Starting phenix.real_space_refine on Thu Jul 24 13:46:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4u_36892/07_2025/8k4u_36892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4u_36892/07_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_36892/07_2025/8k4u_36892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4u_36892/07_2025/8k4u_36892.map" model { file = "/net/cci-nas-00/data/ceres_data/8k4u_36892/07_2025/8k4u_36892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4u_36892/07_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-5711/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: 4.57, per 1000 atoms: 0.72 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: 1.42 Conformation dependent library (CDL) restraints added in 857.8 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: 0.75 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: 1.80 Time building geometry restraints manager: 1.71 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.860 Find NCS groups from input model: 0.070 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:2.860 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 : 0.005 0.200 6515 Z= 0.194 Angle : 0.637 9.768 8849 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 Details of bonding type rmsd hydrogen bonds : bond 0.30761 ( 242) hydrogen bonds : angle 10.98394 ( 690) metal coordination : bond 0.19887 ( 2) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.58772 ( 12) covalent geometry : bond 0.00320 ( 6507) covalent geometry : angle 0.63694 ( 8837) *********************** 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 : 0.691 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: 0.2068 time to fit residues: 55.5931 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 : 0.746 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.191602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157258 restraints weight = 7838.468| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.31 r_work: 0.3749 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 6515 Z= 0.145 Angle : 0.620 9.841 8849 Z= 0.316 Chirality : 0.043 0.220 921 Planarity : 0.005 0.050 1137 Dihedral : 6.509 59.081 866 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.62 % Allowed : 14.04 % Favored : 82.34 % 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: -2.43 (0.27), residues: 774 helix: -1.92 (0.22), residues: 382 sheet: -1.00 (0.82), residues: 41 loop : -1.13 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 427 HIS 0.006 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 Details of bonding type rmsd hydrogen bonds : bond 0.05296 ( 242) hydrogen bonds : angle 5.94710 ( 690) metal coordination : bond 0.00205 ( 2) SS BOND : bond 0.00645 ( 6) SS BOND : angle 3.44871 ( 12) covalent geometry : bond 0.00332 ( 6507) covalent geometry : angle 0.60757 ( 8837) *********************** 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 161 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8243 (tppt) cc_final: 0.7818 (tppt) REVERT: A 446 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7840 (mtp85) REVERT: A 460 VAL cc_start: 0.7670 (t) cc_final: 0.7406 (p) REVERT: A 471 SER cc_start: 0.8145 (t) cc_final: 0.7728 (p) REVERT: A 478 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: B 94 LYS cc_start: 0.8540 (tttt) cc_final: 0.8069 (ttmt) REVERT: B 518 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7042 (ppt90) REVERT: B 601 ASN cc_start: 0.8268 (m-40) cc_final: 0.7669 (t0) outliers start: 25 outliers final: 13 residues processed: 152 average time/residue: 0.2147 time to fit residues: 42.8254 Evaluate side-chains 132 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR 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 A residue 501 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 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: 0.9980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.182284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147943 restraints weight = 7849.085| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.34 r_work: 0.3656 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6515 Z= 0.139 Angle : 0.593 10.633 8849 Z= 0.301 Chirality : 0.043 0.219 921 Planarity : 0.005 0.046 1137 Dihedral : 5.697 53.180 859 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.63 % Allowed : 14.33 % Favored : 81.04 % 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: -1.78 (0.29), residues: 774 helix: -1.19 (0.25), residues: 373 sheet: -0.75 (0.83), residues: 41 loop : -1.08 (0.32), residues: 360 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 0.020 0.001 PHE B 525 TYR 0.015 0.001 TYR B 385 ARG 0.008 0.000 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 242) hydrogen bonds : angle 5.22054 ( 690) metal coordination : bond 0.00123 ( 2) SS BOND : bond 0.00955 ( 6) SS BOND : angle 4.03865 ( 12) covalent geometry : bond 0.00318 ( 6507) covalent geometry : angle 0.57414 ( 8837) *********************** 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: 32 poor