Starting phenix.real_space_refine on Wed Jul 30 10:10:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7soy_25363/07_2025/7soy_25363.cif Found real_map, /net/cci-nas-00/data/ceres_data/7soy_25363/07_2025/7soy_25363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7soy_25363/07_2025/7soy_25363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7soy_25363/07_2025/7soy_25363.map" model { file = "/net/cci-nas-00/data/ceres_data/7soy_25363/07_2025/7soy_25363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7soy_25363/07_2025/7soy_25363.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 7799 2.51 5 N 2053 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12180 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4543 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain: "B" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2963 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 22, 'TRANS': 332} Chain breaks: 1 Chain: "C" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2322 Classifications: {'peptide': 288} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 276} Chain: "P" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2352 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 15, 'TRANS': 287} Chain breaks: 2 Time building chain proxies: 9.03, per 1000 atoms: 0.74 Number of scatterers: 12180 At special positions: 0 Unit cell: (113.95, 112.36, 108.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2256 8.00 N 2053 7.00 C 7799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2916 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 6 sheets defined 73.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 50 through 59 removed outlier: 3.636A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 81 through 84 removed outlier: 4.142A pdb=" N GLU A 84 " --> pdb=" O GLY A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 84' Processing helix chain 'A' and resid 85 through 99 removed outlier: 3.789A pdb=" N LEU A 89 " --> pdb=" O TYR A 85 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 3.764A pdb=" N LEU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 119 removed outlier: 3.770A pdb=" N ARG A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 140 through 155 removed outlier: 3.830A pdb=" N ARG A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER A 152 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 178 through 196 removed outlier: 4.427A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 4.292A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 235 removed outlier: 3.850A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 4.324A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.633A pdb=" N ARG A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.573A pdb=" N ALA A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.922A pdb=" N CYS A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 4.414A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.909A pdb=" N ILE A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.762A pdb=" N ARG A 381 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.795A pdb=" N LEU A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.664A pdb=" N ARG A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.544A pdb=" N LYS A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 452 removed outlier: 3.923A pdb=" N LEU A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 474 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.916A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.681A pdb=" N LYS A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.670A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.513A pdb=" N HIS A 520 " --> pdb=" O ILE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.866A pdb=" N THR A 524 " --> pdb=" O HIS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 569 Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'B' and resid 35 through 51 Processing helix chain 'B' and resid 62 through 83 Processing helix chain 'B' and resid 90 through 104 removed outlier: 4.338A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 196 through 214 Processing helix chain 'B' and resid 220 through 234 removed outlier: 3.866A pdb=" N GLY B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.672A pdb=" N HIS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 4.522A pdb=" N TYR B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Proline residue: B 265 - end of