oldfield, 0 Emsley, 1772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.410 Fit side-chains REVERT: A 194 HIS cc_start: 0.7703 (t70) cc_final: 0.7355 (t-90) REVERT: A 478 TYR cc_start: 0.7871 (t80) cc_final: 0.7619 (t80) REVERT: B 71 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8015 (mp) REVERT: B 264 MET cc_start: 0.8031 (mmm) cc_final: 0.7778 (mmm) REVERT: B 448 MET cc_start: 0.8142 (tpp) cc_final: 0.7519 (tpt) REVERT: M 408 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7622 (tm-30) REVERT: M 417 ASP cc_start: 0.7295 (m-30) cc_final: 0.6959 (t0) REVERT: N 53 LYS cc_start: 0.8450 (mttt) cc_final: 0.8124 (mmtt) outliers start: 18 outliers final: 16 residues processed: 167 average time/residue: 0.1256 time to fit residues: 30.6475 Evaluate side-chains 166 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 328 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 84 ILE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 73 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 14 optimal weight: 0.9990 chunk 169 optimal weight: 0.0060 chunk 95 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113952 restraints weight = 23232.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117529 restraints weight = 12410.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.119860 restraints weight = 7815.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.121433 restraints weight = 5500.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122552 restraints weight = 4159.095| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14669 Z= 0.112 Angle : 0.532 9.180 19864 Z= 0.268 Chirality : 0.042 0.206 2314 Planarity : 0.003 0.046 2522 Dihedral : 4.248 21.074 1956 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 1.32 % Allowed : 9.84 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1772 helix: 0.25 (0.16), residues: 995 sheet: -0.67 (0.34), residues: 231 loop : -0.34 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 62 TYR 0.014 0.001 TYR S 80 PHE 0.016 0.001 PHE S 4 TRP 0.016 0.001 TRP A 462 HIS 0.006 0.001 HIS M 10 Details of bonding type rmsd covalent geometry : bond 0.00267 (14669) covalent geometry : angle 0.53232 (19864) hydrogen bonds : bond 0.02803 ( 651) hydrogen bonds : angle 4.23925 ( 1953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1937.74 seconds wall clock time: 34 minutes 31.02 seconds (2071.02 seconds total)