Starting phenix.real_space_refine on Wed May 14 06:13:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c7g_16457/05_2025/8c7g_16457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c7g_16457/05_2025/8c7g_16457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c7g_16457/05_2025/8c7g_16457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c7g_16457/05_2025/8c7g_16457.map" model { file = "/net/cci-nas-00/data/ceres_data/8c7g_16457/05_2025/8c7g_16457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c7g_16457/05_2025/8c7g_16457.cif" } resolution = 3.2 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= 0.001 sd= 0.023 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 57 5.16 5 C 7410 2.51 5 N 1963 2.21 5 O 2095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11525 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4802 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 25, 'TRANS': 581} Chain breaks: 2 Chain: "B" Number of atoms: 3311 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3301 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 402, 3301 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 6 bond proxies already assigned to first conformer: 3359 Chain: "C" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3412 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 406} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS B 392 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 392 " occ=0.50 Time building chain proxies: 7.73, per 1000 atoms: 0.67 Number of scatterers: 11525 At special positions: 0 Unit cell: (74.844, 103.488, 194.964, 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 57 16.00 O 2095 8.00 N 1963 7.00 C 7410 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: 2.24 Conformation dependent library (CDL) restraints added in 1.8 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2746 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 15 sheets defined 41.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 365 through 374 Processing helix chain 'A' and resid 379 through 393 Processing helix chain 'A' and resid 399 through 423 removed outlier: 3.650A pdb=" N LYS A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.687A pdb=" N GLN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.502A pdb=" N LEU A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 498 Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.824A pdb=" N LEU A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.595A pdb=" N HIS A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 544 removed outlier: 4.032A pdb=" N SER A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.853A pdb=" N ILE A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.629A pdb=" N ASN A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.779A pdb=" N LYS A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.603A pdb=" N PHE A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 619 removed outlier: 3.598A pdb=" N GLN A 619 " --> pdb=" O LYS A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.821A pdb=" N ILE A 624 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 31 removed outlier: 3.505A pdb=" N LYS B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 31' Processing helix chain 'B' and resid 42 through 61 removed outlier: 3.788A pdb=" N ASP B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.592A pdb=" N CYS B 69 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 removed outlier: 3.530A pdb=" N ILE B 116 " --> pdb=" O GLY B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 117 through 137 removed outlier: 4.100A pdb=" N TYR B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN B 135 " --> pdb=" O MET B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.857A pdb=" N CYS B 142 " --> pdb=" O PHE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 removed outlier: 3.932A pdb=" N LEU B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 192 through 201 removed outlier: 3.533A pdb=" N PHE B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.996A pdb=" N THR B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 245 Processing helix chain 'B' and resid 332 through 361 removed outlier: 3.813A pdb=" N TYR B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Proline residue: B 345 - end of helix removed outlier: 3.657A pdb=" N THR B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 415 removed outlier: 3.504A pdb=" N LEU B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 477 removed outlier: 3.695A pdb=" N VAL B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 140 through 155 Processing helix chain 'C' and resid 189 through 208 removed outlier: 3.607A pdb=" N LEU C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.608A pdb=" N ARG C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 240 removed outlier: 3.945A pdb=" N PHE C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 267 through 282 Processing helix chain 'C' and resid 311 through 325 Processing helix chain 'C' and resid 326 through 330 removed outlier: 4.152A pdb=" N LYS C 329 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 390 Processing helix chain 'C' and resid 392 through 402 removed outlier: 3.602A pdb=" N ILE C 396 " --> pdb=" O CYS C 392 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 414 