helix Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.613A pdb=" N MET B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 315 Processing helix chain 'B' and resid 316 through 336 removed outlier: 3.718A pdb=" N LYS B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Proline residue: B 326 - end of helix Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.783A pdb=" N TRP B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 362 removed outlier: 3.536A pdb=" N ASN B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 380 removed outlier: 3.995A pdb=" N ILE B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 383 through 401 Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 153 removed outlier: 3.604A pdb=" N TYR C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.858A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 removed outlier: 4.038A pdb=" N CYS C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.562A pdb=" N ARG C 268 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.542A pdb=" N TYR P 49 " --> pdb=" O PRO P 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 91 Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 127 through 143 Processing helix chain 'P' and resid 156 through 169 removed outlier: 3.524A pdb=" N ALA P 160 " --> pdb=" O ALA P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 190 Processing helix chain 'P' and resid 190 through 200 removed outlier: 3.610A pdb=" N MET P 194 " --> pdb=" O ALA P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 223 through 234 removed outlier: 3.911A pdb=" N VAL P 232 " --> pdb=" O ARG P 228 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY P 233 " --> pdb=" O VAL P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 290 through 302 removed outlier: 3.575A pdb=" N THR P 294 " --> pdb=" O GLU P 290 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP P 299 " --> pdb=" O GLU P 295 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLY P 300 " --> pdb=" O LYS P 296 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP P 301 " --> pdb=" O TYR P 297 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE P 302 " --> pdb=" O TRP P 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 304 through 312 Processing helix chain 'P' and resid 327 through 336 Processing helix chain 'P' and resid 350 through 355 removed outlier: 4.076A pdb=" N ALA P 355 " --> pdb=" O VAL P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 370 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.424A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.102A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N MET C 83 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N CYS C 55 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY C 56 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N ALA C 274 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'P' and resid 52 through 54 removed outlier: 6.098A pdb=" N VAL P 78 " --> pdb=" O MET P 151 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE P 153 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU P 80 " --> pdb=" O ILE P 153 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N HIS P 155 " --> pdb=" O LEU P 80 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU P 82 " --> pdb=" O HIS P 155 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU P 177 " --> pdb=" O LEU P 317 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU P 319 " --> pdb=" O LEU P 177 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET P 179 " --> pdb=" O LEU P 319 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN P 340 " --> pdb=" O LYS P 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 57 through 59 Processing sheet with id=AA6, first strand: chain 'P' and resid 235 through 237 719 hydrogen bonds defined for protein. 2127 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: 4.16 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3856 1.34 - 1.46: 1618 1.46 - 1.58: 6859 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 12444 Sorted by residual: bond pdb=" N VAL P 183 " pdb=" CA VAL P 183 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.19e-02 7.06e+03 8.36e+00 bond pdb=" N VAL P 120 " pdb=" CA VAL P 120 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.17e-02 7.31e+03 8.05e+00 bond pdb=" N ILE A 355 " pdb=" CA ILE A 355 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.94e+00 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 7.91e+00 bond pdb=" N CYS A 