Starting phenix.real_space_refine on Fri Oct 10 13:49:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4u_36892/10_2025/8k4u_36892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4u_36892/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k4u_36892/10_2025/8k4u_36892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4u_36892/10_2025/8k4u_36892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k4u_36892/10_2025/8k4u_36892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4u_36892/10_2025/8k4u_36892.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.61, per 1000 atoms: 0.25 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: 0.50 Conformation dependent library (CDL) restraints added in 364.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.20 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: 0.86 Time building geometry restraints manager: 0.68 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: 4.080 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.980 ------------------------------------------------------------------------------- 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 : 3.80 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 460 TYR 0.023 0.001 TYR B 385 PHE 0.008 0.001 PHE B 230 TRP 0.008 0.001 TRP A 427 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6507) covalent geometry : angle 0.63694 ( 8837) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.58772 ( 12) hydrogen bonds : bond 0.30761 ( 242) hydrogen bonds : angle 10.98394 ( 690) metal coordination : bond 0.19887 ( 2) *********************** 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 : 0.252 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: 0.8827 (mm) REVERT: A 471 SER cc_start: 0.8031 (t) cc_final: 0.7811 (p) REVERT: A 478 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6101 (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: 0.8145 (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: 0.0863 time to fit residues: 23.5355 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 : 0.238 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 397 ASN B 493 HIS B 524 GLN B 535 HIS B 556 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.189994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.155249 restraints weight = 7990.469| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.34 r_work: 0.3723 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6515 Z= 0.165 Angle : 0.643 9.626 8849 Z= 0.328 Chirality : 0.044 0.228 921 Planarity : 0.005 0.053 1137 Dihedral : 6.573 58.197 866 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.76 % Allowed : 14.04 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.27), residues: 774 helix: -1.89 (0.23), residues: 383 sheet: -0.96 (0.82), residues: 41 loop : -1.09 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 531 TYR 0.020 0.002 TYR A 442 PHE 0.015 0.001 PHE B 525 TRP 0.011 0.001 TRP B 477 HIS 0.006 0.001 HIS B 493 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6507) covalent geometry : angle 0.63090 ( 8837) SS BOND : bond 0.00498 ( 6) SS BOND : angle 3.45836 ( 12) hydrogen bonds : bond 0.05170 ( 242) hydrogen bonds : angle 5.90417 ( 690) metal coordination : bond 0.00068 ( 2) *********************** 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 158 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8257 (tppt) cc_final: 0.7817 (tppt) REVERT: A 446 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7937 (mtp85) REVERT: A 460 VAL cc_start: 0.7759 (t) cc_final: 0.7490 (p) REVERT: A 471 SER cc_start: 0.8138 (t) cc_final: 0.7729 (p) REVERT: A 478 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: B 94 LYS cc_start: 0.8571 (tttt) cc_final: 0.8079 (ttmt) REVERT: B 518 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7054 (ppt90) REVERT: B 601 ASN cc_start: 0.8289 (m-40) cc_final: 0.7689 (t0) outliers start: 26 outliers final: 14 residues processed: 149 average time/residue: 0.0808 time to fit residues: 15.9035 Evaluate side-chains 137 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL 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 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 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 307 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 568 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 0.0170 chunk 6 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.0020 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 0.2964 ------------------------------------------------------------------------------- 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 345 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 = 0.4293 r_free = 0.4293 target = 0.192422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158038 restraints weight = 7902.955| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.36 r_work: 0.3711 