Starting phenix.real_space_refine on Tue Feb 11 16:44:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4u_36892/02_2025/8k4u_36892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4u_36892/02_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_36892/02_2025/8k4u_36892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4u_36892/02_2025/8k4u_36892.map" model { file = "/net/cci-nas-00/data/ceres_data/8k4u_36892/02_2025/8k4u_36892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4u_36892/02_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-5592/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: 4.84, per 1000 atoms: 0.77 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: 1.58 Conformation dependent library (CDL) restraints added in 843.4 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: 0.67 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: 1.86 Time building geometry restraints manager: 1.83 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: 3.870 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.910 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- 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 : 0.673 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: 0.2043 time to fit residues: 54.7719 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 : 0.681 ------------------------------------------------------------------------------- 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: 4.9990 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 = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156964 restraints weight = 7841.030| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.41 r_work: 0.3738 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 9.791 8837 Z= 0.309 Chirality : 0.043 0.225 921 Planarity : 0.005 0.051 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 : 0.693 Fit side-chains revert: symmetry clash REVERT: A 446 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7867 (mtp85) REVERT: A 460 VAL cc_start: 0.7643 (t) cc_final: 0.7389 (p) REVERT: A 471 SER cc_start: 0.8162 (t) cc_final: 0.7750 (p) REVERT: A 478 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: B 94 LYS cc_start: 0.8579 (tttt) cc_final: 0.8124 (ttmt) REVERT: B 518 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7071 (ppt90) REVERT: B 601 ASN cc_start: 0.8279 (m-40) cc_final: 0.7688 (t0) outliers start: 25 outliers final: 12 residues processed: 158 average time/residue: 0.1901 time to fit residues: 39.2825 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 : 0.669 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.182093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147973 restraints weight = 7843.221| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.34 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: 0.2815 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= 0.207 Angle : 0.573 8.863 8837 Z= 0.289 Chirality : 0.042 0.154 921 Planarity : 0.005 0.047 1137 Dihedral : 5.655 54.892 859 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.49 % Allowed : 13.89 % Favored : 81.62 % 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: -1.85 (0.28), residues: 774 helix: -1.27 (0.25), residues: 372 sheet: -0.78 (0.83), residues: 41 loop : -1.08 (0.32), residues: 361 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 0.021 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 159 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8305 (tppt) cc_final: 0.8084 (tppt) REVERT: A 446 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8042 (mtp85) REVERT: A 460 VAL cc_start: 0.7717 (t) cc_final: 0.7453 (p) REVERT: A 471 SER cc_start: 0.8138 (t) cc_final: 0.7684 (p) REVERT: A 478 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: B 94 LYS cc_start: 0.8494 (tttt) cc_final: 0.8025 (ttmt) REVERT: B 160 GLU cc_start: 0.7749 (tp30) cc_final: 0.7523 (tp30) REVERT: B 518 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7031 (ppt90) REVERT: B 600 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7631 (mtm-85) REVERT: B 601 ASN cc_start: 0.8293 (m-40) cc_final: 0.7723 (t0) outliers start: 31 outliers final: 21 residues processed: 149 average time/residue: 0.1889 time to fit residues: 37.6720 Evaluate side-chains 143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 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 378 LEU 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 Chi-restraints excluded: chain B residue 568 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ** 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 = 0.4158 r_free = 0.4158 target = 0.179362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.144463 restraints weight = 