317 " pdb=" CA CYS A 317 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.33e-02 5.65e+03 7.57e+00 ... (remaining 12439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 16105 1.32 - 2.65: 597 2.65 - 3.97: 128 3.97 - 5.30: 39 5.30 - 6.62: 6 Bond angle restraints: 16875 Sorted by residual: angle pdb=" N LEU B 305 " pdb=" CA LEU B 305 " pdb=" C LEU B 305 " ideal model delta sigma weight residual 111.02 105.91 5.11 1.22e+00 6.72e-01 1.75e+01 angle pdb=" N LEU A 522 " pdb=" CA LEU A 522 " pdb=" C LEU A 522 " ideal model delta sigma weight residual 112.75 107.30 5.45 1.36e+00 5.41e-01 1.60e+01 angle pdb=" N LEU B 46 " pdb=" CA LEU B 46 " pdb=" C LEU B 46 " ideal model delta sigma weight residual 111.07 107.24 3.83 1.07e+00 8.73e-01 1.28e+01 angle pdb=" CA GLU A 197 " pdb=" C GLU A 197 " pdb=" O GLU A 197 " ideal model delta sigma weight residual 121.94 117.92 4.02 1.15e+00 7.56e-01 1.22e+01 angle pdb=" N LYS B 300 " pdb=" CA LYS B 300 " pdb=" C LYS B 300 " ideal model delta sigma weight residual 111.28 107.73 3.55 1.09e+00 8.42e-01 1.06e+01 ... (remaining 16870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 6884 16.96 - 33.92: 551 33.92 - 50.88: 87 50.88 - 67.84: 18 67.84 - 84.80: 9 Dihedral angle restraints: 7549 sinusoidal: 3065 harmonic: 4484 Sorted by residual: dihedral pdb=" CA TYR A 155 " pdb=" C TYR A 155 " pdb=" N PRO A 156 " pdb=" CA PRO A 156 " ideal model delta harmonic sigma weight residual -180.00 -157.58 -22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA MET B 324 " pdb=" C MET B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta harmonic sigma weight residual 180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP A 57 " pdb=" C ASP A 57 " pdb=" N THR A 58 " pdb=" CA THR A 58 " ideal model delta harmonic sigma weight residual 180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1497 0.047 - 0.094: 324 0.094 - 0.142: 81 0.142 - 0.189: 10 0.189 - 0.236: 4 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CA LEU B 305 " pdb=" N LEU B 305 " pdb=" C LEU B 305 " pdb=" CB LEU B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 13 " pdb=" N ILE A 13 " pdb=" C ILE A 13 " pdb=" CB ILE A 13 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU B 46 " pdb=" N LEU B 46 " pdb=" C LEU B 46 " pdb=" CB LEU B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.94e-01 ... (remaining 1913 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 349 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C ILE A 349 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE A 349 " 0.013 2.00e-02 2.50e+03 pdb=" N MET A 350 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU P 344 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO P 345 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO P 345 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO P 345 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS P 119 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C LYS P 119 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS P 119 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL P 120 " -0.009 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2199 2.76 - 3.30: 13422 3.30 - 3.83: 21774 3.83 - 4.37: 25935 4.37 - 4.90: 42156 Nonbonded interactions: 105486 Sorted by model distance: nonbonded pdb=" O LEU B 254 " pdb=" OH TYR B 263 " model vdw 2.231 3.040 nonbonded pdb=" O LEU C 23 " pdb=" OH TYR C 137 " model vdw 2.306 3.040 nonbonded pdb=" N VAL P 78 " pdb=" O PRO P 149 " model vdw 2.317 3.120 nonbonded pdb=" O LEU B 305 " pdb=" OH TYR B 349 " model vdw 2.318 3.040 nonbonded pdb=" O CYS P 312 " pdb=" NZ LYS P 316 " model vdw 2.326 3.120 ... (remaining 105481 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.560 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.003 0.037 12444 Z= 0.219 Angle : 0.627 6.621 16875 Z= 0.387 Chirality : 0.043 0.236 1916 Planarity : 0.004 0.048 2163 Dihedral : 12.631 84.797 4633 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.37 % Allowed : 0.37 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.22), residues: 1515 helix: 1.41 (0.16), residues: 1009 sheet: -0.46 (0.64), residues: 72 loop : 0.04 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 214 HIS 0.006 0.001 HIS C 230 PHE 0.019 0.001 PHE A 128 TYR 0.015 0.001 TYR A 426 ARG 0.004 0.000 ARG C 89 Details of bonding type rmsd hydrogen bonds : bond 0.14607 ( 719) hydrogen bonds : angle 5.78274 ( 2127) covalent geometry : bond 0.00338 (12444) covalent geometry : angle 0.62688 (16875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.9651 (m-30) cc_final: 0.9238 (p0) REVERT: A 426 TYR cc_start: 0.8978 (m-80) cc_final: 0.8374 (m-80) REVERT: A 489 MET cc_start: 0.9392 (tmm) cc_final: 0.9095 (tmm) REVERT: B 356 MET cc_start: 0.9386 (mmp) cc_final: 0.9131 (mmt) REVERT: C 267 TYR cc_start: 0.8938 (m-80) cc_final: 0.8624 (m-80) REVERT: P 131 MET cc_start: 0.9451 (mmt) cc_final: 0.9058 (mmm) REVERT: P 142 MET cc_start: 0.9750 (tpp) cc_final: 0.9342 (tpp) REVERT: P 285 TYR cc_start: 0.9392 (m-80) cc_final: 0.9111 (m-80) REVERT: P 297 TYR cc_start: 0.7340 (m-80) cc_final: 0.6577 (t80) outliers start: 5 outliers final: 1 residues processed: 119 average time/residue: 0.3007 time to fit residues: 53.3365 Evaluate side-chains 78 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 172 ASN B 330 GLN ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.050944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.035432 restraints weight = 83150.842| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 5.51 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12444 Z= 0.169 Angle : 0.586 6.965 16875 Z= 0.307 Chirality : 0.040 0.150 1916 Planarity : 0.004 0.037 2163 Dihedral : 4.521 29.809 1644 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.59 % Allowed : 5.70 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1515 helix: 1.49 (0.16), residues: 1032 sheet: -0.69 (0.62), residues: 73 loop : 0.10 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP P 301 HIS 0.004 0.001 HIS C 230 PHE 0.015 0.001 PHE P 95 TYR 0.012 0.001 TYR B 138 ARG 0.003 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 719) hydrogen bonds : angle 4.93516 ( 2127) covalent geometry : bond 0.00359 (12444) covalent geometry : angle 0.58617 (16875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.9284 (m-80) cc_final: 0.8988 (m-80) REVERT: A 389 ASP cc_start: 0.9674 (m-30) cc_final: 0.9273 (p0) REVERT: B 98 MET cc_start: 0.8675 (tpp) cc_final: 0.8401 (tpp) REVERT: B 356 MET cc_start: 0.9287 (mmp) cc_final: 0.9048 (mmp) REVERT: C 267 TYR cc_start: 0.8958 (m-80) cc_final: 0.8654 (m-80) REVERT: P 131 MET cc_start: 0.9413 (mmt) cc_final: 0.9090 (mmm) REVERT: P 297 TYR cc_start: 0.7741 (m-80) cc_final: 0.7338 (t80) REVERT: P 301 TRP cc_start: 0.7885 (m-90) cc_final: 0.7519 (m-90) outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.2391 time to fit residues: 34.5883 Evaluate side-chains 74 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 177 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.0020 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 130 optimal weight: 0.0010 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN B 82 HIS B 401 ASN ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.051157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.035554 restraints weight = 83954.482| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 5.57 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12444 Z= 0.133 Angle : 0.547 7.798 16875 Z= 0.281 Chirality : 0.039 0.148 1916 Planarity : 0.004 0.034 2163 Dihedral : 4.346 25.692 1641 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.52 % Allowed : 8.00 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1515 helix: 1.51 (0.16), residues: 1032 sheet: -0.77 (0.62), residues: 73 loop : 0.17 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 214 HIS 0.003 0.001 HIS C 230 PHE 0.020 0.001 PHE A 76 TYR 0.012 0.001 TYR A 426 ARG 0.004 0.000 ARG P 228 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 719) hydrogen bonds : angle 4.67664 ( 2127) covalent geometry : bond 0.00282 (12444) covalent geometry : angle 0.54675 (16875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9338 (m-10) cc_final: 0.9108 (m-10) REVERT: A 85 TYR cc_start: 0.9272 (m-80) cc_final: 0.8965 (m-80) REVERT: A 389 ASP cc_start: 0.9686 (m-30) cc_final: 0.9255 (p0) REVERT: B 98 MET cc_start: 0.8831 (tpp) cc_final: 0.8622 (tpp) REVERT: C 66 MET cc_start: 0.9048 (tpt) cc_final: 0.8757 (tpp) REVERT: C 267 TYR cc_start: 0.8973 (m-80) cc_final: 0.8645 (m-80) REVERT: P 131 MET cc_start: 0.9375 (mmt) cc_final: 0.9058 (mmm) REVERT: P 297 TYR cc_start: 0.7487 (m-80) cc_final: 0.7064 (t80) REVERT: P 301 TRP cc_start: 0.7622 (m-90) cc_final: 0.7013 (m-90) REVERT: P 307 ASN cc_start: 0.9273 (t0) cc_final: 0.9061 (p0) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.2464 time to fit residues: 34.6043 Evaluate side-chains 79 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 