Starting phenix.real_space_refine on Wed Mar 4 00:49:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xec_33155/03_2026/7xec_33155.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xec_33155/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xec_33155/03_2026/7xec_33155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xec_33155/03_2026/7xec_33155.map" model { file = "/net/cci-nas-00/data/ceres_data/7xec_33155/03_2026/7xec_33155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xec_33155/03_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-5986/lib/python3.9/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: 2.34, per 1000 atoms: 0.25 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: 0.79 Conformation dependent library (CDL) restraints added in 499.5 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: 0.30 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: 1.50 Time building geometry restraints manager: 1.09 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: 5017 17.18 - 34.36: 612 34.36 - 51.54: 125 51.54 - 68.73: 37 68.73 - 85.91: 18 Dihedral angle restraints: 5809 sinusoidal: 2359 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 5806 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: 6.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.480 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 16.443 85.906 3591 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 covalent geometry : bond 0.00881 ( 9693) covalent geometry : angle 1.42569 (13134) hydrogen bonds : bond 0.20907 ( 498) hydrogen bonds : angle 8.98177 ( 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 : 0.358 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: 0.1090 time to fit residues: 22.6099 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 : 0.326 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4598 r_free = 0.4598 target = 0.241708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 171)---------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157295 restraints weight = 9408.778| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.90 r_work: 0.3474 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9693 Z= 0.158 Angle : 0.712 9.191 13134 Z= 0.377 Chirality : 0.043 0.181 1465 Planarity : 0.005 0.043 1662 Dihedral : 10.211 84.683 1390 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Rotamer: Outliers : 2.41 % Allowed : 11.85 % Favored : 85.74 % 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: -2.96 (0.22), residues: 1178 helix: -1.22 (0.18), residues: 770 sheet: -2.99 (0.59), residues: 46 loop : -3.26 (0.28), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 259 TYR 0.019 0.002 TYR B 357 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 covalent geometry : bond 0.00339 ( 9693) covalent geometry : angle 0.71182 (13134) hydrogen bonds : bond 0.05555 ( 498) hydrogen bonds : angle 5.66947 ( 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 131 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6307 (ttt180) cc_final: 0.5622 (ttp-170) REVERT: A 281 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5812 (t80) REVERT: A 406 TYR cc_start: 0.7677 (t80) cc_final: 0.6673 (m-80) REVERT: A 501 MET cc_start: 0.8267 (mmm) cc_final: 0.8014 (mmm) REVERT: A 537 GLN cc_start: 0.8397 (pt0) cc_final: 0.8149 (pm20) REVERT: A 566 MET cc_start: 0.8424 (tmm) cc_final: 0.8042 (tmm) REVERT: A 603 ASP cc_start: 0.8241 (m-30) cc_final: 0.7937 (m-30) REVERT: B 250 VAL cc_start: 0.7565 (t) cc_final: 0.7049 (m) REVERT: B 278 GLU cc_start: 0.7678 (tt0) cc_final: 0.7392 (tt0) REVERT: B 321 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7357 (mt) REVERT: B 329 MET cc_start: 0.8234 (ttp) cc_final: 0.7926 (ttp) REVERT: B 380 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: B 539 MET cc_start: 0.5546 (mtp) cc_final: 0.5211 (mtp) REVERT: B 610 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6502 (mmtp) REVERT: B 680 LYS cc_start: 0.5081 (OUTLIER) cc_final: 0.4856 (mptt) outliers start: 24 outliers final: 8 residues processed: 126 average time/residue: 0.1120 time to fit residues: 18.9330 Evaluate side-chains 107 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 321 LEU Chi-restraints excluded: chain B residue 346 MET 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: 0.9980 chunk 96 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4583 r_free = 0.4583 target = 0.239842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.166665 restraints weight = 9476.682| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.83 r_work: 0.3488 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2214 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= 0.167 Angle : 0.658 8.494 13134 Z= 0.343 Chirality : 0.042 0.152 1465 Planarity : 0.004 0.047 1662 Dihedral : 9.147 89.097 1378 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.81 % Allowed : 12.55 % Favored : 84.64 % 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: -2.23 (0.24), residues: 1178 helix: -0.63 (0.19), residues: 768 sheet: -2.46 (0.66), residues: 46 loop : -3.07 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 568 TYR 0.019 0.002 TYR B 357 PHE 0.015 0.002 PHE B 265 TRP 0.012 0.001 TRP B 326 HIS 0.008 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9693) covalent geometry : angle 0.65816 (13134) hydrogen bonds : bond 0.04860 ( 498) hydrogen bonds : angle 5.23016 ( 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: 28 poor density : 111 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6289 (ttt180) cc_final: 0.5584 (ttp-170) REVERT: A 281 TYR cc_start: 0.5959 (OUTLIER) cc_final: 0.5686 (t80) REVERT: A 537 GLN cc_start: 0.8387 (pt0) cc_final: 0.8135 (pm20) REVERT: A 566 MET cc_start: 0.8521 (tmm) cc_final: 0.8188 (tmm) REVERT: B 329 MET cc_start: 0.8355 (ttp) cc_final: 0.8029 (ttp) REVERT: B 539 MET cc_start: 0.5466 (mtp) cc_final: 0.5064 (mtp) REVERT: B 548 MET cc_start: 0.5215 (mmp) cc_final: 0.2851 (tmm) REVERT: B 610 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6579 (mmtp) outliers start: 28 outliers final: 17 residues processed: 134 average time/residue: 0.1142 time to fit residues: 20.6178 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 320 ILE Chi-restraints excluded: chain A residue 427 GLU 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 346 MET 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 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: 5.9990 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4608 r_free = 0.4608 target = 0.242844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.176659 restraints weight = 9510.234| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.14 r_work: 0.3507 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9693 Z= 0.151 Angle : 0.626 10.917 13134 Z= 0.322 Chirality : 0.041 0.154 1465 Planarity : 0.004 0.052 1662 Dihedral : 8.313 81.998 1368 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.21 % Allowed : 14.86 % Favored : 81.93 % 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: -1.77 (0.24), residues: 1178 helix: -0.28 (0.19), residues: 772 sheet: -2.06 (0.74), residues: 46 loop : -2.92 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 568 TYR 0.026 0.002 TYR A 406 PHE 0.015 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 covalent geometry : bond 0.00347 ( 9693) covalent geometry : angle 0.62562 (13134) hydrogen bonds : bond 0.04524 ( 498) hydrogen bonds : angle 4.99413 ( 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 142 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8279 (mmm) cc_final: 0.8048 (mmt) REVERT: A 191 ARG cc_start: 0.8460 (mtp85) cc_final: 0.7977 (mmt90) REVERT: A 234 ARG cc_start: 0.6345 (ttt180) cc_final: 0.5580 (ttp-170) REVERT: A 281 TYR cc_start: 0.5987 (OUTLIER) cc_final: 0.5735 (t80) REVERT: A 501 MET cc_start: 0.8374 (mmm) cc_final: 0.8125 (mmm) REVERT: A 537 GLN cc_start: 0.8427 (pt0) cc_final: 0.8197 (pm20) REVERT: B 539 MET cc_start: 0.5359 (mtp) cc_final: 0.4967 (mtp) REVERT: B 610 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6130 (mmtp) outliers start: 32 outliers final: 15 residues processed: 135 average time/residue: 0.1138 time to fit residues: 20.5878 Evaluate side-chains 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 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 179 THR Chi-restraints excluded: chain B residue 250 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 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: 0.9990 chunk 58 optimal weight: 0.4980 chunk 93 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 433 HIS A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.241076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148069 restraints weight = 9417.462| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.37 r_work: 0.3363 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9693 Z= 0.147 Angle : 0.603 10.531 13134 Z= 0.310 Chirality : 0.041 0.148 1465 Planarity : 0.004 0.052 1662 Dihedral : 7.985 78.429 1368 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.91 % Allowed : 16.97 % Favored : 80.12 % 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: -1.44 (0.24), residues: 1178 helix: -0.04 (0.19), residues: 773 sheet: -1.83 (0.78), residues: 46 loop : -2.76 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 568 TYR 0.019 0.001 TYR B 357 PHE 0.014 0.001 PHE B 265 TRP 0.020 0.001 TRP A 595 HIS 0.005 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9693) covalent geometry : angle 0.60320 (13134) hydrogen bonds : bond 0.04319 ( 498) hydrogen bonds : angle 4.83553 ( 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 138 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8201 (mmm) cc_final: 0.7991 (mmt) REVERT: A 191 ARG cc_start: 0.8488 (mtp85) cc_final: 0.7910 (mmt90) REVERT: A 234 ARG cc_start: 0.6251 (ttt180) cc_final: 0.5406 (ttp-170) REVERT: A 517 PHE cc_start: 0.7492 (m-10) cc_final: 0.7208 (m-80) REVERT: A 537 GLN cc_start: 0.8430 (pt0) cc_final: 0.8042 (pm20) REVERT: B 539 MET cc_start: 0.5306 (mtp) cc_final: 0.4904 (mtp) REVERT: B 