Starting phenix.real_space_refine on Tue Mar 11 16:16:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4u_36892/03_2025/8k4u_36892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4u_36892/03_2025/8k4u_36892.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/8k4u_36892/03_2025/8k4u_36892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4u_36892/03_2025/8k4u_36892.map" model { file = "/net/cci-nas-00/data/ceres_data/8k4u_36892/03_2025/8k4u_36892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4u_36892/03_2025/8k4u_36892.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= -0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4052 2.51 5 N 1045 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6323 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1451 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "B" Number of atoms: 4871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4871 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 563} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.09, per 1000 atoms: 0.65 Number of scatterers: 6323 At special positions: 0 Unit cell: (75.597, 82.287, 115.737, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1189 8.00 N 1045 7.00 C 4052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 469 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 798.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 378 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 374 " 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 51.7% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.892A pdb=" N LEU A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.943A pdb=" N VAL A 398 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 401 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 51 removed outlier: 3.569A pdb=" N ALA B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASN B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 3.851A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.683A pdb=" N GLN B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 removed outlier: 3.653A pdb=" N THR B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 157 through 167 removed outlier: 4.094A pdb=" N TRP B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 removed outlier: 3.675A pdb=" N GLY B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 removed outlier: 3.588A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 220 through 252 removed outlier: 3.637A pdb=" N GLU B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.681A pdb=" N GLN B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.596A pdb=" N TYR B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 303 through 318 removed outlier: 3.758A pdb=" N PHE B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 311 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.223A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 379 removed outlier: 3.602A pdb=" N PHE B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 370 " --> pdb=" O MET B 366 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.259A pdb=" N SER B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 412 removed outlier: 3.670A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.660A pdb=" N PHE B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 464 removed outlier: 4.695A pdb=" N TRP B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.519A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 4.026A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.562A pdb=" N LYS B 552 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.632A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 598 " --> pdb=" O TRP B 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 348 removed outlier: 3.851A pdb=" N GLU A 344 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 390 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 389 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS A 423 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 369 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN A 428 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N PHE A 365 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA4, first strand: chain 'B' and resid 132 through 133 removed outlier: 3.718A pdb=" N LEU B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.440A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.203A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 690 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: 1.52 Time building geometry restraints manager: 1.64 