177 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** P 223 ASN ** 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 = 0.3490 r_free = 0.3490 target = 0.050844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.035301 restraints weight = 83763.135| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 5.44 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12444 Z= 0.134 Angle : 0.544 7.044 16875 Z= 0.279 Chirality : 0.039 0.211 1916 Planarity : 0.004 0.044 2163 Dihedral : 4.319 25.189 1641 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.59 % Allowed : 9.70 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.22), residues: 1515 helix: 1.55 (0.16), residues: 1030 sheet: -0.84 (0.62), residues: 73 loop : 0.14 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 214 HIS 0.005 0.001 HIS A 119 PHE 0.018 0.001 PHE B 141 TYR 0.013 0.001 TYR A 261 ARG 0.006 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 719) hydrogen bonds : angle 4.61470 ( 2127) covalent geometry : bond 0.00288 (12444) covalent geometry : angle 0.54377 (16875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.9227 (m-80) cc_final: 0.8899 (m-80) REVERT: A 389 ASP cc_start: 0.9634 (m-30) cc_final: 0.9258 (p0) REVERT: B 98 MET cc_start: 0.8847 (tpp) cc_final: 0.8577 (tpp) REVERT: B 324 MET cc_start: 0.8861 (mtt) cc_final: 0.8336 (mmm) REVERT: B 356 MET cc_start: 0.9472 (mmp) cc_final: 0.9017 (mmt) REVERT: C 66 MET cc_start: 0.9021 (tpt) cc_final: 0.8682 (tpp) REVERT: C 267 TYR cc_start: 0.9016 (m-80) cc_final: 0.8667 (m-80) REVERT: P 131 MET cc_start: 0.9376 (mmt) cc_final: 0.9061 (mmm) REVERT: P 297 TYR cc_start: 0.7375 (m-80) cc_final: 0.6929 (t80) REVERT: P 301 TRP cc_start: 0.7678 (m-90) cc_final: 0.6990 (m-90) REVERT: P 307 ASN cc_start: 0.9284 (t0) cc_final: 0.9064 (p0) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.2391 time to fit residues: 30.4716 Evaluate side-chains 78 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 85 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 48 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 223 ASN ** 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 = 0.3519 r_free = 0.3519 target = 0.051562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.036113 restraints weight = 80859.699| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 5.50 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12444 Z= 0.105 Angle : 0.548 8.266 16875 Z= 0.275 Chirality : 0.039 0.174 1916 Planarity : 0.004 0.041 2163 Dihedral : 4.241 25.092 1641 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.67 % Allowed : 10.44 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1515 helix: 1.56 (0.16), residues: 1036 sheet: -0.80 (0.63), residues: 73 loop : 0.23 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 214 HIS 0.004 0.000 HIS A 119 PHE 0.016 0.001 PHE B 42 TYR 0.011 0.001 TYR A 426 ARG 0.004 0.000 ARG P 228 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 719) hydrogen bonds : angle 4.43521 ( 2127) covalent geometry : bond 0.00219 (12444) covalent geometry : angle 0.54762 (16875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9198 (m-80) cc_final: 0.8967 (m-80) REVERT: A 85 TYR cc_start: 0.9190 (m-80) cc_final: 0.8904 (m-80) REVERT: A 389 ASP cc_start: 0.9629 (m-30) cc_final: 0.9186 (p0) REVERT: A 427 MET cc_start: 0.9452 (tpt) cc_final: 0.9250 (tpt) REVERT: B 98 MET cc_start: 0.8840 (tpp) cc_final: 0.8558 (tpp) REVERT: B 324 MET cc_start: 0.8847 (mtt) cc_final: 0.8501 (mtt) REVERT: B 356 MET cc_start: 0.9492 (mmp) cc_final: 0.9046 (mmt) REVERT: C 66 MET cc_start: 0.8965 (tpt) cc_final: 0.8642 (tpp) REVERT: C 267 TYR cc_start: 0.9006 (m-80) cc_final: 0.8674 (m-80) REVERT: P 131 MET cc_start: 0.9400 (mmt) cc_final: 0.9088 (mmm) REVERT: P 297 TYR cc_start: 0.7275 (m-80) cc_final: 0.6783 (t80) REVERT: P 301 TRP cc_start: 0.7602 (m-90) cc_final: 0.6874 (m-90) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.2459 time to fit residues: 35.4323 Evaluate side-chains 77 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 86 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 147 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 223 ASN ** 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 = 0.3515 r_free = 0.3515 target = 0.051358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.035779 restraints weight = 81060.819| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 5.62 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12444 