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6515 Z= 0.113 Angle : 0.574 11.074 8849 Z= 0.292 Chirality : 0.041 0.232 921 Planarity : 0.004 0.044 1137 Dihedral : 5.637 53.455 860 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.20 % Allowed : 15.34 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.28), residues: 774 helix: -1.16 (0.25), residues: 372 sheet: -0.86 (0.80), residues: 41 loop : -1.10 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 531 TYR 0.013 0.001 TYR B 385 PHE 0.009 0.001 PHE B 525 TRP 0.010 0.001 TRP B 165 HIS 0.005 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6507) covalent geometry : angle 0.55704 ( 8837) SS BOND : bond 0.00281 ( 6) SS BOND : angle 3.84243 ( 12) hydrogen bonds : bond 0.04156 ( 242) hydrogen bonds : angle 5.22040 ( 690) metal coordination : bond 0.00066 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 415 LYS cc_start: 0.8205 (tppt) cc_final: 0.7960 (tppt) REVERT: A 446 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8062 (mtp85) REVERT: A 471 SER cc_start: 0.8141 (t) cc_final: 0.7693 (p) REVERT: A 478 TYR cc_start: 0.6672 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: B 94 LYS cc_start: 0.8528 (tttt) cc_final: 0.8070 (ttmt) REVERT: B 518 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7073 (ppt90) REVERT: B 601 ASN cc_start: 0.8300 (m-40) cc_final: 0.7739 (t0) outliers start: 29 outliers final: 16 residues processed: 147 average time/residue: 0.0843 time to fit residues: 16.3963 Evaluate side-chains 134 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 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 307 ILE 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 4 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.177644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142992 restraints weight = 7967.774| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.33 r_work: 0.3643 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3126 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= 0.207 Angle : 0.633 11.114 8849 Z= 0.321 Chirality : 0.045 0.202 921 Planarity : 0.005 0.048 1137 Dihedral : 5.729 49.312 859 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.20 % Allowed : 15.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.29), residues: 774 helix: -0.91 (0.26), residues: 381 sheet: -0.89 (0.79), residues: 41 loop : -0.73 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 531 TYR 0.019 0.002 TYR B 385 PHE 0.013 0.001 PHE B 400 TRP 0.013 0.001 TRP B 477 HIS 0.005 0.001 HIS B 535 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 6507) covalent geometry : angle 0.61774 ( 8837) SS BOND : bond 0.00750 ( 6) SS BOND : angle 3.84998 ( 12) hydrogen bonds : bond 0.04306 ( 242) hydrogen bonds : angle 5.10858 ( 690) metal coordination : bond 0.00224 ( 2) *********************** 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 152 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 387 TYR cc_start: 0.7129 (m-10) cc_final: 0.6789 (m-10) REVERT: A 415 LYS cc_start: 0.8243 (tppt) cc_final: 0.7975 (tppt) REVERT: A 446 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8062 (mtp85) REVERT: A 471 SER cc_start: 0.8151 (t) cc_final: 0.7677 (p) REVERT: A 478 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.6326 (m-80) REVERT: B 94 LYS cc_start: 0.8540 (tttt) cc_final: 0.8024 (ttmt) REVERT: B 160 GLU cc_start: 0.7739 (tp30) cc_final: 0.7499 (tp30) REVERT: B 518 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7064 (ppt90) REVERT: B 601 ASN cc_start: 0.8265 (m-40) cc_final: 0.7834 (t0) outliers start: 29 outliers final: 19 residues processed: 142 average time/residue: 0.0847 time to fit residues: 15.8937 Evaluate side-chains 139 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 568 SER 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 31 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.179555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144990 restraints weight = 8001.990| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.34 r_work: 0.3620 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 0.070 6515 Z= 0.146 Angle : 0.599 11.752 8849 Z= 0.301 Chirality : 0.043 0.188 921 Planarity : 0.004 0.044 1137 Dihedral : 5.572 43.566 859 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.34 % Allowed : 15.63 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.30), residues: 774 helix: -0.56 (0.26), residues: 380 sheet: -0.65 (0.82), residues: 41 loop : -0.65 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 531 TYR 0.016 0.002 TYR B 385 PHE 0.013 0.001 PHE A 420 TRP 0.015 0.001 TRP B 168 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6507) covalent geometry : angle 0.58333 ( 8837) SS BOND : bond 0.00602 ( 6) SS BOND : angle 3.75551 ( 12) hydrogen bonds : bond 0.03972 ( 242) hydrogen bonds : angle 4.86909 ( 690) metal coordination : bond 0.00113 ( 2) *********************** 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 152 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.257 Fit side-chains REVERT: A 415 LYS cc_start: 0.8247 (tppt) cc_final: 0.7820 (tppt) REVERT: A 446 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8133 (mtp85) REVERT: A 471 SER cc_start: 0.8134 (t) cc_final: 0.7631 (p) REVERT: A 478 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: B 74 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: B 94 LYS cc_start: 0.8499 (tttt) cc_final: 0.7954 (ttmt) REVERT: B 160 GLU cc_start: 0.7851 (tp30) cc_final: 0.7506 (tp30) REVERT: B 518 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7105 (ppt90) REVERT: B 600 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7597 (mtm-85) REVERT: B 601 ASN cc_start: 0.8341 (m-40) cc_final: 0.7855 (t0) outliers start: 30 outliers final: 20 residues processed: 139 average time/residue: 0.0863 time to fit residues: 15.8285 Evaluate side-chains 137 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.179042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.144251 restraints weight = 8040.023| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.36 r_work: 0.3612 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6515 Z= 0.154 Angle : 0.613 12.720 8849 Z= 0.306 Chirality : 0.043 0.184 921 Planarity : 0.004 0.044 1137 Dihedral : 5.254 43.149 857 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.30), residues: 774 helix: -0.45 (0.27), residues: 382 sheet: -0.58 (0.82), residues: 41 loop : -0.52 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 531 TYR 0.016 0.002 TYR B 385 PHE 0.021 0.001 PHE B 327 TRP 0.012 0.001 TRP B 168 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6507) covalent geometry : angle 0.59801 ( 8837) SS BOND : bond 0.00737 ( 6) SS BOND : angle 3.71394 ( 12) hydrogen bonds : bond 0.03954 ( 242) hydrogen bonds : angle 4.82091 ( 690) metal coordination : bond 0.00145 ( 2) *********************** 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 150 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.267 Fit side-chains REVERT: A 345 ARG cc_start: 0.8342 (tpp80) cc_final: 0.8100 (tpt-90) REVERT: A 415 LYS cc_start: 0.8255 (tppt) cc_final: 0.7829 (tppt) REVERT: A 446 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8182 (mtp85) REVERT: A 471 SER cc_start: 0.8117 (t) cc_final: 0.7596 (p) REVERT: A 478 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: B 74 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7097 (mm-30) REVERT: B 94 LYS cc_start: 0.8499 (tttt) cc_final: 0.7952 (ttmt) REVERT: B 366 MET cc_start: 0.7031 (mmm) cc_final: 0.6738 (tpt) REVERT: B 518 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7102 (ppt90) REVERT: B 600 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7596 (mtm-85) REVERT: B 601 ASN cc_start: 0.8364 (m-40) cc_final: 0.7920 (t0) outliers start: 33 outliers final: 22 residues processed: 137 average time/residue: 0.0927 time to fit residues: 16.5220 Evaluate side-chains 142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 469 CYS Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 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 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 Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.183257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147521 restraints weight = 7998.861| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.41 r_work: 0.3622 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6515 Z= 0.136 Angle : 0.616 13.623 8849 Z= 0.305 Chirality : 0.043 0.184 921 Planarity : 0.004 0.048 1137 Dihedral : 5.155 42.912 856 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.07 % Allowed : 16.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.31), residues: 774 helix: -0.32 (0.27), residues: 387 sheet: -0.32 (0.85), residues: 40 loop : -0.52 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 531 TYR 0.015 0.002 TYR B 385 PHE 0.020 0.001 PHE A 420 TRP 0.011 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6507) covalent geometry : angle 0.60225 ( 8837) SS BOND : bond 0.00998 ( 6) SS BOND : angle 3.60308 ( 12) hydrogen bonds : bond 0.03837 ( 242) hydrogen bonds : angle 4.75003 ( 690) metal coordination : bond 0.00089 ( 2) *********************** 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 152 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.262 Fit side-chains REVERT: A 401 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8868 (mm) REVERT: A 415 LYS cc_start: 0.8215 (tppt) cc_final: 0.7920 (tppt) REVERT: A 446 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8161 (mtp85) REVERT: A 471 SER cc_start: 0.8151 (t) cc_final: 0.7633 (p) REVERT: A 478 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: B 74 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: B 94 LYS cc_start: 0.8469 (tttt) cc_final: 0.7944 (ttmt) REVERT: B 160 GLU cc_start: 0.7778 (tp30) cc_final: 0.7530 (tp30) REVERT: B 518 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7122 (ppt90) REVERT: B 600 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7646 (mtm-85) REVERT: B 601 ASN cc_start: 0.8347 (m-40) cc_final: 0.7908 (t0) outliers start: 35 outliers final: 25 residues processed: 135 average time/residue: 0.0820 time to fit residues: 14.8309 Evaluate side-chains 142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 371 TYR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 401 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 142 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 434 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.180359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145542 restraints weight = 7956.454| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.35 r_work: 0.3638 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6515 Z= 0.136 Angle : 0.618 14.369 8849 Z= 0.305 Chirality : 0.043 0.182 921 Planarity : 0.004 0.052 1137 Dihedral : 5.120 43.070 856 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.63 % Allowed : 17.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.31), residues: 774 helix: -0.26 (0.26), residues: 388 sheet: -0.30 (0.86), residues: 40 loop : -0.51 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 531 TYR 0.015 0.001 TYR B 385 PHE 0.034 0.001 PHE B 525 TRP 0.011 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6507) covalent geometry : angle 0.60463 ( 8837) SS BOND : bond 0.00783 ( 6) SS BOND : angle 3.49413 ( 12) hydrogen bonds : bond 0.03851 ( 242) hydrogen bonds : angle 4.68484 ( 690) metal coordination : bond 0.00130 ( 2) *********************** 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 148 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.227 Fit side-chains REVERT: A 401 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8876 (mm) REVERT: A 415 LYS cc_start: 0.8218 (tppt) cc_final: 0.7870 (tppt) REVERT: A 446 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8115 (mtp85) REVERT: A 471 SER cc_start: 0.8114 (t) cc_final: 0.7604 (p) REVERT: A 478 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6507 (m-80) REVERT: B 94 LYS cc_start: 0.8442 (tttt) cc_final: 0.7895 (ttmt) REVERT: B 160 GLU cc_start: 0.7787 (tp30) cc_final: 0.7464 (tp30) REVERT: B 367 GLU cc_start: 0.6956 (tt0) cc_final: 0.6683 (mt-10) REVERT: B 408 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.6520 (mpt) REVERT: B 455 MET cc_start: 0.8052 (tmm) cc_final: 0.7656 (tmm) REVERT: B 518 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7113 (ppt90) REVERT: B 600 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: B 601 ASN cc_start: 0.8364 (m-40) cc_final: 0.7908 (t0) outliers start: 32 outliers final: 24 residues processed: 132 average time/residue: 0.0875 time to fit residues: 15.1800 Evaluate side-chains 142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 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 291 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 408 MET 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 568 SER Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.177875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142716 restraints weight = 8006.360| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.36 r_work: 0.3593 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6515 Z= 0.186 Angle : 0.647 14.215 8849 Z= 0.322 Chirality : 0.044 0.183 921 Planarity : 0.004 0.053 1137 Dihedral : 5.207 42.872 856 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.78 % Allowed : 17.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.31), residues: 774 helix: -0.29 (0.26), residues: 388 sheet: -0.45 (0.84), residues: 40 loop : -0.49 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 531 TYR 0.018 0.002 TYR B 385 PHE 0.031 0.002 PHE B 525 TRP 0.013 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 6507) covalent geometry : angle 0.63512 ( 8837) SS BOND : bond 0.00830 ( 6) SS BOND : angle 3.47506 ( 12) hydrogen bonds : bond 0.04037 ( 242) hydrogen bonds : angle 4.77575 ( 690) metal coordination : bond 0.00211 ( 2) *********************** 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: 33 poor density : 115 time to evaluate : 0.246 Fit side-chains REVERT: A 401 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8901 (mm) REVERT: A 415 LYS cc_start: 0.8241 (tppt) cc_final: 0.7893 (tppt) REVERT: A 446 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8218 (mtp85) REVERT: A 471 SER cc_start: 0.8078 (t) cc_final: 0.7545 (p) REVERT: A 478 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.6179 (m-80) REVERT: B 94 LYS cc_start: 0.8460 (tttt) cc_final: 0.7912 (ttmt) REVERT: B 160 GLU cc_start: 0.7851 (tp30) cc_final: 0.7539 (tp30) REVERT: B 208 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8334 (tp30) REVERT: B 367 GLU cc_start: 0.7001 (tt0) cc_final: 0.6728 (mt-10) REVERT: B 408 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.6579 (mpt) REVERT: B 455 MET cc_start: 0.8072 (tmm) cc_final: 0.7725 (tmm) REVERT: B 518 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7123 (ppt90) REVERT: B 601 ASN cc_start: 0.8369 (m-40) cc_final: 0.7955 (t0) outliers start: 33 outliers final: 23 residues processed: 133 average time/residue: 0.0842 time to fit residues: 14.8352 Evaluate side-chains 141 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 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 133 CYS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 208 GLU 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 408 MET 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 568 SER 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 75 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.180925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146442 restraints weight = 7854.566| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.33 r_work: 0.3630 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3693 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= 0.129 Angle : 0.622 14.076 8849 Z= 0.308 Chirality : 0.043 0.196 921 Planarity : 0.004 0.058 1137 Dihedral : 5.067 42.783 856 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.34 % Allowed : 17.80 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.31), residues: 774 helix: -0.12 (0.27), residues: 389 sheet: -0.64 (0.84), residues: 40 loop : -0.46 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 531 TYR 0.017 0.001 TYR A 387 PHE 0.037 0.001 PHE B 525 TRP 0.010 0.001 TRP B 477 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6507) covalent geometry : angle 0.61025 ( 8837) SS BOND : bond 0.00790 ( 6) SS BOND : angle 3.30390 ( 12) hydrogen bonds : bond 0.03826 ( 242) hydrogen bonds : angle 4.70919 ( 690) metal coordination : bond 0.00152 ( 2) ********************** 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 147 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.230 Fit side-chains REVERT: A 401 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8873 (mm) REVERT: A 415 LYS cc_start: 0.8222 (tppt) cc_final: 0.7884 (tppt) REVERT: A 446 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8169 (mtp85) REVERT: A 471 SER cc_start: 0.8026 (t) cc_final: 0.7494 (p) REVERT: A 478 TYR cc_start: 0.6464 (OUTLIER) cc_final: 0.6064 (m-80) REVERT: B 94 LYS cc_start: 0.8382 (tttt) cc_final: 0.7850 (ttmt) REVERT: B 160 GLU cc_start: 0.7853 (tp30) cc_final: 0.7545 (tp30) REVERT: B 358 ILE cc_start: 0.8895 (mm) cc_final: 0.8586 (mt) REVERT: B 408 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.6394 (mpt) REVERT: B 455 MET cc_start: 0.8031 (tmm) cc_final: 0.7639 (tmm) REVERT: B 518 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7127 (ppt90) REVERT: B 573 PHE cc_start: 0.8213 (t80) cc_final: 0.7963 (t80) REVERT: B 600 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7423 (mtm-85) REVERT: B 601 ASN cc_start: 0.8335 (m-40) cc_final: 0.7942 (t0) outliers start: 30 outliers final: 22 residues processed: 131 average time/residue: 0.0871 time to fit residues: 15.0699 Evaluate side-chains 140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 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 334 THR Chi-restraints excluded: chain B residue 408 MET 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 568 SER 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 48 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.0670 chunk 9 optimal weight: 0.3980 chunk 33 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.181636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147274 restraints weight = 8015.990| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.36 r_work: 0.3640 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3750 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= 0.122 Angle : 0.615 13.875 8849 Z= 0.305 Chirality : 0.042 0.187 921 Planarity : 0.004 0.059 1137 Dihedral : 4.995 42.961 856 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.20 % Allowed : 17.80 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.31), residues: 774 helix: -0.01 (0.27), residues: 389 sheet: -0.61 (0.85), residues: 40 loop : -0.45 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 531 TYR 0.015 0.001 TYR B 385 PHE 0.035 0.001 PHE B 525 TRP 0.010 0.001 TRP B 477 HIS 0.005 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6507) covalent geometry : angle 0.60372 ( 8837) SS BOND : bond 0.00770 ( 6) SS BOND : angle 3.21992 ( 12) hydrogen bonds : bond 0.03727 ( 242) hydrogen bonds : angle 4.65412 ( 690) metal coordination : bond 0.00079 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1747.82 seconds wall clock time: 30 minutes 45.69 seconds (1845.69 seconds total)