Starting phenix.real_space_refine on Thu Jul 2 18:17:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xec_33155/07_2026/7xec_33155.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xec_33155/07_2026/7xec_33155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xec_33155/07_2026/7xec_33155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xec_33155/07_2026/7xec_33155.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xec_33155/07_2026/7xec_33155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xec_33155/07_2026/7xec_33155.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xec_33155/07_2026/7xec_33155.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xec_33155/07_2026/7xec_33155.cif" } resolution = 3.34 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= -0.001 sd= 0.025 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 P 3 5.49 5 S 43 5.16 5 C 6074 2.51 5 N 1670 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9485 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4759 Classifications: {'peptide': 597} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 574} Chain breaks: 1 Chain: "B" Number of atoms: 4695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4695 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.16, per 1000 atoms: 0.23 Number of scatterers: 9485 At special positions: 0 Unit cell: (77.19, 105.41, 140.27, 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) S 43 16.00 P 3 15.00 O 1695 8.00 N 1670 7.00 C 6074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 342.3 milliseconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 3 sheets defined 63.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 68 through 79 removed outlier: 3.696A pdb=" N LEU A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 110 through 124 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.934A pdb=" N VAL A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 175 removed outlier: 3.873A pdb=" N LEU A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 200 through 237 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 242 through 252 removed outlier: 4.262A pdb=" N GLY A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 262 through 289 removed outlier: 4.299A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 302 through 334 removed outlier: 3.505A pdb=" N ASP A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.539A pdb=" N SER A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.932A pdb=" N THR A 355 " --> pdb=" O ILE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 removed outlier: 4.012A pdb=" N LYS A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 411 through 429 removed outlier: 4.076A pdb=" N GLU A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 513 through 521 removed outlier: 3.570A pdb=" N PHE A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 562 through 569 removed outlier: 3.735A pdb=" N ARG A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 585 through 592 removed outlier: 4.276A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 621 removed outlier: 3.837A pdb=" N GLN A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 removed outlier: 3.967A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 667 removed outlier: 3.831A pdb=" N LEU A 663 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 removed outlier: 3.893A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 4.430A pdb=" N ARG B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 145 through 173 removed outlier: 4.463A pdb=" N ARG B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 195 through 234 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 241 through 260 removed outlier: 4.351A pdb=" N ALA B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 289 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.526A pdb=" N PHE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 336 removed outlier: 3.864A pdb=" N LEU B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 348 Processing helix chain 'B' and resid 349 through 359 removed outlier: 5.000A pdb=" N THR B 355 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 4.668A pdb=" N ALA B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 432 removed outlier: 3.725A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.099A pdb=" N GLY B 512 " --> pdb=" O ASN B 509 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LYS B 513 " --> pdb=" O GLY B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 Processing helix chain 'B' and resid 553 