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: 2010 1.34 - 1.46: 1635 1.46 - 1.58: 2805 1.58 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 6507 Sorted by residual: bond pdb=" CA GLY B 582 " pdb=" C GLY B 582 " ideal model delta sigma weight residual 1.511 1.523 -0.013 6.90e-03 2.10e+04 3.38e+00 bond pdb=" C ASP B 499 " pdb=" N PRO B 500 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.28e-02 6.10e+03 2.64e+00 bond pdb=" C VAL B 581 " pdb=" N GLY B 582 " ideal model delta sigma weight residual 1.340 1.330 0.010 6.60e-03 2.30e+04 2.33e+00 bond pdb=" C LEU B 320 " pdb=" N PRO B 321 " ideal model delta sigma weight residual 1.330 1.347 -0.017 1.25e-02 6.40e+03 1.94e+00 bond pdb=" C ARG B 177 " pdb=" N PRO B 178 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.23e-02 6.61e+03 1.72e+00 ... (remaining 6502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 8679 1.95 - 3.91: 135 3.91 - 5.86: 16 5.86 - 7.81: 4 7.81 - 9.77: 3 Bond angle restraints: 8837 Sorted by residual: angle pdb=" C ILE B 379 " pdb=" N GLN B 380 " pdb=" CA GLN B 380 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" N ILE B 291 " pdb=" CA ILE B 291 " pdb=" C ILE B 291 " ideal model delta sigma weight residual 111.91 108.44 3.47 8.90e-01 1.26e+00 1.52e+01 angle pdb=" N GLY A 448 " pdb=" CA GLY A 448 " pdb=" C GLY A 448 " ideal model delta sigma weight residual 110.56 115.53 -4.97 1.36e+00 5.41e-01 1.34e+01 angle pdb=" C LEU B 143 " pdb=" N LEU B 144 " pdb=" CA LEU B 144 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" N LYS B 234 " pdb=" CA LYS B 234 " pdb=" C LYS B 234 " ideal model delta sigma weight residual 109.81 116.56 -6.75 2.21e+00 2.05e-01 9.34e+00 ... (remaining 8832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 3545 16.39 - 32.78: 216 32.78 - 49.18: 68 49.18 - 65.57: 11 65.57 - 81.96: 1 Dihedral angle restraints: 3841 sinusoidal: 1558 harmonic: 2283 Sorted by residual: dihedral pdb=" CA ALA B 396 " pdb=" C ALA B 396 " pdb=" N ASN B 397 " pdb=" CA ASN B 397 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLN B 380 " pdb=" C GLN B 380 " pdb=" N TYR B 381 " pdb=" CA TYR B 381 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP B 149 " pdb=" C ASP B 149 " pdb=" N ASN B 150 " pdb=" CA ASN B 150 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 494 0.031 - 0.061: 292 0.061 - 0.092: 86 0.092 - 0.123: 38 0.123 - 0.153: 11 Chirality restraints: 921 Sorted by residual: chirality pdb=" CA ASP B 499 " pdb=" N ASP B 499 " pdb=" C ASP B 499 " pdb=" CB ASP B 499 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ARG B 177 " pdb=" N ARG B 177 " pdb=" C ARG B 177 " pdb=" CB ARG B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" CA LEU B 450 " pdb=" N LEU B 450 " pdb=" C LEU B 450 " pdb=" CB LEU B 450 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 918 not shown) Planarity restraints: 1137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 582 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO B 583 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 279 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO B 280 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 234 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 235 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " 0.031 5.00e-02 4.00e+02 ... (remaining 1134 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 88 2.66 - 3.22: 5451 3.22 - 3.78: 9947 3.78 - 4.34: 14019 4.34 - 4.90: 22909 Nonbonded interactions: 52414 Sorted by model distance: nonbonded pdb=" OE2 GLU B 402 " pdb="ZN ZN B 701 " model vdw 2.101 2.230 nonbonded pdb=" OG1 THR B 362 " pdb=" OD2 ASP B 368 " model vdw 2.309 3.040 nonbonded pdb=" OD1 ASP B 382 " pdb=" OH TYR B 385 " model vdw 2.320 3.040 nonbonded pdb=" O ASN B 150 " pdb=" OG1 THR B 154 " model vdw 2.321 3.040 nonbonded pdb=" O ASN B 121 " pdb=" OG1 THR B 125 " model vdw 2.324 3.040 ... (remaining 52409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.300 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6507 Z= 0.199 Angle : 0.637 9.768 8837 Z= 0.352 Chirality : 0.045 0.153 921 Planarity : 0.006 0.069 1137 Dihedral : 11.919 81.959 2359 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.92 % Allowed : 7.96 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -4.11 (0.24), residues: 774 helix: -3.74 (0.14), residues: 383 sheet: -1.03 (0.85), residues: 42 loop : -1.49 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 427 HIS 0.004 0.001 HIS B 322 PHE 0.008 0.001 PHE B 230 TYR 0.023 0.001 TYR B 385 ARG 0.002 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8123 (mtpp) REVERT: A 401 