Z= 0.108 Angle : 0.561 13.601 16875 Z= 0.275 Chirality : 0.040 0.327 1916 Planarity : 0.004 0.040 2163 Dihedral : 4.189 24.918 1641 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.89 % Allowed : 11.56 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1515 helix: 1.61 (0.16), residues: 1027 sheet: -0.92 (0.60), residues: 78 loop : 0.21 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 214 HIS 0.007 0.001 HIS B 264 PHE 0.010 0.001 PHE A 287 TYR 0.012 0.001 TYR B 138 ARG 0.005 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 719) hydrogen bonds : angle 4.42065 ( 2127) covalent geometry : bond 0.00229 (12444) covalent geometry : angle 0.56054 (16875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9167 (m-10) cc_final: 0.8954 (m-80) REVERT: A 85 TYR cc_start: 0.9214 (m-80) cc_final: 0.8876 (m-80) REVERT: A 389 ASP cc_start: 0.9639 (m-30) cc_final: 0.9231 (p0) REVERT: A 427 MET cc_start: 0.9482 (tpt) cc_final: 0.9223 (tpp) REVERT: A 489 MET cc_start: 0.9538 (tmm) cc_final: 0.9194 (tmm) REVERT: A 520 HIS cc_start: 0.9272 (OUTLIER) cc_final: 0.8556 (m90) REVERT: A 538 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.9040 (p90) REVERT: B 98 MET cc_start: 0.8894 (tpp) cc_final: 0.8571 (tpp) REVERT: B 143 ARG cc_start: 0.8996 (tpt170) cc_final: 0.8748 (tpt90) REVERT: B 324 MET cc_start: 0.8873 (mtt) cc_final: 0.8546 (mtt) REVERT: B 356 MET cc_start: 0.9523 (mmp) cc_final: 0.9047 (mmt) REVERT: C 66 MET cc_start: 0.9015 (tpt) cc_final: 0.8661 (tpp) REVERT: C 267 TYR cc_start: 0.9048 (m-80) cc_final: 0.8712 (m-80) REVERT: P 131 MET cc_start: 0.9370 (mmt) cc_final: 0.9088 (mmm) REVERT: P 297 TYR cc_start: 0.7226 (m-80) cc_final: 0.6709 (t80) REVERT: P 301 TRP cc_start: 0.7583 (m-90) cc_final: 0.6837 (m-90) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 0.2691 time to fit residues: 36.9883 Evaluate side-chains 85 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 138 optimal weight: 6.9990 chunk 136 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 223 ASN ** 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 = 0.3454 r_free = 0.3454 target = 0.049608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.034042 restraints weight = 86702.496| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 5.42 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12444 Z= 0.210 Angle : 0.615 10.285 16875 Z= 0.309 Chirality : 0.040 0.208 1916 Planarity : 0.004 0.040 2163 Dihedral : 4.334 25.272 1641 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.74 % Allowed : 12.52 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1515 helix: 1.53 (0.16), residues: 1023 sheet: -1.19 (0.59), residues: 78 loop : 0.12 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 214 HIS 0.005 0.001 HIS C 118 PHE 0.015 0.001 PHE B 42 TYR 0.009 0.001 TYR A 426 ARG 0.005 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 719) hydrogen bonds : angle 4.66596 ( 2127) covalent geometry : bond 0.00442 (12444) covalent geometry : angle 0.61524 (16875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.9710 (tpm170) cc_final: 0.9493 (tpp-160) REVERT: A 85 TYR cc_start: 0.9182 (m-80) cc_final: 0.8822 (m-80) REVERT: A 350 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7791 (ptt) REVERT: A 389 ASP cc_start: 0.9607 (m-30) cc_final: 0.9199 (p0) REVERT: A 427 MET cc_start: 0.9406 (tpt) cc_final: 0.9150 (tpp) REVERT: A 520 HIS cc_start: 0.9218 (OUTLIER) cc_final: 0.8478 (m90) REVERT: B 98 MET cc_start: 0.8719 (tpp) cc_final: 0.8513 (tpp) REVERT: B 143 ARG cc_start: 0.8960 (tpt170) cc_final: 0.8617 (tpt90) REVERT: B 356 MET cc_start: 0.9476 (mmp) cc_final: 0.8998 (mmt) REVERT: C 66 MET cc_start: 0.8829 (tpt) cc_final: 0.8481 (tpp) REVERT: C 267 TYR cc_start: 0.9038 (m-80) cc_final: 0.8676 (m-80) REVERT: C 276 MET cc_start: 0.9085 (ttp) cc_final: 0.8699 (ttm) REVERT: P 131 MET cc_start: 0.9391 (mmt) cc_final: 0.9094 (mmm) REVERT: P 143 TYR cc_start: 0.8971 (m-80) cc_final: 0.8729 (m-80) REVERT: P 297 TYR cc_start: 0.7206 (m-80) cc_final: 0.6683 (t80) REVERT: P 301 TRP cc_start: 0.7540 (m-90) cc_final: 0.6817 (m-90) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.3240 time to fit residues: 41.0677 Evaluate side-chains 79 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 75 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 110 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 223 ASN ** 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 = 0.3501 r_free = 0.3501 target = 