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 442 through 462 removed outlier: 4.068A pdb=" N ARG C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 521 removed outlier: 3.723A pdb=" N VAL C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 503 " --> pdb=" O LYS C 499 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASP C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.935A pdb=" N CYS A 348 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 77 removed outlier: 4.043A pdb=" N SER A 74 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 88 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SER A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 122 removed outlier: 3.656A pdb=" N GLY A 119 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 136 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A 153 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL A 138 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 142 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 147 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 215 removed outlier: 3.725A pdb=" N HIS A 251 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 239 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS A 249 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N THR A 296 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N CYS A 250 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N HIS A 298 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 252 " --> pdb=" O HIS A 298 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 290 " --> pdb=" O TYR A 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 262 through 266 removed outlier: 3.668A pdb=" N ALA A 262 " --> pdb=" O HIS A 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.599A pdb=" N LEU A 312 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 324 " --> pdb=" O LEU A 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AB2, first strand: chain 'B' and resid 33 through 36 removed outlier: 5.407A pdb=" N VAL B 33 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN B 19 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU B 12 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN B 95 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 14 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 78 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 77 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 162 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N THR C 161 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER C 123 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 187 removed outlier: 6.224A pdb=" N ILE B 186 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N THR B 393 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 390 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 445 " --> pdb=" O GLU B 429 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 429 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLU B 430 " --> pdb=" O GLU C 472 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU C 472 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLN B 432 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE C 470 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS B 434 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS C 468 " --> pdb=" O ALA C 483 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 483 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS C 420 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 222 through 225 removed outlier: 5.105A pdb=" N VAL B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR B 219 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS B 225 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 214 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET B 295 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 261 through 262 removed outlier: 6.582A pdb=" N ILE C 261 " --> pdb=" O LEU C 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 333 through 337 removed outlier: 3.604A pdb=" N PHE C 290 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 301 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 526 " --> pdb=" O LEU C 302 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3730 1.34 - 1.46: 2125 1.46 - 1.58: 5824 1.58 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 11761 Sorted by residual: bond pdb=" N SER C 250 " pdb=" CA SER C 250 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" CG1 ILE B 57 " pdb=" CD1 ILE B 57 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.34e+00 bond pdb=" CA SER C 250 " pdb=" CB SER C 250 " ideal model delta sigma weight residual 1.530 1.507 0.023 2.00e-02 2.50e+03 1.28e+00 bond pdb=" CB THR B 74 " pdb=" CG2 THR B 74 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.72e-01 bond pdb=" C ILE C 310 " pdb=" N HIS C 311 " ideal model delta sigma weight residual 1.331 1.312 0.019 2.07e-02 2.33e+03 8.66e-01 ... (remaining 11756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 15882 4.05 - 8.11: 39 8.11 - 12.16: 2 12.16 - 16.22: 0 16.22 - 20.27: 1 Bond angle restraints: 15924 Sorted by residual: angle pdb=" N ASN C 251 " pdb=" CA ASN C 251 " pdb=" C ASN C 251 " ideal model delta sigma weight residual 107.60 127.87 -20.27 1.83e+00 2.99e-01 1.23e+02 angle pdb=" N ASN C 251 " pdb=" CA ASN