8041.112| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.37 r_work: 0.3655 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3051 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= 0.261 Angle : 0.592 9.861 8837 Z= 0.298 Chirality : 0.043 0.136 921 Planarity : 0.004 0.047 1137 Dihedral : 5.673 51.425 859 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.63 % Allowed : 14.76 % Favored : 80.61 % 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: -1.47 (0.29), residues: 774 helix: -0.97 (0.26), residues: 381 sheet: -0.90 (0.81), residues: 41 loop : -0.81 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 168 HIS 0.004 0.001 HIS B 417 PHE 0.026 0.001 PHE B 525 TYR 0.017 0.002 TYR B 385 ARG 0.009 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 159 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 345 ARG cc_start: 0.8029 (tpt-90) cc_final: 0.7714 (tpt-90) REVERT: A 415 LYS cc_start: 0.8283 (tppt) cc_final: 0.7992 (tppt) REVERT: A 446 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8139 (mtp85) REVERT: A 460 VAL cc_start: 0.7770 (t) cc_final: 0.7535 (p) REVERT: A 471 SER cc_start: 0.8126 (t) cc_final: 0.7659 (p) REVERT: A 478 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: B 94 LYS cc_start: 0.8519 (tttt) cc_final: 0.8024 (ttmt) REVERT: B 160 GLU cc_start: 0.7748 (tp30) cc_final: 0.7485 (tp30) REVERT: B 518 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7060 (ppt90) REVERT: B 601 ASN cc_start: 0.8276 (m-40) cc_final: 0.7815 (t0) outliers start: 32 outliers final: 20 residues processed: 150 average time/residue: 0.1838 time to fit residues: 36.8421 Evaluate side-chains 144 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 411 SER Chi-restraints excluded: chain B residue 518 ARG 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: 0.0970 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.180902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.146482 restraints weight = 7952.805| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.33 r_work: 0.3678 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6507 Z= 0.188 Angle : 0.559 11.248 8837 Z= 0.281 Chirality : 0.042 0.126 921 Planarity : 0.004 0.043 1137 Dihedral : 5.486 47.721 859 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.49 % Allowed : 15.63 % Favored : 79.88 % 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: -1.03 (0.30), residues: 774 helix: -0.55 (0.27), residues: 381 sheet: -0.67 (0.81), residues: 41 loop : -0.66 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 168 HIS 0.005 0.001 HIS B 417 PHE 0.010 0.001 PHE B 525 TYR 0.015 0.001 TYR B 385 ARG 0.010 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 161 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.839 Fit side-chains REVERT: A 415 LYS cc_start: 0.8248 (tppt) cc_final: 0.7949 (tppt) REVERT: A 446 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8059 (mtp85) REVERT: A 460 VAL cc_start: 0.7704 (t) cc_final: 0.7495 (p) REVERT: A 471 SER cc_start: 0.8103 (t) cc_final: 0.7632 (p) REVERT: A 478 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.6262 (m-80) REVERT: A 502 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8731 (mm) REVERT: B 74 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7122 (mm-30) REVERT: B 94 LYS cc_start: 0.8480 (tttt) cc_final: 0.7976 (ttmt) REVERT: B 160 GLU cc_start: 0.7734 (tp30) cc_final: 0.7519 (tp30) REVERT: B 518 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7062 (ppt90) REVERT: B 600 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7605 (mtm-85) REVERT: B 601 ASN cc_start: 0.8290 (m-40) cc_final: 0.7861 (t0) outliers start: 31 outliers final: 20 residues processed: 149 average time/residue: 0.1855 time to fit residues: 36.9336 Evaluate side-chains 143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 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 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 502 LEU 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 411 SER Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG 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: 4.9990 chunk 6 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.179058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144525 restraints weight = 7882.686| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.33 r_work: 0.3609 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3387 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= 0.263 Angle : 0.596 12.630 8837 Z= 0.299 Chirality : 0.044 0.130 921 Planarity : 0.004 0.045 1137 Dihedral : 5.491 45.431 858 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.07 % Allowed : 15.92 % Favored : 79.02 % 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: -0.49 (0.26), residues: 