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8830 (mm) REVERT: A 471 SER cc_start: 0.8031 (t) cc_final: 0.7810 (p) REVERT: A 478 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6104 (m-80) REVERT: B 94 LYS cc_start: 0.8433 (tttt) cc_final: 0.8039 (ttmt) REVERT: B 163 TRP cc_start: 0.7593 (t60) cc_final: 0.7253 (t60) REVERT: B 276 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8294 (p) REVERT: B 408 MET cc_start: 0.8354 (mpt) cc_final: 0.8146 (mpt) REVERT: B 518 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6831 (ppt90) REVERT: B 601 ASN cc_start: 0.7834 (m-40) cc_final: 0.7531 (t0) outliers start: 34 outliers final: 6 residues processed: 209 average time/residue: 0.2008 time to fit residues: 54.0503 Evaluate side-chains 126 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 518 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 0.0980 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 463 ASN A 495 GLN B 345 HIS B 397 ASN B 493 HIS B 524 GLN B 535 HIS B 556 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.192015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.157052 restraints weight = 7841.037| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.40 r_work: 0.3734 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 6507 Z= 0.207 Angle : 0.605 9.790 8837 Z= 0.309 Chirality : 0.043 0.225 921 Planarity : 0.005 0.050 1137 Dihedral : 6.472 59.134 866 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.62 % Allowed : 13.75 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.38 (0.27), residues: 774 helix: -1.87 (0.23), residues: 373 sheet: -0.98 (0.82), residues: 41 loop : -1.15 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 427 HIS 0.005 0.001 HIS B 493 PHE 0.015 0.001 PHE B 525 TYR 0.019 0.001 TYR A 442 ARG 0.007 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 446 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7866 (mtp85) REVERT: A 460 VAL cc_start: 0.7640 (t) cc_final: 0.7386 (p) REVERT: A 471 SER cc_start: 0.8163 (t) cc_final: 0.7751 (p) REVERT: A 478 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: B 94 LYS cc_start: 0.8577 (tttt) cc_final: 0.8124 (ttmt) REVERT: B 518 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7071 (ppt90) REVERT: B 601 ASN cc_start: 0.8269 (m-40) cc_final: 0.7681 (t0) outliers start: 25 outliers final: 12 residues processed: 158 average time/residue: 0.1937 time to fit residues: 40.0594 Evaluate side-chains 131 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 568 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.0370 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN B 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.182067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147950 restraints weight = 7835.928| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.33 r_work: 0.3650 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6507 Z= 0.204 Angle : 0.571 8.839 8837 Z= 0.288 Chirality : 0.042 0.156 921 Planarity : 0.005 0.046 1137 Dihedral : 5.649 54.754 859 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.34 % Allowed : 14.18 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.28), residues: 774 helix: -1.21 (0.25), residues: 373 sheet: -0.76 (0.83), residues: 41 loop : -1.07 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 PHE 0.022 0.001 PHE B 525 TYR 0.015 0.001 TYR B 385 ARG 0.008 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8296 (tppt) cc_final: 0.8074 (tppt) REVERT: A 446 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8044 (mtp85) REVERT: A 471 SER cc_start: 0.8132 (t) cc_final: 0.7678 (p) REVERT: A 478 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.6191 (m-80) REVERT: B 94 LYS cc_start: 0.8493 (tttt) cc_final: 0.8024 (ttmt) REVERT: B 160 GLU cc_start: 0.7731 (tp30) cc_final: 0.7494 (tp30) REVERT: B 518 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7030 (ppt90) REVERT: B 600 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7653 (mtm-85) REVERT: B 601 ASN cc_start: 0.8292 (m-40) cc_final: 0.7717 (t0) outliers start: 30 outliers final: 19 residues processed: 150 average time/residue: 0.1801 time to fit residues: 35.8476 Evaluate side-chains 142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 459 ASN Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 518 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN ** B 535 HIS ** 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 = 0.4144 r_free = 0.4144 target = 0.178158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.143326 restraints weight = 8033.740| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.35 