0.050884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035494 restraints weight = 84036.897| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 5.57 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12444 Z= 0.112 Angle : 0.589 14.408 16875 Z= 0.287 Chirality : 0.039 0.198 1916 Planarity : 0.004 0.042 2163 Dihedral : 4.239 25.336 1641 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.89 % Allowed : 12.59 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1515 helix: 1.59 (0.16), residues: 1034 sheet: -0.98 (0.61), residues: 77 loop : 0.19 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 214 HIS 0.004 0.001 HIS A 119 PHE 0.011 0.001 PHE B 42 TYR 0.007 0.001 TYR B 79 ARG 0.004 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 719) hydrogen bonds : angle 4.46371 ( 2127) covalent geometry : bond 0.00240 (12444) covalent geometry : angle 0.58899 (16875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.9083 (m-80) cc_final: 0.8804 (m-80) REVERT: A 85 TYR cc_start: 0.9239 (m-80) cc_final: 0.8867 (m-80) REVERT: A 389 ASP cc_start: 0.9654 (m-30) cc_final: 0.9247 (p0) REVERT: A 427 MET cc_start: 0.9493 (tpt) cc_final: 0.9225 (tpp) REVERT: A 520 HIS cc_start: 0.9278 (OUTLIER) cc_final: 0.8530 (m90) REVERT: A 538 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.9075 (p90) REVERT: B 98 MET cc_start: 0.8903 (tpp) cc_final: 0.8654 (tpp) REVERT: B 138 TYR cc_start: 0.9026 (m-80) cc_final: 0.8777 (m-80) REVERT: B 143 ARG cc_start: 0.9020 (tpt170) cc_final: 0.8661 (tpt90) REVERT: B 182 LEU cc_start: 0.9684 (mt) cc_final: 0.9452 (mt) REVERT: B 324 MET cc_start: 0.8913 (mtt) cc_final: 0.8381 (mmm) REVERT: B 356 MET cc_start: 0.9420 (mmp) cc_final: 0.9000 (mmp) REVERT: C 66 MET cc_start: 0.8966 (tpt) cc_final: 0.8583 (tpp) REVERT: C 245 MET cc_start: 0.8948 (mmm) cc_final: 0.8691 (mmm) REVERT: C 267 TYR cc_start: 0.9051 (m-80) cc_final: 0.8660 (m-80) REVERT: C 276 MET cc_start: 0.9222 (ttp) cc_final: 0.8893 (ttt) REVERT: P 131 MET cc_start: 0.9351 (mmt) cc_final: 0.9058 (mmm) REVERT: P 143 TYR cc_start: 0.8948 (m-80) cc_final: 0.8671 (m-80) REVERT: P 297 TYR cc_start: 0.7155 (m-80) cc_final: 0.6633 (t80) REVERT: P 301 TRP cc_start: 0.7507 (m-90) cc_final: 0.6784 (m-90) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.2102 time to fit residues: 29.3802 Evaluate side-chains 84 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 0.0030 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 0.0040 chunk 51 optimal weight: 0.1980 chunk 113 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 23 optimal weight: 0.0370 overall best weight: 0.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** P 223 ASN ** 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 = 0.3528 r_free = 0.3528 target = 0.051706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.036342 restraints weight = 81036.127| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 5.51 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12444 Z= 0.105 Angle : 0.598 12.840 16875 Z= 0.287 Chirality : 0.039 0.219 1916 Planarity : 0.004 0.044 2163 Dihedral : 4.181 24.765 1641 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.89 % Allowed : 12.74 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1515 helix: 1.59 (0.16), residues: 1030 sheet: -0.79 (0.63), residues: 77 loop : 0.21 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 214 HIS 0.004 0.000 HIS A 119 PHE 0.011 0.001 PHE B 42 TYR 0.009 0.001 TYR B 138 ARG 0.004 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 719) hydrogen bonds : angle 4.34342 ( 2127) covalent geometry : bond 0.00211 (12444) covalent geometry : angle 0.59779 (16875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.8953 (m-80) cc_final: 0.8694 (m-80) REVERT: A 85 TYR cc_start: 0.9216 (m-80) cc_final: 0.8829 (m-80) REVERT: A 291 MET cc_start: 0.9235 (ptt) cc_final: 0.9000 (ppp) REVERT: A 350 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7800 (ptt) REVERT: A 389 ASP cc_start: 0.9631 (m-30) cc_final: 0.9261 (p0) REVERT: A 427 MET cc_start: 0.9439 (tpt) cc_final: 0.9214 (tpp) REVERT: A 520 HIS cc_start: 0.9270 (OUTLIER) cc_final: 0.8536 (m90) REVERT: A 538 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.9074 (p90) REVERT: B 98 MET cc_start: 0.8867 (tpp) cc_final: 0.8598 (tpp) REVERT: B 324 MET cc_start: 0.8872 (mtt) cc_final: 0.8394 (mmm) REVERT: B 356 MET cc_start: 0.9347 (mmp) cc_final: 0.9026 (mmp) REVERT: C 66 MET cc_start: 0.8948 (tpt) cc_final: 0.8566 (tpp) REVERT: C 245 MET cc_start: 0.8894 (mmm) cc_final: 0.8660 (mmm) REVERT: C 267 TYR cc_start: 0.9033 (m-80) cc_final: 0.8635 (m-80) REVERT: C 276 MET cc_start: 0.9217 (ttp) cc_final: 0.8893 (ttt) REVERT: P 131 MET cc_start: 0.9353 (mmt) cc_final: 0.9056 (mmm) REVERT: P 143 TYR cc_start: 0.8940 (m-80) cc_final: 0.8648 (m-80) REVERT: P 297 TYR cc_start: 0.7148 (m-80) cc_final: 0.6595 (t80) REVERT: P 301 TRP cc_start: 0.7516 (m-90) cc_final: 0.6752 (m-90) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 0.2131 time to fit residues: 29.5479 Evaluate side-chains 83 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 122 optimal weight: 8.9990 chunk 140 optimal weight: 30.0000 chunk 59 optimal weight: 0.0010 chunk 21 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** P 223 ASN ** 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 = 0.3503 r_free = 0.3503 target = 0.051185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035717 restraints weight = 84200.340| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 5.52 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12444 Z= 0.117 Angle : 0.601 11.282 16875 Z= 0.291 Chirality : 0.039 0.189 1916 Planarity : 0.004 0.061 2163 Dihedral : 4.158 24.604 1641 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.81 % Allowed : 13.04 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.22), residues: 1515 helix: 1.59 (0.16), residues: 1030 sheet: -0.74 (0.63), residues: 77 loop : 0.18 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 214 HIS 0.003 0.001 HIS A 119 PHE 0.013 0.001 PHE B 104 TYR 0.010 0.001 TYR B 92 ARG 0.008 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 719) hydrogen bonds : angle 4.39762 ( 2127) covalent geometry : bond 0.00256 (12444) covalent geometry : angle 0.60110 (16875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.8949 (m-80) cc_final: 0.8686 (m-80) REVERT: A 85 TYR cc_start: 0.9233 (m-80) cc_final: 0.8844 (m-80) REVERT: A 291 MET cc_start: 0.9233 (ptt) cc_final: 0.9004 (ppp) REVERT: A 350 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8033 (ptt) REVERT: A 389 ASP cc_start: 0.9648 (m-30) cc_final: 0.9280 (p0) REVERT: A 427 MET cc_start: 0.9460 (tpt) cc_final: 0.9249 (tpp) REVERT: A 520 HIS cc_start: 0.9308 (OUTLIER) cc_final: 0.8559 (m90) REVERT: A 538 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9090 (p90) REVERT: B 98 MET cc_start: 0.8883 (tpp) cc_final: 0.8617 (tpp) REVERT: B 324 MET cc_start: 0.8902 (mtt) cc_final: 0.8347 (mmm) REVERT: B 356 MET cc_start: 0.9381 (mmp) cc_final: 0.9041 (mmp) REVERT: C 66 MET cc_start: 0.8984 (tpt) cc_final: 0.8596 (tpp) REVERT: C 245 MET cc_start: 0.8926 (mmm) cc_final: 0.8705 (mmm) REVERT: C 267 TYR cc_start: 0.9058 (m-80) cc_final: 0.8662 (m-80) REVERT: C 276 MET cc_start: 0.9209 (ttp) cc_final: 0.8905 (ttt) REVERT: P 131 MET cc_start: 0.9342 (mmt) cc_final: 0.9054 (mmm) REVERT: P 143 TYR cc_start: 0.8960 (m-80) cc_final: 0.8657 (m-80) REVERT: P 297 TYR cc_start: 0.7135 (m-80) cc_final: 0.6590 (t80) REVERT: P 301 TRP cc_start: 0.7461 (m-90) cc_final: 0.6739 (m-90) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.2030 time to fit residues: 26.8566 Evaluate side-chains 81 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 520 HIS Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 chunk 140 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN ** P 223 ASN ** 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 = 0.3476 r_free = 0.3476 target = 0.050371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.034878 restraints weight = 85154.222| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 5.45 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12444 Z= 0.150 Angle : 0.623 10.255 16875 Z= 0.303 Chirality : 0.039 0.198 1916 Planarity : 0.004 0.050 2163 Dihedral : 4.223 24.738 1641 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.81 % Allowed : 13.19 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1515 helix: 1.53 (0.16), residues: 1035 sheet: -0.80 (0.62), residues: 77 loop : 0.24 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 214 HIS 0.003 0.001 HIS A 119 PHE 0.010 0.001 PHE A 209 TYR 0.008 0.001 TYR B 158 ARG 0.009 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 719) hydrogen bonds : angle 4.49336 ( 2127) covalent geometry : bond 0.00325 (12444) covalent geometry : angle 0.62328 (16875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6417.18 seconds wall clock time: 117 minutes 30.47 seconds (7050.47 seconds total)