387 sheet: -0.56 (0.83), residues: 40 loop : -0.55 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 477 HIS 0.004 0.001 HIS B 322 PHE 0.021 0.001 PHE B 327 TYR 0.018 0.002 TYR B 385 ARG 0.010 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 157 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.701 Fit side-chains REVERT: A 415 LYS cc_start: 0.8261 (tppt) cc_final: 0.7945 (tppt) REVERT: A 446 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8060 (mtp85) REVERT: A 460 VAL cc_start: 0.7818 (t) cc_final: 0.7596 (p) REVERT: A 471 SER cc_start: 0.8120 (t) cc_final: 0.7624 (p) REVERT: A 478 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6365 (m-80) REVERT: A 502 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8789 (mm) REVERT: B 74 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: B 94 LYS cc_start: 0.8498 (tttt) cc_final: 0.7987 (ttmt) REVERT: B 518 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7049 (ppt90) REVERT: B 600 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7557 (mtm-85) REVERT: B 601 ASN cc_start: 0.8332 (m-40) cc_final: 0.7897 (t0) outliers start: 35 outliers final: 22 residues processed: 143 average time/residue: 0.1999 time to fit residues: 37.4124 Evaluate side-chains 142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 A residue 502 LEU 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 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: 2.9990 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.179414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144721 restraints weight = 7875.492| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.33 r_work: 0.3612 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6507 Z= 0.244 Angle : 0.609 13.621 8837 Z= 0.303 Chirality : 0.043 0.148 921 Planarity : 0.004 0.047 1137 Dihedral : 5.207 43.143 856 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.78 % Allowed : 16.50 % 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: -0.79 (0.31), residues: 774 helix: -0.39 (0.27), residues: 387 sheet: -0.62 (0.81), residues: 40 loop : -0.48 (0.35), residues: 347 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 0.019 0.001 PHE B 327 TYR 0.017 0.002 TYR B 385 ARG 0.012 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 155 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.062 Fit side-chains REVERT: A 415 LYS cc_start: 0.8251 (tppt) cc_final: 0.7689 (tppt) REVERT: A 446 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8089 (mtp85) REVERT: A 471 SER cc_start: 0.8159 (t) cc_final: 0.7645 (p) REVERT: A 478 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.6397 (m-80) REVERT: B 74 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: B 94 LYS cc_start: 0.8461 (tttt) cc_final: 0.7935 (ttmt) REVERT: B 160 GLU cc_start: 0.7795 (tp30) cc_final: 0.7449 (tp30) REVERT: B 518 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7059 (ppt90) REVERT: B 600 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7571 (mtm-85) REVERT: B 601 ASN cc_start: 0.8340 (m-40) cc_final: 0.7897 (t0) outliers start: 33 outliers final: 22 residues processed: 141 average time/residue: 0.2192 time to fit residues: 40.7342 Evaluate side-chains 140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 68 optimal weight: 0.6980 chunk 13 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.181560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.147261 restraints weight = 7873.727| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.33 r_work: 0.3655 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6507 Z= 0.178 Angle : 0.588 14.202 8837 Z= 0.291 Chirality : 0.042 0.148 921 Planarity : 0.004 0.053 1137 Dihedral : 5.065 43.127 856 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.91 % Allowed : 17.95 % Favored : 78.15 % 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: -0.63 (0.31), residues: 774 helix: -0.23 (0.27), residues: 387 sheet: -0.46 (0.82), residues: 40 loop : -0.46 (0.35), residues: 347 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 0.019 0.001 PHE B 327 TYR 0.013 0.001 TYR B 385 ARG 0.012 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 143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.699 Fit side-chains REVERT: A 415 LYS cc_start: 0.8228 (tppt) cc_final: 0.7665 (tppt) REVERT: A 446 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8109 (mtp85) REVERT: A 471 SER cc_start: 0.8077 (t) cc_final: 0.7565 (p) REVERT: A 478 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: B 94 LYS cc_start: 0.8420 (tttt) cc_final: 0.7901 (ttmt) REVERT: B 160 GLU cc_start: 0.7784 (tp30) cc_final: 0.7379 (tp30) REVERT: B 518 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7057 (ppt90) REVERT: B 600 