C 251 " pdb=" CB ASN C 251 " ideal model delta sigma weight residual 112.27 100.57 11.70 1.77e+00 3.19e-01 4.37e+01 angle pdb=" C ASN C 251 " pdb=" CA ASN C 251 " pdb=" CB ASN C 251 " ideal model delta sigma weight residual 111.70 104.69 7.01 1.52e+00 4.33e-01 2.13e+01 angle pdb=" N SER C 244 " pdb=" CA SER C 244 " pdb=" C SER C 244 " ideal model delta sigma weight residual 111.00 120.02 -9.02 2.80e+00 1.28e-01 1.04e+01 angle pdb=" OG1 THR A 426 " pdb=" CB THR A 426 " pdb=" CG2 THR A 426 " ideal model delta sigma weight residual 109.30 103.35 5.95 2.00e+00 2.50e-01 8.85e+00 ... (remaining 15919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 6465 17.62 - 35.24: 527 35.24 - 52.86: 109 52.86 - 70.47: 8 70.47 - 88.09: 8 Dihedral angle restraints: 7117 sinusoidal: 2899 harmonic: 4218 Sorted by residual: dihedral pdb=" CA LEU C 288 " pdb=" C LEU C 288 " pdb=" N VAL C 289 " pdb=" CA VAL C 289 " ideal model delta harmonic sigma weight residual -180.00 -161.86 -18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASN A 200 " pdb=" C ASN A 200 " pdb=" N PRO A 201 " pdb=" CA PRO A 201 " ideal model delta harmonic sigma weight residual 180.00 162.31 17.69 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA MET B 182 " pdb=" C MET B 182 " pdb=" N LEU B 183 " pdb=" CA LEU B 183 " ideal model delta harmonic sigma weight residual 180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 7114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1626 0.071 - 0.141: 199 0.141 - 0.212: 4 0.212 - 0.283: 1 0.283 - 0.354: 1 Chirality restraints: 1831 Sorted by residual: chirality pdb=" CA SER C 244 " pdb=" N SER C 244 " pdb=" C SER C 244 " pdb=" CB SER C 244 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA ASN C 252 " pdb=" N ASN C 252 " pdb=" C ASN C 252 " pdb=" CB ASN C 252 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB THR A 426 " pdb=" CA THR A 426 " pdb=" OG1 THR A 426 " pdb=" CG2 THR A 426 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 1828 not shown) Planarity restraints: 2019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 293 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO B 294 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 294 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 294 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 246 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 247 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 200 " 0.034 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO A 201 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.029 5.00e-02 4.00e+02 ... (remaining 2016 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 93 2.67 - 3.23: 10057 3.23 - 3.78: 15519 3.78 - 4.34: 20747 4.34 - 4.90: 36295 Nonbonded interactions: 82711 Sorted by model distance: nonbonded pdb=" O ASN C 251 " pdb=" OD1 ASN C 251 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR A 531 " pdb=" OE1 GLN B 387 " model vdw 2.232 3.040 nonbonded pdb=" NH1 ARG A 73 " pdb=" OE1 GLU A 90 " model vdw 2.258 3.120 nonbonded pdb=" ND2 ASN A 227 " pdb=" OE2 GLU A 234 " model vdw 2.258 3.120 nonbonded pdb=" NH1 ARG A 260 " pdb=" OE1 GLN A 275 " model vdw 2.281 3.120 ... (remaining 82706 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=0.50 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.360 Find NCS groups from input model: 0.150 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.004 0.045 11761 Z= 0.160 Angle : 0.631 20.273 15924 Z= 0.335 Chirality : 0.046 0.354 1831 Planarity : 0.005 0.062 2019 Dihedral : 13.278 88.092 4371 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.22), residues: 1408 helix: 1.38 (0.23), residues: 513 sheet: 0.65 (0.29), residues: 327 loop : -1.54 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 160 HIS 0.009 0.001 HIS C 351 PHE 0.016 0.002 PHE C 170 TYR 0.013 0.001 TYR B 16 ARG 0.005 0.000 ARG C 419 Details of bonding type rmsd hydrogen bonds : bond 0.15705 ( 541) hydrogen bonds : angle 5.50019 ( 1542) covalent geometry : bond 0.00375 (11761) covalent geometry : angle 0.63108 (15924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.202 Fit side-chains REVERT: A 127 GLU cc_start: 0.7839 (pm20) cc_final: 0.7526 (pm20) REVERT: A 145 LYS cc_start: 0.8155 (ptpt) cc_final: 0.7944 (ttpp) REVERT: A 197 ASP cc_start: 0.7208 (p0) cc_final: 0.6985 (p0) REVERT: A 236 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6243 (mt-10) REVERT: B 32 LYS cc_start: 0.8144 (ptpt) cc_final: 0.7783 (ptpt) REVERT: B 178 ASP cc_start: 0.6013 (m-30) cc_final: 0.5748 (m-30) REVERT: C 332 GLU cc_start: 0.6972 (tp30) cc_final: 0.6688 (mm-30) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3195 time to fit residues: 98.1804 Evaluate side-chains 215 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.0050 chunk 36 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 128 optimal weight: 0.0670 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS C 251 ASN C 420 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.154855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130692 restraints weight = 43776.604| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 4.54 r_work: 0.3425 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11761 Z= 0.114 Angle : 0.515 6.625 15924 Z= 0.270 Chirality : 0.043 0.156 1831 Planarity : 0.004 0.051 2019 Dihedral : 4.034 18.210 1542 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.70 % Allowed : 8.20 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.23), residues: 1408 helix: 1.67 (0.23), residues: 524 sheet: 0.63 (0.29), residues: 332 loop : -1.41 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 160 HIS 0.006 0.001 HIS C 351 PHE 0.022 0.001 PHE C 290 TYR 0.016 0.001 TYR B 240 ARG 0.003 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.04445 ( 541) hydrogen bonds : angle 4.44393 ( 1542) covalent geometry : bond 0.00255 (11761) covalent geometry : angle 0.51460 (15924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 1.156 Fit side-chains REVERT: A 197 ASP cc_start: 0.7807 (p0) cc_final: 0.7486 (p0) REVERT: B 98 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7898 (ttpt) REVERT: B 194 THR cc_start: 0.8045 (m) cc_final: 0.7841 (p) REVERT: C 251 ASN cc_start: 0.5641 (OUTLIER) cc_final: 0.5363 (p0) outliers start: 9 outliers final: 6 residues processed: 217 average time/residue: 0.3179 time to fit residues: 90.1919 Evaluate side-chains 221 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 251 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.0970 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 437 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 = 0.3946 r_free = 0.3946 target = 0.153267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.129397 restraints weight = 42925.214| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 4.42 r_work: 0.3407 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11761 Z= 0.136 Angle : 0.527 6.044 15924 Z= 0.275 Chirality : 0.043 0.152 1831 Planarity : 0.004 0.044 2019 Dihedral : 4.052 18.928 1542 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.01 % Allowed : 9.51 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.23), residues: 1408 helix: 1.72 (0.23), residues: 524 sheet: 0.63 (0.29), residues: 328 loop : -1.36 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 334 HIS 0.004 0.001 HIS A 273 PHE 0.019 0.002 PHE C 290 TYR 0.016 0.001 TYR B 240 ARG 0.004 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.04809 ( 541) hydrogen bonds : angle 4.35487 ( 1542) covalent geometry : bond 0.00323 (11761) covalent geometry : angle 0.52714 (15924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 1.258 Fit side-chains REVERT: A 11 GLU cc_start: 0.7085 (pm20) cc_final: 0.6599 (pm20) REVERT: A 197 ASP cc_start: 0.7787 (p0) cc_final: 0.7447 (p0) REVERT: A 248 ARG cc_start: 0.7517 (mpt180) cc_final: 0.7244 (mpt180) REVERT: B 57 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7404 (mp) REVERT: B 133 ARG cc_start: 0.7836 (ttm170) cc_final: 0.7548 (ttp-170) REVERT: C 332 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6992 (mm-30) outliers start: 13 outliers final: 9 residues processed: 229 average time/residue: 0.3251 time to fit residues: 97.2453 Evaluate side-chains 225 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 215 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 480 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 35 optimal weight: 0.5980 chunk 93 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 111 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN ** B 437 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 = 0.3955 r_free = 0.3955 target = 0.154243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130161 restraints weight = 40652.932| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 4.05 r_work: 0.3446 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11761 Z= 0.117 Angle : 0.494 5.775 15924 Z= 0.260 Chirality : 0.042 0.145 1831 Planarity : 0.004 0.042 2019 Dihedral : 3.942 18.012 1542 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.08 % Allowed : 10.75 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.23), residues: 1408 helix: 1.84 (0.23), residues: 524 sheet: 0.63 (0.29), residues: 334 loop : -1.36 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 334 HIS 0.003 0.001 HIS A 273 PHE 0.022 0.001 PHE C 290 TYR 0.016 0.001 TYR B 240 ARG 0.004 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 541) hydrogen bonds : angle 4.18899 ( 1542) covalent geometry : bond 0.00272 (11761) covalent geometry : angle 0.49385 (15924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6877 (pm20) cc_final: 0.6466 (pm20) REVERT: A 197 ASP cc_start: 0.7747 (p0) cc_final: 0.7414 (p0) REVERT: A 343 ASP cc_start: 0.8160 (t0) cc_final: 0.7847 (t70) REVERT: B 98 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7945 (ttpt) REVERT: B 133 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7492 (ttp-170) REVERT: C 332 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6880 (mm-30) outliers start: 14 outliers final: 12 residues processed: 216 average time/residue: 0.3392 time to fit residues: 96.9270 Evaluate side-chains 225 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 480 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 437 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 = 0.3929 r_free = 0.3929 target = 0.151997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127999 restraints weight = 39876.517| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 4.14 r_work: 0.3406 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11761 Z= 0.163 Angle : 0.546 6.211 15924 Z= 0.286 Chirality : 