r_work: 0.3614 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6507 Z= 0.280 Angle : 0.604 9.843 8837 Z= 0.306 Chirality : 0.044 0.136 921 Planarity : 0.005 0.047 1137 Dihedral : 5.706 51.081 859 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.49 % Allowed : 15.05 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.29), residues: 774 helix: -0.93 (0.25), residues: 381 sheet: -0.87 (0.80), residues: 41 loop : -0.71 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 168 HIS 0.004 0.001 HIS B 535 PHE 0.028 0.002 PHE B 525 TYR 0.018 0.002 TYR B 385 ARG 0.008 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 345 ARG cc_start: 0.8030 (tpt-90) cc_final: 0.7688 (tpt-90) REVERT: A 415 LYS cc_start: 0.8286 (tppt) cc_final: 0.7994 (tppt) REVERT: A 446 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8189 (mtp85) REVERT: A 460 VAL cc_start: 0.7667 (t) cc_final: 0.7436 (p) REVERT: A 471 SER cc_start: 0.8153 (t) cc_final: 0.7668 (p) REVERT: A 478 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.6322 (m-80) REVERT: B 94 LYS cc_start: 0.8543 (tttt) cc_final: 0.8024 (ttmt) REVERT: B 160 GLU cc_start: 0.7771 (tp30) cc_final: 0.7499 (tp30) REVERT: B 518 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7059 (ppt90) REVERT: B 601 ASN cc_start: 0.8302 (m-40) cc_final: 0.7829 (t0) outliers start: 31 outliers final: 20 residues processed: 145 average time/residue: 0.1846 time to fit residues: 35.4707 Evaluate side-chains 140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 0.0270 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN B 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.180410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145880 restraints weight = 7958.190| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.34 r_work: 0.3671 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6507 Z= 0.194 Angle : 0.566 11.217 8837 Z= 0.284 Chirality : 0.042 0.129 921 Planarity : 0.004 0.043 1137 Dihedral : 5.521 48.194 859 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.78 % Allowed : 15.92 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.30), residues: 774 helix: -0.58 (0.26), residues: 381 sheet: -0.64 (0.81), residues: 41 loop : -0.64 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 168 HIS 0.004 0.001 HIS B 417 PHE 0.010 0.001 PHE B 314 TYR 0.016 0.001 TYR B 194 ARG 0.008 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.720 Fit side-chains REVERT: A 415 LYS cc_start: 0.8247 (tppt) cc_final: 0.7940 (tppt) REVERT: A 446 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8144 (mtp85) REVERT: A 460 VAL cc_start: 0.7640 (t) cc_final: 0.7412 (p) REVERT: A 471 SER cc_start: 0.8133 (t) cc_final: 0.7656 (p) REVERT: A 478 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: B 74 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: B 94 LYS cc_start: 0.8494 (tttt) cc_final: 0.7987 (ttmt) REVERT: B 160 GLU cc_start: 0.7736 (tp30) cc_final: 0.7492 (tp30) REVERT: B 518 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7051 (ppt90) REVERT: B 600 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7559 (mtm-85) REVERT: B 601 ASN cc_start: 0.8295 (m-40) cc_final: 0.7867 (t0) outliers start: 33 outliers final: 20 residues processed: 151 average time/residue: 0.1781 time to fit residues: 36.0461 Evaluate side-chains 138 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN B 322 HIS B 535 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.177651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.143007 restraints weight = 7887.652| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.32 r_work: 0.3607 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6507 Z= 0.278 Angle : 0.609 12.866 8837 Z= 0.306 Chirality : 0.044 0.120 921 Planarity : 0.004 0.046 1137 Dihedral : 5.556 44.875 858 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.92 % Allowed : 16.35 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.91 (0.30), residues: 774 helix: -0.53 (0.26), residues: 381 sheet: -0.67 (0.80), residues: 41 loop : -0.49 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 PHE 0.031 0.002 PHE B 525 TYR 0.018 0.002 TYR B 385 ARG 0.012 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.742 Fit side-chains REVERT: A 415 LYS cc_start: 0.8247 (tppt) cc_final: 0.7940 (tppt) REVERT: A 446 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8123 (mtp85) REVERT: A 460 VAL cc_start: 0.7760 (t) cc_final: 0.7512 (p) REVERT: A 471 SER cc_start: 0.8155 (t) cc_final: 0.7629 (p) REVERT: A 478 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6395 (m-80) REVERT: B 74 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: B 94 LYS cc_start: 0.8530 (tttt) cc_final: 0.7997 (ttmt) REVERT: B 160 GLU cc_start: 0.7819 (tp30) cc_final: 0.7598 (tp30) REVERT: B 366 MET cc_start: 0.7093 (mmm) cc_final: 0.6887 (tpt) REVERT: B 518 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7074 (ppt90) REVERT: B 600 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7651 (mtm-85) REVERT: B 601 ASN cc_start: 0.8318 (m-40) cc_final: 0.7940 (t0) outliers start: 34 outliers final: 21 residues processed: 139 average time/residue: 0.2017 time to fit residues: 36.5175 Evaluate side-chains 140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 580 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143513 restraints weight = 7907.390| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.31 r_work: 0.3633 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6507 Z= 0.259 Angle : 0.618 13.926 8837 Z= 0.306 Chirality : 0.044 0.149 921 Planarity : 0.004 0.048 1137 Dihedral : 5.263 42.688 856 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.63 % Allowed : 16.79 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.83 (0.30), residues: 774 helix: -0.45 (0.27), residues: 382 sheet: -0.61 (0.81), residues: 40 loop : -0.47 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 PHE 0.032 0.001 PHE B 525 TYR 0.017 0.002 TYR B 385 ARG 0.011 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.747 Fit side-chains REVERT: A 415 LYS cc_start: 0.8247 (tppt) cc_final: 0.7949 (tppt) REVERT: A 446 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8166 (mtp85) REVERT: A 460 VAL cc_start: 0.7803 (t) cc_final: 0.7556 (p) REVERT: A 471 SER cc_start: 0.8143 (t) cc_final: 0.7600 (p) REVERT: A 478 TYR cc_start: 0.6865 (OUTLIER) cc_final: 0.6461 (m-80) REVERT: B 74 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: B 94 LYS cc_start: 0.8505 (tttt) cc_final: 0.7957 (ttmt) REVERT: B 160 GLU cc_start: 0.7845 (tp30) cc_final: 0.7615 (tp30) REVERT: B 408 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.6556 (mpt) REVERT: B 518 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7120 (ppt90) REVERT: B 601 ASN cc_start: 0.8323 (m-40) cc_final: 0.7938 (t0) outliers start: 32 outliers final: 24 residues processed: 138 average time/residue: 0.2029 time to fit residues: 36.8355 Evaluate side-chains 141 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 580 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 68 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 51 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.180483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145986 restraints weight = 7900.192| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.32 r_work: 0.3632 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6507 Z= 0.197 Angle : 0.599 14.297 8837 Z= 0.295 Chirality : 0.042 0.155 921 Planarity : 0.004 0.051 1137 Dihedral : 5.144 42.778 856 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.20 % Allowed : 17.51 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.72 (0.31), residues: 774 helix: -0.34 (0.27), residues: 390 sheet: -0.47 (0.82), residues: 40 loop : -0.45 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 PHE 0.040 0.001 PHE B 525 TYR 0.015 0.001 TYR B 385 ARG 0.013 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.749 Fit side-chains REVERT: A 415 LYS cc_start: 0.8262 (tppt) cc_final: 0.7696 (tppt) REVERT: A 446 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8152 (mtp85) REVERT: A 460 VAL cc_start: 0.7717 (t) cc_final: 0.7474 (p) REVERT: A 471 SER cc_start: 0.8089 (t) cc_final: 0.7549 (p) REVERT: A 478 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: B 94 LYS cc_start: 0.8413 (tttt) cc_final: 0.7891 (ttmt) REVERT: B 160 GLU cc_start: 0.7882 (tp30) cc_final: 0.7630 (tp30) REVERT: B 408 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.6493 (mpt) REVERT: B 518 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7112 (ppt90) REVERT: B 600 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.7489 (mtm-85) REVERT: B 601 ASN cc_start: 0.8379 (m-40) cc_final: 0.7941 (t0) outliers start: 29 outliers final: 20 residues processed: 135 average time/residue: 0.1976 time to fit residues: 34.6718 Evaluate side-chains 136 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 580 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.176869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.141969 restraints weight = 7996.704| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.36 r_work: 0.3598 