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7559 (mtm-85) REVERT: B 601 ASN cc_start: 0.8340 (m-40) cc_final: 0.7898 (t0) outliers start: 27 outliers final: 22 residues processed: 131 average time/residue: 0.1992 time to fit residues: 34.0258 Evaluate side-chains 138 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.177699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.142799 restraints weight = 7987.935| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.35 r_work: 0.3589 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6507 Z= 0.319 Angle : 0.645 14.109 8837 Z= 0.323 Chirality : 0.045 0.161 921 Planarity : 0.005 0.051 1137 Dihedral : 5.260 43.313 856 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.20 % Allowed : 17.37 % Favored : 78.44 % 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: -0.75 (0.30), residues: 774 helix: -0.37 (0.26), residues: 390 sheet: -0.58 (0.79), residues: 40 loop : -0.45 (0.35), residues: 344 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 0.018 0.002 PHE A 420 TYR 0.019 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 143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.779 Fit side-chains REVERT: A 415 LYS cc_start: 0.8246 (tppt) cc_final: 0.7699 (tppt) REVERT: A 446 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8188 (mtp85) REVERT: A 471 SER cc_start: 0.8071 (t) cc_final: 0.7513 (p) REVERT: A 478 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.6052 (m-80) REVERT: B 94 LYS cc_start: 0.8469 (tttt) cc_final: 0.7932 (ttmt) REVERT: B 518 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7061 (ppt90) REVERT: B 597 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7807 (tm-30) REVERT: B 600 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7575 (mtm-85) REVERT: B 601 ASN cc_start: 0.8344 (m-40) cc_final: 0.7939 (t0) outliers start: 29 outliers final: 22 residues processed: 134 average time/residue: 0.2132 time to fit residues: 37.7260 Evaluate side-chains 135 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.179924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145399 restraints weight = 7933.997| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.34 r_work: 0.3618 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3727 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= 0.221 Angle : 0.622 13.928 8837 Z= 0.308 Chirality : 0.043 0.150 921 Planarity : 0.004 0.059 1137 Dihedral : 5.168 42.641 856 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.76 % Allowed : 18.09 % Favored : 78.15 % 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: -0.64 (0.31), residues: 774 helix: -0.22 (0.27), residues: 389 sheet: -0.61 (0.81), residues: 40 loop : -0.46 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 477 HIS 0.005 0.001 HIS B 417 PHE 0.018 0.001 PHE B 327 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: 26 poor density : 114 time to evaluate : 0.580 Fit side-chains REVERT: A 415 LYS cc_start: 0.8223 (tppt) cc_final: 0.7677 (tppt) REVERT: A 446 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8108 (mtp85) REVERT: A 471 SER cc_start: 0.8053 (t) cc_final: 0.7490 (p) REVERT: A 478 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.5957 (m-80) REVERT: B 94 LYS cc_start: 0.8410 (tttt) cc_final: 0.7892 (ttmt) REVERT: B 160 GLU cc_start: 0.7654 (tp30) cc_final: 0.7374 (tp30) REVERT: B 518 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7075 (ppt90) REVERT: B 597 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 600 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7593 (mtm-85) REVERT: B 601 ASN cc_start: 0.8340 (m-40) cc_final: 0.7926 (t0) outliers start: 26 outliers final: 20 residues processed: 130 average time/residue: 0.2155 time to fit residues: 36.4663 Evaluate side-chains 136 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 chunk 38 optimal weight: 0.0030 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.181117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.146448 restraints weight = 8065.272| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.37 r_work: 0.3637 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6507 Z= 0.203 Angle : 0.613 13.725 8837 Z= 0.305 Chirality : 0.042 0.146 921 Planarity : 0.004 0.058 1137 Dihedral : 5.073 42.905 856 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.62 % Allowed : 18.81 % 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: -0.57 (0.31), residues: 774 helix: -0.16 (0.27), residues: 390 sheet: -0.64 (0.82), residues: 40 loop : -0.42 (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 0.018 0.001 PHE B 327 TYR 0.015 0.001 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: 3414.85 seconds wall clock time: 61 minutes 40.36 seconds (3700.36 seconds total)