0.044 0.150 1831 Planarity : 0.004 0.043 2019 Dihedral : 4.093 19.092 1542 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.47 % Allowed : 11.99 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.23), residues: 1408 helix: 1.74 (0.23), residues: 524 sheet: 0.74 (0.29), residues: 336 loop : -1.45 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 334 HIS 0.005 0.001 HIS B 238 PHE 0.017 0.002 PHE C 170 TYR 0.021 0.002 TYR A 9 ARG 0.005 0.000 ARG B 445 Details of bonding type rmsd hydrogen bonds : bond 0.05240 ( 541) hydrogen bonds : angle 4.31233 ( 1542) covalent geometry : bond 0.00397 (11761) covalent geometry : angle 0.54645 (15924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6927 (pm20) cc_final: 0.6608 (pm20) REVERT: A 145 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8353 (ttpp) REVERT: A 197 ASP cc_start: 0.7738 (p0) cc_final: 0.7424 (p0) REVERT: A 248 ARG cc_start: 0.7449 (mpt180) cc_final: 0.7160 (mpt180) REVERT: C 332 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6799 (mm-30) outliers start: 19 outliers final: 14 residues processed: 227 average time/residue: 0.3340 time to fit residues: 98.7239 Evaluate side-chains 228 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain C residue 480 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 60 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 102 optimal weight: 0.0970 chunk 127 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 86 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** B 437 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 = 0.3966 r_free = 0.3966 target = 0.154968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132079 restraints weight = 31414.027| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.04 r_work: 0.3503 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11761 Z= 0.098 Angle : 0.469 6.846 15924 Z= 0.247 Chirality : 0.042 0.146 1831 Planarity : 0.004 0.041 2019 Dihedral : 3.845 17.104 1542 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.39 % Allowed : 12.30 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1408 helix: 1.96 (0.23), residues: 526 sheet: 0.72 (0.30), residues: 332 loop : -1.30 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 334 HIS 0.003 0.001 HIS C 351 PHE 0.026 0.001 PHE C 290 TYR 0.016 0.001 TYR B 240 ARG 0.005 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 541) hydrogen bonds : angle 4.06261 ( 1542) covalent geometry : bond 0.00215 (11761) covalent geometry : angle 0.46890 (15924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6803 (pm20) cc_final: 0.6473 (pm20) REVERT: A 197 ASP cc_start: 0.7665 (p0) cc_final: 0.7319 (p0) REVERT: C 332 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6744 (mm-30) REVERT: C 347 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.6809 (m-10) outliers start: 18 outliers final: 11 residues processed: 216 average time/residue: 0.3201 time to fit residues: 89.9492 Evaluate side-chains 222 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 480 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 126 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN ** B 437 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 = 0.3918 r_free = 0.3918 target = 0.151241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128775 restraints weight = 33931.795| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.21 r_work: 0.3459 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11761 Z= 0.196 Angle : 0.580 6.898 15924 Z= 0.300 Chirality : 0.045 0.157 1831 Planarity : 0.004 0.044 2019 Dihedral : 4.157 19.593 1542 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.24 % Allowed : 13.30 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.23), residues: 1408 helix: 1.80 (0.23), residues: 524 sheet: 0.78 (0.29), residues: 333 loop : -1.47 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 417 HIS 0.006 0.001 HIS B 238 PHE 0.025 0.002 PHE C 290 TYR 0.024 0.002 TYR A 9 ARG 0.006 0.000 ARG B 445 Details of bonding type rmsd hydrogen bonds : bond 0.05714 ( 541) hydrogen bonds : angle 4.33681 ( 1542) covalent geometry : bond 0.00488 (11761) covalent geometry : angle 0.58014 (15924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7615 (p0) cc_final: 0.7296 (p0) REVERT: C 332 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6727 (mt-10) REVERT: C 347 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.6727 (m-10) outliers start: 16 outliers final: 12 residues processed: 228 average time/residue: 0.3453 time to fit residues: 102.9620 Evaluate side-chains 230 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 480 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 60 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 0.0370 chunk 95 optimal weight: 0.9990 chunk 130 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 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 = 0.3949 r_free = 0.3949 target = 0.153594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129770 restraints weight = 40421.666| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 4.07 r_work: 0.3438 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11761 Z= 0.118 Angle : 0.499 7.486 15924 Z= 0.262 Chirality : 0.042 0.143 1831 Planarity : 0.004 0.042 2019 Dihedral : 3.943 18.071 1542 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.31 % Allowed : 13.46 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.23), residues: 1408 helix: 1.94 (0.23), residues: 526 sheet: 0.75 (0.29), residues: 339 loop : -1.42 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 334 HIS 0.003 0.001 HIS C 118 PHE 0.027 0.001 PHE C 290 TYR 0.016 0.001 TYR B 240 ARG 0.005 0.000 ARG B 445 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 541) hydrogen bonds : angle 4.14406 ( 1542) covalent geometry : bond 0.00274 (11761) covalent geometry : angle 0.49929 (15924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7763 (p0) cc_final: 0.7426 (p0) REVERT: A 554 MET cc_start: 0.7657 (mtm) cc_final: 0.7291 (mtp) REVERT: C 173 MET cc_start: 0.8249 (ttt) cc_final: 0.7925 (ttt) REVERT: C 332 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6771 (mt-10) REVERT: C 347 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.6765 (m-10) outliers start: 17 outliers final: 14 residues processed: 222 average time/residue: 0.3308 time to fit residues: 95.7960 Evaluate side-chains 231 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 69 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.150315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127739 restraints weight = 25710.198| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.77 r_work: 0.3463 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 11761 Z= 0.221 Angle : 0.611 7.589 15924 Z= 0.315 Chirality : 0.046 0.162 1831 Planarity : 0.004 0.044 2019 Dihedral : 4.278 20.306 1542 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.16 % Allowed : 14.08 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.23), residues: 1408 helix: 1.65 (0.23), residues: 530 sheet: 0.70 (0.30), residues: 321 loop : -1.48 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 417 HIS 0.007 0.001 HIS B 238 PHE 0.027 0.002 PHE C 290 TYR 0.026 0.002 TYR A 9 ARG 0.006 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.06069 ( 541) hydrogen bonds : angle 4.43280 ( 1542) covalent geometry : bond 0.00553 (11761) covalent geometry : angle 0.61105 (15924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7621 (p0) cc_final: 0.7292 (p0) REVERT: A 374 LEU cc_start: 0.7984 (mt) cc_final: 0.7783 (mt) REVERT: C 332 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6761 (mt-10) REVERT: C 347 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.6912 (m-10) outliers start: 15 outliers final: 14 residues processed: 229 average time/residue: 0.3225 time to fit residues: 96.3314 Evaluate side-chains 238 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 77 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: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.151826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129233 restraints weight = 28085.034| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.84 r_work: 0.3474 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11761 Z= 0.161 Angle : 0.560 8.190 15924 Z= 0.292 Chirality : 0.044 0.152 1831 Planarity : 0.004 0.044 2019 Dihedral : 4.165 19.604 1542 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.39 % Allowed : 14.31 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.23), residues: 1408 helix: 1.79 (0.23), residues: 524 sheet: 0.69 (0.29), residues: 333 loop : -1.52 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 334 HIS 0.004 0.001 HIS B 238 PHE 0.029 0.002 PHE C 290 TYR 0.020 0.002 TYR A 9 ARG 0.006 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.05083 ( 541) hydrogen bonds : angle 4.31563 ( 1542) covalent geometry : bond 0.00393 (11761) covalent geometry : angle 0.56046 (15924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7647 (p0) cc_final: 0.7293 (p0) REVERT: C 332 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6769 (mt-10) REVERT: C 347 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.6856 (m-10) outliers start: 18 outliers final: 14 residues processed: 223 average time/residue: 0.3195 time to fit residues: 92.8697 Evaluate side-chains 231 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 0.0050 chunk 82 optimal weight: 0.9980 chunk 83 optimal weight: 0.0040 chunk 15 optimal weight: 0.4980 chunk 85 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN B 390 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.155058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132448 restraints weight = 30388.951| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.97 r_work: 0.3493 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11761 Z= 0.099 Angle : 0.488 8.110 15924 Z= 0.257 Chirality : 0.042 0.154 1831 Planarity : 0.004 0.040 2019 Dihedral : 3.867 17.045 1542 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.31 % Allowed : 14.39 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.23), residues: 1408 helix: 1.98 (0.23), residues: 526 sheet: 0.66 (0.29), residues: 333 loop : -1.34 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 334 HIS 0.004 0.001 HIS C 351 PHE 0.037 0.001 PHE C 290 TYR 0.016 0.001 TYR B 240 ARG 0.005 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 541) hydrogen bonds : angle 4.08047 ( 1542) covalent geometry : bond 0.00218 (11761) covalent geometry : angle 0.48827 (15924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6077.84 seconds wall clock time: 106 minutes 4.00 seconds (6364.00 seconds total)