through 558 Processing helix chain 'B' and resid 572 through 584 Processing helix chain 'B' and resid 585 through 592 Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 606 through 621 Processing helix chain 'B' and resid 637 through 651 removed outlier: 3.991A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 664 Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.541A pdb=" N GLN A 466 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LYS A 533 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A 468 " --> pdb=" O LYS A 533 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AA3, first strand: chain 'B' and resid 467 through 469 498 hydrogen bonds defined for protein. 1458 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: 1.74 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1508 1.31 - 1.44: 2649 1.44 - 1.57: 5457 1.57 - 1.70: 7 1.70 - 1.82: 72 Bond restraints: 9693 Sorted by residual: bond pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " ideal model delta sigma weight residual 1.526 1.323 0.203 1.10e-02 8.26e+03 3.40e+02 bond pdb=" C1' ATP A 801 " pdb=" C2' ATP A 801 " ideal model delta sigma weight residual 1.531 1.365 0.166 1.20e-02 6.94e+03 1.92e+02 bond pdb=" C4' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.444 1.596 -0.152 1.10e-02 8.26e+03 1.92e+02 bond pdb=" C6 ATP A 801 " pdb=" N6 ATP A 801 " ideal model delta sigma weight residual 1.337 1.446 -0.109 1.10e-02 8.26e+03 9.89e+01 bond pdb=" C1' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.416 1.536 -0.120 1.30e-02 5.92e+03 8.59e+01 ... (remaining 9688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 12876 3.80 - 7.60: 241 7.60 - 11.40: 15 11.40 - 15.20: 0 15.20 - 19.01: 2 Bond angle restraints: 13134 Sorted by residual: angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 117.82 19.01 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 123.62 16.25 1.00e+00 1.00e+00 2.64e+02 angle pdb=" C5 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 126.80 118.03 8.77 1.00e+00 1.00e+00 7.69e+01 angle pdb=" N ILE A 402 " pdb=" CA ILE A 402 " pdb=" C ILE A 402 " ideal model delta sigma weight residual 112.29 104.35 7.94 9.40e-01 1.13e+00 7.14e+01 angle pdb=" N SER B 562 " pdb=" CA SER B 562 " pdb=" C SER B 562 " ideal model delta sigma weight residual 111.07 119.57 -8.50 1.07e+00 8.73e-01 6.31e+01 ... (remaining 13129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5013 17.18 - 34.36: 605 34.36 - 51.54: 119 51.54 - 68.73: 26 68.73 - 85.91: 15 Dihedral angle restraints: 5778 sinusoidal: 2328 harmonic: 3450 Sorted by residual: dihedral pdb=" CA MET B 186 " pdb=" C MET B 186 " pdb=" N ASP B 187 " pdb=" CA ASP B 187 " ideal model delta harmonic sigma weight residual -180.00 -103.58 -76.42 0 5.00e+00 4.00e-02 2.34e+02 dihedral pdb=" CA ASP A 361 " pdb=" C ASP A 361 " pdb=" N ALA A 362 " pdb=" CA ALA A 362 " ideal model delta harmonic sigma weight residual 0.00 30.86 -30.86 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA ASP B 194 " pdb=" C ASP B 194 " pdb=" N GLN B 195 " pdb=" CA GLN B 195 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 5775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1019 0.092 - 0.184: 373 0.184 - 0.277: 62 0.277 - 0.369: 9 0.369 - 0.461: 2 Chirality restraints: 1465 Sorted by residual: chirality pdb=" CA PHE A 295 " pdb=" N PHE A 295 " pdb=" C PHE A 295 " pdb=" CB PHE A 295 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA GLN B 177 " pdb=" N GLN B 177 " pdb=" C GLN B 177 " pdb=" CB GLN B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA LEU A 160 " pdb=" N LEU A 160 " pdb=" C LEU A 160 " pdb=" CB LEU A 160 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1462 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 218 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C PRO B 218 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO B 218 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 219 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 181 " -0.035 2.00e-02 2.50e+03 2.18e-02 9.54e+00 pdb=" CG TYR B 181 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 181 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 181 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 181 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 181 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 181 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 181 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 186 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C MET B 186 " -0.049 2.00e-02 