density : 127 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8254 (tppt) cc_final: 0.7987 (tppt) REVERT: A 446 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8038 (mtp85) REVERT: A 460 VAL cc_start: 0.7741 (t) cc_final: 0.7487 (p) REVERT: A 471 SER cc_start: 0.8147 (t) cc_final: 0.7672 (p) REVERT: A 478 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.6334 (m-80) REVERT: B 94 LYS cc_start: 0.8502 (tttt) cc_final: 0.8036 (ttmt) REVERT: B 160 GLU cc_start: 0.7753 (tp30) cc_final: 0.7514 (tp30) REVERT: B 518 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7056 (ppt90) REVERT: B 600 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: B 601 ASN cc_start: 0.8247 (m-40) cc_final: 0.7715 (t0) outliers start: 32 outliers final: 18 residues processed: 146 average time/residue: 0.2465 time to fit residues: 48.0228 Evaluate side-chains 139 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 141 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 434 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: 4.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN B 322 HIS ** 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 = 0.4126 r_free = 0.4126 target = 0.176266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141169 restraints weight = 8040.550| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.36 r_work: 0.3585 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 6515 Z= 0.232 Angle : 0.654 10.699 8849 Z= 0.333 Chirality : 0.046 0.203 921 Planarity : 0.005 0.049 1137 Dihedral : 5.855 48.638 859 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.49 % Allowed : 15.34 % Favored : 80.17 % 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 (0.30), residues: 774 helix: -0.93 (0.26), residues: 381 sheet: -0.92 (0.81), residues: 41 loop : -0.71 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 477 HIS 0.005 0.001 HIS B 535 PHE 0.027 0.002 PHE B 525 TYR 0.020 0.002 TYR B 385 ARG 0.008 0.001 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 242) hydrogen bonds : angle 5.19760 ( 690) metal coordination : bond 0.00280 ( 2) SS BOND : bond 0.00512 ( 6) SS BOND : angle 3.75114 ( 12) covalent geometry : bond 0.00545 ( 6507) covalent geometry : angle 0.63975 ( 8837) *********************** 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 155 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: A 345 ARG cc_start: 0.8132 (tpt-90) cc_final: 0.7653 (tpt-90) REVERT: A 415 LYS cc_start: 0.8305 (tppt) cc_final: 0.7824 (tppt) REVERT: A 416 LEU cc_start: 0.8770 (mt) cc_final: 0.8187 (mt) REVERT: A 446 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8202 (mtp85) REVERT: A 460 VAL cc_start: 0.7921 (t) cc_final: 0.7668 (p) REVERT: A 471 SER cc_start: 0.8150 (t) cc_final: 0.7660 (p) REVERT: A 478 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: B 94 LYS cc_start: 0.8567 (tttt) cc_final: 0.8044 (ttmt) REVERT: B 474 MET cc_start: 0.7981 (mmp) cc_final: 0.7777 (mmp) REVERT: B 518 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7096 (ppt90) REVERT: B 600 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7711 (mtm-85) REVERT: B 601 ASN cc_start: 0.8296 (m-40) cc_final: 0.7807 (t0) outliers start: 31 outliers final: 20 residues processed: 145 average time/residue: 0.3066 time to fit residues: 59.7101 Evaluate side-chains 137 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 133 CYS 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 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: 2.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN B 322 HIS B 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.179831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145316 restraints weight = 7939.899| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.34 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: 0.7929 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6515 Z= 0.136 Angle : 0.605 11.190 8849 Z= 0.303 Chirality : 0.042 0.188 921 Planarity : 0.004 0.048 1137 Dihedral : 5.658 44.566 859 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.63 % Allowed : 15.77 % Favored : 79.59 % 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: -1.08 (0.30), residues: 774 helix: -0.59 (0.26), residues: 381 sheet: -0.82 (0.82), residues: 41 loop : -0.68 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 168 HIS 0.005 0.001 HIS B 417 PHE 0.022 0.001 PHE B 525 TYR 0.015 0.002 TYR B 194 ARG 0.010 0.001 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 242) hydrogen bonds : angle 4.93873 ( 690) metal coordination : bond 0.00116 ( 2) SS BOND : bond 0.00947 ( 6) SS BOND : angle 3.71439 ( 12) covalent geometry : bond 0.00316 ( 6507) covalent geometry : angle 0.58945 ( 8837) *********************** 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 159 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.759 Fit side-chains REVERT: A 415 LYS cc_start: 0.8258 (tppt) cc_final: 0.7832 (tppt) REVERT: A 416 LEU cc_start: 0.8699 (mt) cc_final: 0.8247 (mt) REVERT: A 446 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8175 (mtp85) REVERT: A 460 VAL cc_start: 0.7849 (t) cc_final: 0.7623 (p) REVERT: A 471 SER cc_start: 0.8093 (t) cc_final: 0.7584 (p) REVERT: A 478 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: B 74 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: B 94 LYS cc_start: 0.8508 (tttt) cc_final: 0.7973 (ttmt) REVERT: B 160 GLU cc_start: 0.7792 (tp30) cc_final: 0.7538 (tp30) REVERT: B 366 MET cc_start: 0.6989 (mmm) cc_final: 0.6787 (tpt) REVERT: B 518 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7095 (ppt90) REVERT: B 600 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7758 (mtm-85) REVERT: B 601 ASN cc_start: 0.8363 (m-40) cc_final: 0.7901 (t0) outliers start: 32 outliers final: 20 residues processed: 146 average time/residue: 0.2014 time to fit residues: 38.6554 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 : 0.708 ------------------------------------------------------------------------------- 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 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 133 CYS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 434 THR 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: 0.5980 chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4155 r_free = 0.4155 target = 0.178592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.143388 restraints weight = 7915.353| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.34 r_work: 0.3585 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 6515 Z= 0.198 Angle : 0.647 13.134 8849 Z= 0.323 Chirality : 0.045 0.187 921 Planarity : 0.004 0.046 1137 Dihedral : 5.429 44.391 856 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.07 % Allowed : 15.77 % Favored : 79.16 % 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: -0.95 (0.30), residues: 774 helix: -0.53 (0.26), residues: 381 sheet: -0.77 (0.80), residues: 41 loop : -0.55 (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 322 PHE 0.029 0.002 PHE B 525 TYR 0.018 0.002 TYR B 385 ARG 0.011 0.001 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 242) hydrogen bonds : angle 4.97796 ( 690) metal coordination : bond 0.00248 ( 2) SS BOND : bond 0.00895 ( 6) SS BOND : angle 3.71283 ( 12) covalent geometry : bond 0.00469 ( 6507) covalent geometry : angle 0.63315 ( 8837) *********************** 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 156 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.913 Fit side-chains REVERT: A 401 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8941 (mm) REVERT: A 446 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8220 (mtp85) REVERT: A 460 VAL cc_start: 0.7929 (t) cc_final: 0.7721 (p) REVERT: A 471 SER cc_start: 0.8109 (t) cc_final: 0.7584 (p) REVERT: A 478 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: B 74 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7123 (mm-30) REVERT: B 94 LYS cc_start: 0.8533 (tttt) cc_final: 0.7976 (ttmt) REVERT: B 160 GLU cc_start: 0.7897 (tp30) cc_final: 0.7511 (tp30) REVERT: B 518 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7115 (ppt90) REVERT: B 600 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7732 (mtm-85) REVERT: B 601 ASN cc_start: 0.8370 (m-40) cc_final: 0.7972 (t0) outliers start: 35 outliers final: 21 residues processed: 140 average time/residue: 0.3401 time to fit residues: 63.4622 Evaluate side-chains 144 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 401 ILE 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 133 CYS 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 434 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 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: 0.0170 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- 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 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.177223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142564 restraints weight = 7926.333| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.31 r_work: 0.3631 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6515 Z= 0.179 Angle : 0.650 14.137 8849 Z= 0.321 Chirality : 0.044 0.184 921 Planarity : 0.004 0.047 1137 Dihedral : 5.410 44.611 856 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.07 % Allowed : 16.06 % Favored : 78.87 % 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: -0.84 (0.30), residues: 774 helix: -0.44 (0.26), residues: 384 sheet: -0.65 (0.80), residues: 40 loop : -0.51 (0.34), residues: 350 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 0.035 0.001 PHE B 525 TYR 0.017 0.002 TYR B 385 ARG 0.012 0.001 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 242) hydrogen bonds : angle 4.92300 ( 690) metal coordination : bond 0.00160 ( 2) SS BOND : bond 0.00719 ( 6) SS BOND : angle 3.61729 ( 12) covalent geometry : bond 0.00425 ( 6507) covalent geometry : angle 0.63672 ( 8837) *********************** 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 153 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.010 Fit side-chains REVERT: A 415 LYS cc_start: 0.8221 (tppt) cc_final: 0.8003 (tppt) REVERT: A 446 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8237 (mtp85) REVERT: A 471 SER cc_start: 0.8126 (t) cc_final: 0.7592 (p) REVERT: A 478 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: B 74 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: B 94 LYS cc_start: 0.8494 (tttt) cc_final: 0.7939 (ttmt) REVERT: B 160 GLU cc_start: 0.7904 (tp30) cc_final: 0.7555 (tp30) REVERT: B 366 MET cc_start: 0.7214 (mmm) cc_final: 0.6972 (tpt) REVERT: B 518 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7134 (ppt90) REVERT: B 600 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7738 (mtm-85) REVERT: B 601 ASN cc_start: 0.8296 (m-40) cc_final: 0.7972 (t0) outliers start: 35 outliers final: 23 residues processed: 137 average time/residue: 0.3712 time to fit residues: 69.9532 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 : 1.065 ------------------------------------------------------------------------------- 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 74 GLU Chi-restraints excluded: chain B residue 133 CYS 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 434 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 68 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.178454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143768 restraints weight = 7919.731| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.33 r_work: 0.3601 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6515 Z= 0.156 Angle : 0.646 14.652 8849 Z= 0.320 Chirality : 0.044 0.180 921 Planarity : 0.004 0.051 1137 Dihedral : 5.338 43.650 856 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.49 % Allowed : 16.64 % Favored : 78.87 % 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: -0.35 (0.26), residues: 390 sheet: -0.26 (0.81), residues: 38 loop : -0.52 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 477 HIS 0.005 0.001 HIS B 417 PHE 0.036 0.001 PHE B 525 TYR 0.016 0.002 TYR B 385 ARG 0.013 0.001 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 242) hydrogen bonds : angle 4.86691 ( 690) metal coordination : bond 0.00133 ( 2) SS BOND : bond 0.00792 ( 6) SS BOND : angle 3.48654 ( 12) covalent geometry : bond 0.00367 ( 6507) covalent geometry : angle 0.63350 ( 8837) *********************** 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 150 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.934 Fit side-chains REVERT: A 401 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8872 (mm) REVERT: A 415 LYS cc_start: 0.8230 (tppt) cc_final: 0.7997 (tppt) REVERT: A 446 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8211 (mtp85) REVERT: A 471 SER cc_start: 0.8101 (t) cc_final: 0.7556 (p) REVERT: A 478 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.6496 (m-80) REVERT: B 94 LYS cc_start: 0.8475 (tttt) cc_final: 0.7903 (ttmt) REVERT: B 160 GLU cc_start: 0.7959 (tp30) cc_final: 0.7576 (tp30) REVERT: B 366 MET cc_start: 0.7140 (mmm) cc_final: 0.6888 (tpt) REVERT: B 518 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7130 (ppt90) REVERT: B 600 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7741 (mtm-85) REVERT: B 601 ASN cc_start: 0.8353 (m-40) cc_final: 0.7966 (t0) outliers start: 31 outliers final: 20 residues processed: 135 average time/residue: 0.2622 time to fit residues: 47.2545 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 : 0.674 ------------------------------------------------------------------------------- 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 401 ILE 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 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 133 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 401 HIS Chi-restraints excluded: chain B residue 434 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 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: 0.8980 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.176046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141042 restraints weight = 7993.624| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.35 r_work: 0.3569 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.005 0.065 6515 Z= 0.212 Angle : 0.684 14.683 8849 Z= 0.342 Chirality : 0.046 0.208 921 Planarity : 0.005 0.051 1137 Dihedral : 5.505 47.797 856 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.63 % Allowed : 16.64 % 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: -0.88 (0.30), residues: 774 helix: -0.49 (0.26), residues: 397 sheet: -0.40 (0.79), residues: 38 loop : -0.52 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 PHE 0.036 0.002 PHE B 525 TYR 0.020 0.002 TYR B 385 ARG 0.013 0.001 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 242) hydrogen bonds : angle 4.99258 ( 690) metal coordination : bond 0.00226 ( 2) SS BOND : bond 0.00901 ( 6) SS BOND : angle 3.37727 ( 12) covalent geometry : bond 0.00502 ( 6507) covalent geometry : angle 0.67285 ( 8837) *********************** 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 148 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.559 Fit side-chains REVERT: A 401 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8933 (mm) REVERT: A 415 LYS cc_start: 0.8252 (tppt) cc_final: 0.8005 (tppt) REVERT: A 446 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8262 (mtp85) REVERT: A 454 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7549 (tt0) REVERT: A 471 SER cc_start: 0.8151 (t) cc_final: 0.7613 (p) REVERT: A 478 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: B 94 LYS cc_start: 0.8495 (tttt) cc_final: 0.7917 (ttmt) REVERT: B 518 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7180 (ppt90) REVERT: B 601 ASN cc_start: 0.8372 (m-40) cc_final: 0.7984 (t0) outliers start: 32 outliers final: 24 residues processed: 134 average time/residue: 0.2985 time to fit residues: 53.6703 Evaluate side-chains 140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 2.570 ------------------------------------------------------------------------------- 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 401 ILE Chi-restraints excluded: chain A residue 409 ILE 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 24 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 133 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 434 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 53 ASN B 277 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.175367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140458 restraints weight = 7942.244| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.32 r_work: 0.3575 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 6515 Z= 0.239 Angle : 1.063 59.197 8849 Z= 0.614 Chirality : 0.046 0.372 921 Planarity : 0.005 0.060 1137 Dihedral : 5.473 47.679 855 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.78 % Allowed : 16.93 % 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: -0.86 (0.30), residues: 774 helix: -0.47 (0.26), residues: 397 sheet: -0.43 (0.79), residues: 38 loop : -0.52 (0.36), residues: 339 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 0.033 0.002 PHE B 525 TYR 0.018 0.002 TYR B 385 ARG 0.012 0.001 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 242) hydrogen bonds : angle 4.99232 ( 690) metal coordination : bond 0.00183 ( 2) SS BOND : bond 0.00850 ( 6) SS BOND : angle 3.56120 ( 12) covalent geometry : bond 0.00539 ( 6507) covalent geometry : angle 1.05541 ( 8837) ********************** 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 145 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.946 Fit side-chains REVERT: A 401 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8935 (mm) REVERT: A 415 LYS cc_start: 0.8247 (tppt) cc_final: 0.7995 (tppt) REVERT: A 446 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8259 (mtp85) REVERT: A 454 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7531 (tt0) REVERT: A 471 SER cc_start: 0.8155 (t) cc_final: 0.7614 (p) REVERT: A 478 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: B 94 LYS cc_start: 0.8488 (tttt) cc_final: 0.7911 (ttmt) REVERT: B 358 ILE cc_start: 0.9067 (mm) cc_final: 0.8777 (mt) REVERT: B 366 MET cc_start: 0.7229 (mmm) cc_final: 0.6790 (tpt) REVERT: B 518 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7162 (ppt90) REVERT: B 601 ASN cc_start: 0.8345 (m-40) cc_final: 0.7984 (t0) outliers start: 33 outliers final: 26 residues processed: 132 average time/residue: 0.3871 time to fit residues: 69.7202 Evaluate side-chains 141 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 401 ILE Chi-restraints excluded: chain A residue 409 ILE 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 24 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 133 CYS 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 401 HIS Chi-restraints excluded: chain B residue 434 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 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: 0.5980 chunk 36 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.175360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140302 restraints weight = 8101.349| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.35 r_work: 0.3571 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 6515 Z= 0.244 Angle : 0.852 24.810 8849 Z= 0.506 Chirality : 0.045 0.207 921 Planarity : 0.006 0.108 1137 Dihedral : 5.473 47.679 855 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.49 % Allowed : 16.93 % 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: -0.86 (0.30), residues: 774 helix: -0.47 (0.26), residues: 397 sheet: -0.43 (0.79), residues: 38 loop : -0.52 (0.36), residues: 339 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 0.033 0.002 PHE B 525 TYR 0.018 0.002 TYR B 385 ARG 0.012 0.001 ARG B 531 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 242) hydrogen bonds : angle 4.99232 ( 690) metal coordination : bond 0.00183 ( 2) SS BOND : bond 0.01489 ( 6) SS BOND : angle 3.60265 ( 12) covalent geometry : bond 0.00541 ( 6507) covalent geometry : angle 0.84248 ( 8837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4393.99 seconds wall clock time: 83 minutes 17.46 seconds (4997.46 seconds total)