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6507 Z= 0.285 Angle : 0.639 14.128 8837 Z= 0.317 Chirality : 0.044 0.159 921 Planarity : 0.005 0.054 1137 Dihedral : 5.231 43.830 856 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.63 % Allowed : 17.51 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.76 (0.30), residues: 774 helix: -0.38 (0.26), residues: 390 sheet: -0.22 (0.81), residues: 38 loop : -0.50 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 477 HIS 0.005 0.001 HIS B 417 PHE 0.043 0.002 PHE B 525 TYR 0.018 0.002 TYR B 385 ARG 0.013 0.001 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.691 Fit side-chains REVERT: A 415 LYS cc_start: 0.8237 (tppt) cc_final: 0.7686 (tppt) REVERT: A 446 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8161 (mtp85) REVERT: A 454 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7438 (tt0) REVERT: A 460 VAL cc_start: 0.7829 (t) cc_final: 0.7572 (p) REVERT: A 471 SER cc_start: 0.8043 (t) cc_final: 0.7483 (p) REVERT: A 478 TYR cc_start: 0.6550 (OUTLIER) cc_final: 0.6010 (m-80) REVERT: B 94 LYS cc_start: 0.8455 (tttt) cc_final: 0.7906 (ttmt) REVERT: B 160 GLU cc_start: 0.7913 (tp30) cc_final: 0.7664 (tp30) REVERT: B 198 ASP cc_start: 0.7149 (m-30) cc_final: 0.6913 (m-30) REVERT: B 408 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.6650 (mpt) REVERT: B 518 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7112 (ppt90) REVERT: B 601 ASN cc_start: 0.8361 (m-40) cc_final: 0.7949 (t0) outliers start: 32 outliers final: 24 residues processed: 131 average time/residue: 0.1970 time to fit residues: 34.1395 Evaluate side-chains 136 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 580 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.179064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144401 restraints weight = 7949.578| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.34 r_work: 0.3612 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6507 Z= 0.228 Angle : 0.621 14.024 8837 Z= 0.308 Chirality : 0.043 0.152 921 Planarity : 0.004 0.057 1137 Dihedral : 5.162 42.405 856 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.49 % Allowed : 17.95 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.65 (0.30), residues: 774 helix: -0.28 (0.26), residues: 390 sheet: -0.19 (0.83), residues: 38 loop : -0.47 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 PHE 0.047 0.002 PHE B 525 TYR 0.016 0.002 TYR B 385 ARG 0.014 0.001 ARG B 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.920 Fit side-chains REVERT: A 415 LYS cc_start: 0.8228 (tppt) cc_final: 0.7671 (tppt) REVERT: A 446 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8132 (mtp85) REVERT: A 454 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7440 (tt0) REVERT: A 460 VAL cc_start: 0.7794 (t) cc_final: 0.7541 (p) REVERT: A 471 SER cc_start: 0.8025 (t) cc_final: 0.7450 (p) REVERT: A 478 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.5953 (m-80) REVERT: B 94 LYS cc_start: 0.8414 (tttt) cc_final: 0.7876 (ttmt) REVERT: B 160 GLU cc_start: 0.7948 (tp30) cc_final: 0.7691 (tp30) REVERT: B 198 ASP cc_start: 0.7116 (m-30) cc_final: 0.6895 (m-30) REVERT: B 367 GLU cc_start: 0.6962 (tt0) cc_final: 0.6682 (mt-10) REVERT: B 408 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.6521 (mpt) REVERT: B 518 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7133 (ppt90) REVERT: B 601 ASN cc_start: 0.8357 (m-40) cc_final: 0.7936 (t0) outliers start: 31 outliers final: 23 residues processed: 128 average time/residue: 0.2018 time to fit residues: 33.8493 Evaluate side-chains 136 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 290 ASN Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 580 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.179507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144801 restraints weight = 8091.667| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.36 r_work: 0.3616 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6507 Z= 0.227 Angle : 0.617 13.910 8837 Z= 0.306 Chirality : 0.043 0.149 921 Planarity : 0.004 0.058 1137 Dihedral : 5.123 42.454 856 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.34 % Allowed : 17.95 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.60 (0.31), residues: 774 helix: -0.20 (0.26), residues: 390 sheet: -0.20 (0.84), residues: 38 loop : -0.48 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 PHE 0.045 0.002 PHE B 525 TYR 0.016 0.002 TYR B 385 ARG 0.014 0.001 ARG B 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3454.94 seconds wall clock time: 59 minutes 58.64 seconds (3598.64 seconds total)