Starting phenix.real_space_refine on Tue Jun 10 08:10:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c7g_16457/06_2025/8c7g_16457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c7g_16457/06_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_16457/06_2025/8c7g_16457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c7g_16457/06_2025/8c7g_16457.map" model { file = "/net/cci-nas-00/data/ceres_data/8c7g_16457/06_2025/8c7g_16457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c7g_16457/06_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-5710/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: 8.65, per 1000 atoms: 0.75 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: 2.63 Conformation dependent library (CDL) restraints added in 1.9 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: 1.34 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: 3.45 Time building geometry restraints manager: 2.97 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: 2.270 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.260 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.320 ------------------------------------------------------------------------------- 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 : 1.403 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: 0.3301 time to fit residues: 102.3610 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 : 1.373 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.154802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131466 restraints weight = 43778.333| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 4.34 r_work: 0.3426 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 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 = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 4.44392 ( 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 : 1.256 Fit side-chains REVERT: A 18 ARG cc_start: 0.7817 (mmm160) cc_final: 0.7614 (mtp180) REVERT: A 197 ASP cc_start: 0.7809 (p0) cc_final: 0.7499 (p0) REVERT: B 98 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7979 (ttpt) REVERT: C 251 ASN cc_start: 0.5773 (OUTLIER) cc_final: 0.5491 (p0) outliers start: 9 outliers final: 6 residues processed: 217 average time/residue: 0.3611 time to fit residues: 103.0886 Evaluate side-chains 220 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 213 time to evaluate : 1.972 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 0.0980 chunk 117 optimal weight: 0.0270 chunk 81 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 0.0000 chunk 44 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 overall best weight: 0.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 390 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.155585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131890 restraints weight = 42899.838| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 4.37 r_work: 0.3443 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1186 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= 0.100 Angle : 0.481 5.621 15924 Z= 0.253 Chirality : 0.042 0.150 1831 Planarity : 0.004 0.043 2019 Dihedral : 3.892 17.679 1542 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.24 % Allowed : 9.05 % Favored : 89.71 % 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: 0.58 (0.23), residues: 1408 helix: 1.82 (0.23), residues: 526 sheet: 0.67 (0.29), residues: 318 loop : -1.20 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 334 HIS 0.003 0.001 HIS A 124 PHE 0.017 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 0.03876 ( 541) hydrogen bonds : angle 4.22438 ( 1542) covalent geometry : bond 0.00218 (11761) covalent geometry : angle 0.48131 (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 237 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 1.413 Fit side-chains REVERT: A 11 GLU cc_start: 0.7069 (pm20) cc_final: 0.6602 (pm20) REVERT: A 197 ASP cc_start: 0.7799 (p0) cc_final: 0.7477 (p0) REVERT: A 236 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 248 ARG cc_start: 0.7486 (mpt180) cc_final: 0.7284 (mpt180) REVERT: B 81 PHE cc_start: 0.8155 (m-80) cc_final: 0.7871 (m-80) REVERT: B 133 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7532 (ttp-170) outliers start: 16 outliers final: 12 residues processed: 225 average time/residue: 0.3574 time to fit residues: 105.5055 Evaluate side-chains 223 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 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 352 VAL 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: 0.0670 chunk 93 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 111 optimal weight: 0.3980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.154541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130432 restraints weight = 40628.056| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 4.07 r_work: 0.3449 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 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 = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11761 Z= 0.115 Angle : 0.496 5.950 15924 Z= 0.259 Chirality : 0.042 0.146 1831 Planarity : 0.004 0.041 2019 Dihedral : 3.867 17.359 1542 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.08 % Allowed : 10.67 % Favored : 88.24 % 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: 0.62 (0.23), residues: 1408 helix: 1.89 (0.23), residues: 524 sheet: 0.72 (0.29), residues: 328 loop : -1.26 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 334 HIS 0.003 0.001 HIS A 273 PHE 0.022 0.001 PHE C 290 TYR 0.015 0.001 TYR B 240 ARG 0.004 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 541) hydrogen bonds : angle 4.17456 ( 1542) covalent geometry : bond 0.00263 (11761) covalent geometry : angle 0.49565 (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 227 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6912 (pm20) cc_final: 0.6501 (pm20) REVERT: A 197 ASP cc_start: 0.7749 (p0) cc_final: 0.7413 (p0) REVERT: A 248 ARG cc_start: 0.7445 (mpt180) cc_final: 0.7177 (mpt180) REVERT: B 133 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7471 (ttp-170) REVERT: C 173 MET cc_start: 0.8174 (ttt) cc_final: 0.7815 (ttt) REVERT: C 332 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6895 (mm-30) outliers start: 14 outliers final: 14 residues processed: 217 average time/residue: 0.3281 time to fit residues: 92.8841 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 : 1.322 ------------------------------------------------------------------------------- 