2.50e+03 pdb=" O MET B 186 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP B 187 " 0.016 2.00e-02 2.50e+03 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 335 2.70 - 3.25: 9572 3.25 - 3.80: 14856 3.80 - 4.35: 19901 4.35 - 4.90: 31801 Nonbonded interactions: 76465 Sorted by model distance: nonbonded pdb=" O ASN A 509 " pdb=" O3B ATP A 801 " model vdw 2.153 3.040 nonbonded pdb=" O VAL B 482 " pdb=" OH TYR B 527 " model vdw 2.356 3.040 nonbonded pdb=" O LEU B 520 " pdb=" OH TYR B 541 " model vdw 2.371 3.040 nonbonded pdb=" N PHE B 295 " pdb=" O PHE B 295 " model vdw 2.373 2.496 nonbonded pdb=" O SER B 103 " pdb=" OG SER B 103 " model vdw 2.376 3.040 ... (remaining 76460 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 68 through 436 or resid 461 through 680)) selection = chain 'B' } 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: 3.780 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.380 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.009 0.203 9693 Z= 0.644 Angle : 1.426 19.006 13134 Z= 0.990 Chirality : 0.094 0.461 1465 Planarity : 0.007 0.032 1662 Dihedral : 15.926 85.906 3560 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.59 % Favored : 90.15 % Rotamer: Outliers : 3.51 % Allowed : 7.83 % Favored : 88.65 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -4.80 (0.20), residues: 1178 helix: -2.71 (0.15), residues: 765 sheet: -3.13 (0.63), residues: 39 loop : -3.88 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 401 TYR 0.043 0.005 TYR B 181 PHE 0.023 0.004 PHE A 295 TRP 0.025 0.004 TRP B 339 HIS 0.014 0.003 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00881 / 0.64 ( 9693) covalent geometry : angle 1.42569 / 0.99 (13134) hydrogen bonds : bond 0.20907 / 14.33 ( 498) hydrogen bonds : angle 8.98177 / 6.29 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6196 (ttt180) cc_final: 0.5848 (ttp-170) REVERT: A 281 TYR cc_start: 0.5604 (OUTLIER) cc_final: 0.5347 (t80) REVERT: A 406 TYR cc_start: 0.7421 (t80) cc_final: 0.7214 (m-80) REVERT: A 537 GLN cc_start: 0.8228 (pt0) cc_final: 0.8025 (pm20) REVERT: A 566 MET cc_start: 0.8254 (tmm) cc_final: 0.7511 (ttt) REVERT: A 568 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7546 (ttp80) REVERT: B 250 VAL cc_start: 0.7814 (t) cc_final: 0.7483 (m) REVERT: B 278 GLU cc_start: 0.6904 (tt0) cc_final: 0.6652 (tt0) REVERT: B 321 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7382 (mt) REVERT: B 322 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8036 (tt) REVERT: B 329 MET cc_start: 0.8007 (ttp) cc_final: 0.7595 (ttt) REVERT: B 539 MET cc_start: 0.5583 (mtp) cc_final: 0.5357 (mtp) REVERT: B 561 ASP cc_start: 0.5338 (OUTLIER) cc_final: 0.4834 (m-30) REVERT: B 610 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6632 (mmtt) REVERT: B 680 LYS cc_start: 0.5097 (OUTLIER) cc_final: 0.4599 (mtmm) outliers start: 35 outliers final: 7 residues processed: 152 average time/residue: 0.0996 time to fit residues: 20.6766 Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 680 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.0060 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 10.0000 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.242351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3995 r_free = 0.3995 target = 0.170921 restraints weight = 9425.060| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.87 r_work: 0.3527 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9693 Z= 0.154 Angle : 0.703 8.755 13134 Z= 0.372 Chirality : 0.043 0.177 1465 Planarity : 0.005 0.043 1662 Dihedral : 8.113 77.942 1359 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 2.41 % Allowed : 11.95 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -2.94 (0.22), residues: 1178 helix: -1.21 (0.18), residues: 768 sheet: -2.90 (0.59), residues: 46 loop : -3.22 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 545 TYR 0.019 0.002 TYR B 310 PHE 0.017 0.002 PHE B 265 TRP 0.013 0.001 TRP B 326 HIS 0.006 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 9693) covalent geometry : angle 0.70254 / 0.37 (13134) hydrogen bonds : bond 0.05329 / 3.54 ( 498) hydrogen bonds : angle 5.61231 / 3.95 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6331 (ttt180) cc_final: 0.5687 (ttp-170) REVERT: A 281 TYR cc_start: 0.5975 (OUTLIER) cc_final: 0.5681 (t80) REVERT: A 324 ARG cc_start: 0.6691 (tpp80) cc_final: 0.5818 (ptm160) REVERT: A 406 TYR cc_start: 0.7664 (t80) cc_final: 0.6722 (m-80) REVERT: A 501 MET cc_start: 0.8322 (mmm) cc_final: 0.8088 (mmm) REVERT: A 537 