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 136 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 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 352 VAL 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: 0.9990 chunk 71 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 51 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.154771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131347 restraints weight = 39900.751| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 4.19 r_work: 0.3462 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1361 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= 0.109 Angle : 0.482 5.767 15924 Z= 0.252 Chirality : 0.042 0.144 1831 Planarity : 0.004 0.041 2019 Dihedral : 3.814 16.950 1542 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.55 % Allowed : 11.37 % Favored : 87.08 % 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: 0.68 (0.23), residues: 1408 helix: 1.95 (0.23), residues: 526 sheet: 0.71 (0.29), residues: 333 loop : -1.25 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 334 HIS 0.003 0.001 HIS A 273 PHE 0.010 0.001 PHE C 264 TYR 0.015 0.001 TYR B 240 ARG 0.005 0.000 ARG B 445 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 541) hydrogen bonds : angle 4.07907 ( 1542) covalent geometry : bond 0.00248 (11761) covalent geometry : angle 0.48223 (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 231 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6882 (pm20) cc_final: 0.6407 (pm20) REVERT: A 197 ASP cc_start: 0.7715 (p0) cc_final: 0.7403 (p0) REVERT: B 133 ARG cc_start: 0.7774 (ttm170) cc_final: 0.7460 (ttp-170) REVERT: C 332 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6861 (mm-30) REVERT: C 360 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6625 (mm110) outliers start: 20 outliers final: 16 residues processed: 215 average time/residue: 0.3277 time to fit residues: 92.0765 Evaluate side-chains 221 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain A residue 136 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 259 ASN Chi-restraints excluded: chain C residue 352 VAL 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: 0.6980 chunk 129 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.152428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129623 restraints weight = 31418.719| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.15 r_work: 0.3472 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 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 = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11761 Z= 0.156 Angle : 0.540 6.269 15924 Z= 0.280 Chirality : 0.043 0.148 1831 Planarity : 0.004 0.043 2019 Dihedral : 3.994 18.466 1542 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.47 % Allowed : 12.14 % Favored : 86.39 % 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: 1.89 (0.23), residues: 524 sheet: 0.84 (0.29), residues: 335 loop : -1.41 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 334 HIS 0.004 0.001 HIS C 118 PHE 0.019 0.002 PHE C 290 TYR 0.021 0.002 TYR A 9 ARG 0.005 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 541) hydrogen bonds : angle 4.23118 ( 1542) covalent geometry : bond 0.00377 (11761) covalent geometry : angle 0.53993 (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 238 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7667 (p0) cc_final: 0.7354 (p0) REVERT: B 133 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7481 (ttp-170) REVERT: C 332 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6750 (mm-30) REVERT: C 347 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.6758 (m-10) outliers start: 19 outliers final: 15 residues processed: 227 average time/residue: 0.3371 time to fit residues: 100.6017 Evaluate side-chains 228 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 136 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 Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 126 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.150644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128201 restraints weight = 33930.243| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.21 r_work: 0.3450 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11761 Z= 0.202 Angle : 0.598 7.044 15924 Z= 0.310 Chirality : 0.045 0.155 1831 Planarity : 0.004 0.045 2019 Dihedral : 4.278 20.285 1542 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.31 % Allowed : 12.99 % Favored : 85.69 % 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: 1.70 (0.23), residues: 524 sheet: 0.80 (0.29), residues: 328 loop : -1.48 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 334 HIS 0.007 0.001 HIS B 238 PHE 0.029 0.002 PHE C 290 TYR 0.026 0.002 TYR A 9 ARG 0.005 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.05948 ( 541) hydrogen bonds : angle 4.42606 ( 1542) covalent geometry : bond 0.00502 (11761) covalent geometry : angle 0.59845 (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 238 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7669 (p0) cc_final: 0.7330 (p0) REVERT: C 259 ASN cc_start: 0.6546 (t0) cc_final: 0.6321 (t0) REVERT: C 332 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6732 (mt-10) REVERT: C 347 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.6783 (m-10) outliers start: 17 outliers final: 14 residues processed: 228 average time/residue: 0.3231 time to fit residues: 96.4839 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 : 1.174 ------------------------------------------------------------------------------- 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 136 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 352 VAL 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: 0.9980 chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 0.0370 chunk 95 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.0030 chunk 1 optimal weight: 1.9990 overall best weight: 0.5468 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.152819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128912 restraints weight = 40429.326| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.09 r_work: 0.3430 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1430 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= 0.131 Angle : 0.517 7.313 15924 Z= 0.271 Chirality : 0.043 0.145 1831 Planarity : 0.004 0.044 2019 Dihedral : 4.035 18.828 1542 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.39 % Allowed : 13.46 % Favored : 85.15 % 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: 0.54 (0.23), residues: 1408 helix: 1.89 (0.23), residues: 524 sheet: 0.74 (0.30), residues: 327 loop : -1.44 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 334 HIS 0.003 0.001 HIS A 273 PHE 0.028 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 0.04512 ( 541) hydrogen bonds : angle 4.21058 ( 1542) covalent geometry : bond 0.00309 (11761) covalent geometry : angle 0.51701 (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 239 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7789 (p0) cc_final: 0.7437 (p0) REVERT: B 98 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7984 (ttpt) REVERT: C 259 ASN cc_start: 0.6536 (t0) cc_final: 0.6266 (t0) REVERT: C 332 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6809 (mt-10) REVERT: C 347 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.6798 (m-10) outliers start: 18 outliers final: 15 residues processed: 230 average time/residue: 0.3108 time to fit residues: 93.8125 Evaluate side-chains 232 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 216 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain A residue 136 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 176 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 69 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 390 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.152365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129829 restraints weight = 25694.354| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.77 r_work: 0.3492 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- 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 = 0.48 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 = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11761 Z= 0.145 Angle : 0.535 7.077 15924 Z= 0.279 Chirality : 0.043 0.147 1831 Planarity : 0.004 0.044 2019 Dihedral : 4.047 18.702 1542 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.39 % Allowed : 13.69 % Favored : 84.92 % 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: 0.55 (0.23), residues: 1408 helix: 1.90 (0.23), residues: 524 sheet: 0.78 (0.29), residues: 333 loop : -1.49 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 334 HIS 0.004 0.001 HIS B 238 PHE 0.033 0.002 PHE C 290 TYR 0.017 0.001 TYR A 9 ARG 0.005 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 541) hydrogen bonds : angle 4.22712 ( 1542) covalent geometry : bond 0.00349 (11761) covalent geometry : angle 0.53540 (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 233 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7631 (p0) cc_final: 0.7279 (p0) REVERT: B 98 LYS cc_start: 0.8236 (ttmm) cc_final: 0.8008 (ttpt) REVERT: C 332 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6752 (mt-10) REVERT: C 347 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.6946 (m-10) outliers start: 18 outliers final: 16 residues processed: 223 average time/residue: 0.3229 time to fit residues: 94.5199 Evaluate side-chains 235 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain A residue 136 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 176 GLN 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 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: 0.5980 chunk 59 optimal weight: 0.3980 chunk 25 optimal weight: 0.1980 chunk 63 optimal weight: 0.4980 chunk 105 optimal weight: 0.4980 chunk 134 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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** C 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.153838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130508 restraints weight = 28104.443| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.06 r_work: 0.3501 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11761 Z= 0.117 Angle : 0.505 6.962 15924 Z= 0.265 Chirality : 0.042 0.142 1831 Planarity : 0.004 0.043 2019 Dihedral : 3.909 17.901 1542 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.24 % Allowed : 14.39 % Favored : 84.38 % 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: 0.64 (0.23), residues: 1408 helix: 1.97 (0.23), residues: 526 sheet: 0.77 (0.29), residues: 337 loop : -1.40 (0.25), residues: 545 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 0.031 0.001 PHE C 290 TYR 0.015 0.001 TYR B 240 ARG 0.005 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 541) hydrogen bonds : angle 4.12060 ( 1542) covalent geometry : bond 0.00272 (11761) covalent geometry : angle 0.50467 (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 227 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7676 (p0) cc_final: 0.7326 (p0) REVERT: A 343 ASP cc_start: 0.7976 (t0) cc_final: 0.7715 (t70) REVERT: B 98 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7975 (ttpt) REVERT: C 173 MET cc_start: 0.8164 (ttt) cc_final: 0.7757 (ttt) REVERT: C 290 PHE cc_start: 0.8418 (m-80) cc_final: 0.8097 (m-80) REVERT: C 332 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6764 (mt-10) REVERT: C 347 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7030 (m-10) outliers start: 16 outliers final: 13 residues processed: 220 average time/residue: 0.3244 time to fit residues: 93.6890 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 : 1.338 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain A residue 136 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 25 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 126 optimal weight: 0.0060 chunk 140 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 259 ASN C 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.153507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130671 restraints weight = 30372.102| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.03 r_work: 0.3489 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11761 Z= 0.121 Angle : 0.509 7.138 15924 Z= 0.267 Chirality : 0.042 0.143 1831 Planarity : 0.004 0.060 2019 Dihedral : 3.897 17.596 1542 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.47 % Allowed : 14.23 % 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: 0.66 (0.23), residues: 1408 helix: 2.00 (0.23), residues: 526 sheet: 0.76 (0.29), residues: 339 loop : -1.41 (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 351 PHE 0.037 0.001 PHE C 290 TYR 0.014 0.001 TYR B 240 ARG 0.005 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 541) hydrogen bonds : angle 4.11904 ( 1542) covalent geometry : bond 0.00281 (11761) covalent geometry : angle 0.50885 (15924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6945.29 seconds wall clock time: 120 minutes 15.10 seconds (7215.10 seconds total)