GLN cc_start: 0.8376 (pt0) cc_final: 0.8142 (pm20) REVERT: A 566 MET cc_start: 0.8501 (tmm) cc_final: 0.8143 (tmm) REVERT: B 96 LEU cc_start: 0.7963 (tp) cc_final: 0.7738 (tt) REVERT: B 278 GLU cc_start: 0.7696 (tt0) cc_final: 0.7411 (tt0) REVERT: B 321 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7378 (mt) REVERT: B 380 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: B 539 MET cc_start: 0.5556 (mtp) cc_final: 0.5203 (mtp) REVERT: B 610 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6508 (mmtp) REVERT: B 680 LYS cc_start: 0.5051 (OUTLIER) cc_final: 0.4842 (mptt) outliers start: 24 outliers final: 9 residues processed: 124 average time/residue: 0.1132 time to fit residues: 19.0990 Evaluate side-chains 106 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 680 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 40.0000 chunk 86 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN B 621 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.240469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.168780 restraints weight = 9475.574| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.85 r_work: 0.3500 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9693 Z= 0.160 Angle : 0.647 8.619 13134 Z= 0.337 Chirality : 0.042 0.147 1465 Planarity : 0.004 0.047 1662 Dihedral : 7.155 83.099 1347 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.01 % Allowed : 12.55 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -2.21 (0.24), residues: 1178 helix: -0.61 (0.19), residues: 768 sheet: -2.40 (0.67), residues: 46 loop : -3.06 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 74 TYR 0.020 0.002 TYR B 357 PHE 0.015 0.001 PHE B 265 TRP 0.012 0.001 TRP B 326 HIS 0.008 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9693) covalent geometry : angle 0.64694 / 0.34 (13134) hydrogen bonds : bond 0.04820 / 3.20 ( 498) hydrogen bonds : angle 5.21042 / 3.66 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6294 (ttt180) cc_final: 0.5591 (ttp-170) REVERT: A 281 TYR cc_start: 0.5953 (OUTLIER) cc_final: 0.5687 (t80) REVERT: A 324 ARG cc_start: 0.6659 (tpp80) cc_final: 0.5809 (ptm160) REVERT: A 537 GLN cc_start: 0.8382 (pt0) cc_final: 0.8137 (pm20) REVERT: A 566 MET cc_start: 0.8512 (tmm) cc_final: 0.8184 (tmm) REVERT: B 539 MET cc_start: 0.5462 (mtp) cc_final: 0.5054 (mtp) REVERT: B 548 MET cc_start: 0.5144 (mmp) cc_final: 0.2790 (tmm) REVERT: B 610 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6580 (mmtp) REVERT: B 680 LYS cc_start: 0.5221 (OUTLIER) cc_final: 0.5004 (mptt) outliers start: 30 outliers final: 17 residues processed: 133 average time/residue: 0.1090 time to fit residues: 19.8218 Evaluate side-chains 114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 680 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.3980 chunk 38 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 chunk 62 optimal weight: 0.0470 chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.244482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.177293 restraints weight = 9473.864| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.22 r_work: 0.3545 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9693 Z= 0.126 Angle : 0.597 10.921 13134 Z= 0.309 Chirality : 0.040 0.161 1465 Planarity : 0.004 0.052 1662 Dihedral : 6.662 89.018 1341 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.11 % Allowed : 15.06 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.53 (0.24), residues: 1178 helix: -0.11 (0.19), residues: 774 sheet: -1.92 (0.76), residues: 46 loop : -2.80 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 568 TYR 0.028 0.002 TYR A 406 PHE 0.014 0.001 PHE B 265 TRP 0.012 0.001 TRP B 326 HIS 0.006 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9693) covalent geometry : angle 0.59707 / 0.31 (13134) hydrogen bonds : bond 0.04283 / 2.83 ( 498) hydrogen bonds : angle 4.91220 / 3.46 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6360 (ttt180) cc_final: 0.5575 (ttp-170) REVERT: A 501 MET cc_start: 0.8402 (mmm) cc_final: 0.8157 (mmm) REVERT: A 517 PHE cc_start: 0.7680 (m-10) cc_final: 0.7439 (m-80) REVERT: A 537 GLN cc_start: 0.8436 (pt0) cc_final: 0.8158 (pm20) REVERT: A 611 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7841 (mt0) REVERT: A 622 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8496 (mtt-85) REVERT: B 539 MET cc_start: 0.5518 (mtp) cc_final: 0.5084 (mtp) REVERT: B 548 MET cc_start: 0.5419 (mmp) cc_final: 0.4485 (tpp) REVERT: B 610 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6238 (mmtp) REVERT: B 680 LYS cc_start: 0.5292 (OUTLIER) cc_final: 0.5051 (mptt) outliers start: 31 outliers final: 14 residues processed: 132 average time/residue: 0.1047 time to fit residues: 19.2808 Evaluate side-chains 114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 680 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 93 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.243149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.174277 restraints weight = 9396.342| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.09 r_work: 0.3505 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9693 Z= 0.154 Angle : 0.610 11.005 13134 Z= 0.313 Chirality : 0.041 0.144 1465 Planarity : 0.004 0.053 1662 Dihedral : 6.456 83.258 1339 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.51 % Allowed : 16.47 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 are not related in a simple way. whole: -1.36 (0.25), residues: 1178 helix: 0.00 (0.19), residues: 773 sheet: -1.74 (0.79), residues: 46 loop : -2.72 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 568 TYR 0.020 0.002 TYR B 357 PHE 0.014 0.001 PHE B 265 TRP 0.020 0.001 TRP A 595 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 9693) covalent geometry : angle 0.60984 / 0.31 (13134) hydrogen bonds : bond 0.04321 / 2.84 ( 498) hydrogen bonds : angle 4.79737 / 3.37 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8166 (mmm) cc_final: 0.7908 (mmt) REVERT: A 234 ARG cc_start: 0.6351 (ttt180) cc_final: 0.5565 (ttp-170) REVERT: A 537 GLN cc_start: 0.8427 (pt0) cc_final: 0.8169 (pm20) REVERT: B 539 MET cc_start: 0.5337 (mtp) cc_final: 0.4901 (mtp) REVERT: B 610 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6030 (mmtp) REVERT: B 680 LYS cc_start: 0.5303 (OUTLIER) cc_final: 0.5083 (mptt) outliers start: 35 outliers final: 20 residues processed: 129 average time/residue: 0.0984 time to fit residues: 17.8441 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 680 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.241339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.169588 restraints weight = 9483.987| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.90 r_work: 0.3495 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9693 Z= 0.152 Angle : 0.601 9.659 13134 Z= 0.306 Chirality : 0.041 0.149 1465 Planarity : 0.004 0.054 1662 Dihedral : 6.381 82.683 1339 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.61 % Allowed : 16.87 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 are not related in a simple way. whole: -1.22 (0.25), residues: 1178 helix: 0.12 (0.19), residues: 771 sheet: -1.56 (0.82), residues: 46 loop : -2.67 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 568 TYR 0.019 0.002 TYR B 357 PHE 0.014 0.001 PHE B 265 TRP 0.025 0.001 TRP A 595 HIS 0.004 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 9693) covalent geometry : angle 0.60115 / 0.31 (13134) hydrogen bonds : bond 0.04241 / 2.79 ( 498) hydrogen bonds : angle 4.70928 / 3.31 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8082 (mmm) cc_final: 0.7834 (mmt) REVERT: A 191 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8053 (mmt90) REVERT: A 234 ARG cc_start: 0.6382 (ttt180) cc_final: 0.5537 (ttp-170) REVERT: A 517 PHE cc_start: 0.7649 (m-10) cc_final: 0.7376 (m-80) REVERT: A 537 GLN cc_start: 0.8394 (pt0) cc_final: 0.8137 (pm20) REVERT: A 622 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.8347 (mtt-85) REVERT: A 655 LEU cc_start: 0.7197 (tt) cc_final: 0.6971 (tt) REVERT: B 321 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7474 (mt) REVERT: B 539 MET cc_start: 0.5231 (mtp) cc_final: 0.4832 (mtp) REVERT: B 548 MET cc_start: 0.4799 (mmp) cc_final: 0.3742 (tpp) REVERT: B 610 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6071 (mmtp) REVERT: B 680 LYS cc_start: 0.5330 (OUTLIER) cc_final: 0.5106 (mptt) outliers start: 36 outliers final: 17 residues processed: 132 average time/residue: 0.0985 time to fit residues: 18.3949 Evaluate side-chains 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 680 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.241629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.172755 restraints weight = 9478.407| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.10 r_work: 0.3522 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9693 Z= 0.147 Angle : 0.596 10.155 13134 Z= 0.301 Chirality : 0.041 0.146 1465 Planarity : 0.004 0.054 1662 Dihedral : 6.289 85.568 1339 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.41 % Allowed : 17.97 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 are not related in a simple way. whole: -1.06 (0.25), residues: 1178 helix: 0.23 (0.19), residues: 772 sheet: -1.30 (0.84), residues: 46 loop : -2.64 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 568 TYR 0.020 0.001 TYR B 357 PHE 0.013 0.001 PHE B 265 TRP 0.029 0.001 TRP A 595 HIS 0.005 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9693) covalent geometry : angle 0.59592 / 0.30 (13134) hydrogen bonds : bond 0.04184 / 2.75 ( 498) hydrogen bonds : angle 4.65052 / 3.26 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8196 (mmm) cc_final: 0.7967 (mmt) REVERT: A 191 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8063 (mmt90) REVERT: A 211 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7808 (tp) REVERT: A 234 ARG cc_start: 0.6328 (ttt180) cc_final: 0.5479 (ttp-170) REVERT: A 517 PHE cc_start: 0.7690 (m-10) cc_final: 0.7432 (m-80) REVERT: A 537 GLN cc_start: 0.8417 (pt0) cc_final: 0.8165 (pm20) REVERT: A 622 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.8364 (mtt-85) REVERT: B 321 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7501 (mt) REVERT: B 539 MET cc_start: 0.5347 (mtp) cc_final: 0.4931 (mtp) REVERT: B 548 MET cc_start: 0.4940 (mmp) cc_final: 0.4051 (tpp) REVERT: B 610 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6047 (mmtp) REVERT: B 680 LYS cc_start: 0.5455 (OUTLIER) cc_final: 0.5201 (mptt) outliers start: 34 outliers final: 18 residues processed: 128 average time/residue: 0.0911 time to fit residues: 16.3637 Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 680 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 55 optimal weight: 0.0980 chunk 65 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 116 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.244418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175574 restraints weight = 9378.934| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.02 r_work: 0.3554 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9693 Z= 0.117 Angle : 0.573 10.777 13134 Z= 0.288 Chirality : 0.040 0.250 1465 Planarity : 0.004 0.054 1662 Dihedral : 6.096 85.863 1339 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.71 % Allowed : 19.68 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 are not related in a simple way. whole: -0.87 (0.25), residues: 1178 helix: 0.39 (0.20), residues: 776 sheet: -1.02 (0.86), residues: 46 loop : -2.63 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 568 TYR 0.020 0.001 TYR B 357 PHE 0.013 0.001 PHE B 265 TRP 0.021 0.001 TRP A 595 HIS 0.006 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9693) covalent geometry : angle 0.57269 / 0.29 (13134) hydrogen bonds : bond 0.03890 / 2.57 ( 498) hydrogen bonds : angle 4.55263 / 3.19 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8165 (mmm) cc_final: 0.7941 (mmt) REVERT: A 191 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8013 (mmt90) REVERT: A 234 ARG cc_start: 0.6319 (ttt180) cc_final: 0.5513 (ttp-170) REVERT: A 517 PHE cc_start: 0.7563 (m-10) cc_final: 0.7236 (m-80) REVERT: A 537 GLN cc_start: 0.8364 (pt0) cc_final: 0.8150 (pm20) REVERT: B 90 GLU cc_start: 0.7441 (mp0) cc_final: 0.7053 (mm-30) REVERT: B 321 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7399 (mt) REVERT: B 539 MET cc_start: 0.5285 (mtp) cc_final: 0.4860 (mtp) REVERT: B 548 MET cc_start: 0.5129 (mmp) cc_final: 0.4399 (tpp) REVERT: B 609 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6424 (pt0) REVERT: B 680 LYS cc_start: 0.5642 (OUTLIER) cc_final: 0.5376 (mptt) outliers start: 27 outliers final: 14 residues processed: 116 average time/residue: 0.0900 time to fit residues: 14.7383 Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 680 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 17 optimal weight: 0.0020 chunk 47 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.242316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.171170 restraints weight = 9469.131| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.92 r_work: 0.3534 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9693 Z= 0.145 Angle : 0.598 9.728 13134 Z= 0.301 Chirality : 0.041 0.182 1465 Planarity : 0.004 0.055 1662 Dihedral : 5.829 86.404 1335 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.21 % Allowed : 19.88 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 are not related in a simple way. whole: -0.82 (0.25), residues: 1178 helix: 0.40 (0.19), residues: 780 sheet: -0.91 (0.88), residues: 46 loop : -2.60 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 568 TYR 0.020 0.001 TYR B 357 PHE 0.013 0.001 PHE B 265 TRP 0.019 0.001 TRP A 595 HIS 0.006 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 9693) covalent geometry : angle 0.59765 / 0.30 (13134) hydrogen bonds : bond 0.04071 / 2.68 ( 498) hydrogen bonds : angle 4.54208 / 3.18 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8131 (mmm) cc_final: 0.7902 (mmt) REVERT: A 191 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8027 (mmt90) REVERT: A 211 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7715 (tp) REVERT: A 517 PHE cc_start: 0.7609 (m-10) cc_final: 0.7288 (m-80) REVERT: A 537 GLN cc_start: 0.8378 (pt0) cc_final: 0.8140 (pm20) REVERT: B 90 GLU cc_start: 0.7452 (mp0) cc_final: 0.7020 (mm-30) REVERT: B 126 ASP cc_start: 0.7155 (t0) cc_final: 0.6822 (m-30) REVERT: B 321 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7432 (mt) REVERT: B 335 MET cc_start: 0.8408 (ttm) cc_final: 0.8198 (mtp) REVERT: B 539 MET cc_start: 0.4949 (mtp) cc_final: 0.4735 (mtp) REVERT: B 548 MET cc_start: 0.5189 (mmp) cc_final: 0.4459 (tpp) REVERT: B 609 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6389 (pt0) outliers start: 22 outliers final: 16 residues processed: 110 average time/residue: 0.0898 time to fit residues: 14.2794 Evaluate side-chains 109 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 609 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.242749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 169)---------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169129 restraints weight = 9311.924| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.67 r_work: 0.3523 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9693 Z= 0.140 Angle : 0.596 9.873 13134 Z= 0.301 Chirality : 0.042 0.389 1465 Planarity : 0.004 0.055 1662 Dihedral : 5.586 83.896 1331 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.51 % Allowed : 19.88 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 are not related in a simple way. whole: -0.78 (0.25), residues: 1178 helix: 0.42 (0.19), residues: 780 sheet: -0.82 (0.89), residues: 46 loop : -2.56 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 568 TYR 0.021 0.001 TYR B 357 PHE 0.013 0.001 PHE B 265 TRP 0.017 0.001 TRP A 595 HIS 0.006 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9693) covalent geometry : angle 0.59575 / 0.30 (13134) hydrogen bonds : bond 0.04043 / 2.66 ( 498) hydrogen bonds : angle 4.55725 / 3.19 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8137 (mmm) cc_final: 0.7904 (mmt) REVERT: A 191 ARG cc_start: 0.8341 (mtp85) cc_final: 0.8005 (mmt90) REVERT: A 211 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7668 (tp) REVERT: A 517 PHE cc_start: 0.7540 (m-10) cc_final: 0.7251 (m-80) REVERT: A 537 GLN cc_start: 0.8331 (pt0) cc_final: 0.8090 (pm20) REVERT: B 126 ASP cc_start: 0.7181 (t0) cc_final: 0.6824 (m-30) REVERT: B 321 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7391 (mt) REVERT: B 539 MET cc_start: 0.5166 (mtp) cc_final: 0.4806 (mtp) REVERT: B 609 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6512 (pt0) outliers start: 25 outliers final: 19 residues processed: 113 average time/residue: 0.0891 time to fit residues: 14.4605 Evaluate side-chains 115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 658 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 76 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.242458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.174547 restraints weight = 9350.685| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.14 r_work: 0.3524 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9693 Z= 0.147 Angle : 0.619 11.039 13134 Z= 0.308 Chirality : 0.042 0.303 1465 Planarity : 0.004 0.054 1662 Dihedral : 5.569 82.825 1331 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.21 % Allowed : 20.38 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 are not related in a simple way. whole: -0.80 (0.25), residues: 1178 helix: 0.40 (0.19), residues: 775 sheet: -0.87 (0.88), residues: 46 loop : -2.52 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 568 TYR 0.020 0.001 TYR B 357 PHE 0.013 0.001 PHE B 265 TRP 0.015 0.001 TRP A 595 HIS 0.005 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9693) covalent geometry : angle 0.61932 / 0.31 (13134) hydrogen bonds : bond 0.04070 / 2.68 ( 498) hydrogen bonds : angle 4.54758 / 3.18 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3168.11 seconds wall clock time: 54 minutes 43.04 seconds (3283.04 seconds total)