548 MET cc_start: 0.4700 (mmp) cc_final: 0.3556 (tpp) REVERT: B 610 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.6114 (mmtp) outliers start: 29 outliers final: 17 residues processed: 131 average time/residue: 0.1125 time to fit residues: 20.0869 Evaluate side-chains 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 320 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 588 ILE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 71 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4601 r_free = 0.4601 target = 0.242532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170930 restraints weight = 9485.250| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.86 r_work: 0.3522 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9693 Z= 0.136 Angle : 0.592 9.277 13134 Z= 0.302 Chirality : 0.040 0.144 1465 Planarity : 0.004 0.054 1662 Dihedral : 7.598 73.781 1366 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.41 % Allowed : 16.87 % Favored : 79.72 % 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: -1.21 (0.25), residues: 1178 helix: 0.12 (0.19), residues: 777 sheet: -1.54 (0.82), residues: 46 loop : -2.69 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 568 TYR 0.019 0.001 TYR B 357 PHE 0.013 0.001 PHE B 265 TRP 0.031 0.001 TRP A 595 HIS 0.005 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9693) covalent geometry : angle 0.59172 (13134) hydrogen bonds : bond 0.04125 ( 498) hydrogen bonds : angle 4.70228 ( 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 146 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8434 (mtp85) cc_final: 0.8038 (mmt90) REVERT: A 211 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7665 (tp) REVERT: A 234 ARG cc_start: 0.6352 (ttt180) cc_final: 0.5523 (ttp-170) REVERT: A 345 LEU cc_start: 0.8115 (mt) cc_final: 0.7599 (mm) REVERT: A 431 ARG cc_start: 0.8189 (ttp-110) cc_final: 0.7707 (ttp80) REVERT: A 517 PHE cc_start: 0.7572 (m-10) cc_final: 0.7242 (m-80) REVERT: A 537 GLN cc_start: 0.8405 (pt0) cc_final: 0.8151 (pm20) REVERT: A 622 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8304 (mtt-85) REVERT: B 126 ASP cc_start: 0.7391 (t0) cc_final: 0.6975 (t0) REVERT: B 321 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7419 (mt) REVERT: B 335 MET cc_start: 0.8341 (ttm) cc_final: 0.8126 (mtp) REVERT: B 379 SER cc_start: 0.8312 (t) cc_final: 0.7858 (m) REVERT: B 539 MET cc_start: 0.5450 (mtp) cc_final: 0.5000 (mtp) REVERT: B 548 MET cc_start: 0.4969 (mmp) cc_final: 0.4054 (tpp) REVERT: B 610 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6067 (mmtp) outliers start: 34 outliers final: 12 residues processed: 138 average time/residue: 0.1033 time to fit residues: 19.3851 Evaluate side-chains 124 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 211 LEU 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 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 140 ILE 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 550 VAL Chi-restraints excluded: chain B residue 610 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 0.0870 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4611 r_free = 0.4611 target = 0.243409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.174361 restraints weight = 9443.017| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.96 r_work: 0.3502 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3315 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 : 0.602 10.260 13134 Z= 0.305 Chirality : 0.041 0.145 1465 Planarity : 0.004 0.054 1662 Dihedral : 7.503 74.869 1366 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.11 % Allowed : 17.77 % Favored : 79.12 % 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: -1.12 (0.25), residues: 1178 helix: 0.18 (0.19), residues: 772 sheet: -1.33 (0.85), 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 0.027 0.001 TRP A 595 HIS 0.005 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9693) covalent geometry : angle 0.60233 (13134) hydrogen bonds : bond 0.04176 ( 498) hydrogen bonds : angle 4.67988 ( 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 135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8045 (mmt90) REVERT: A 211 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7710 (tp) REVERT: A 234 ARG cc_start: 0.6313 (ttt180) cc_final: 0.5482 (ttp-170) REVERT: A 517 PHE cc_start: 0.7609 (m-10) cc_final: 0.7317 (m-80) REVERT: A 537 GLN cc_start: 0.8386 (pt0) cc_final: 0.8144 (pm20) REVERT: A 622 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8343 (mtt-85) REVERT: B 321 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7456 (mt) REVERT: B 539 MET cc_start: 0.5346 (mtp) cc_final: 0.4911 (mtp) REVERT: B 610 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.5880 (mmtp) outliers start: 31 outliers final: 14 residues processed: 125 average time/residue: 0.0977 time to fit residues: 16.7577 Evaluate side-chains 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 211 LEU 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 427 GLU Chi-restraints excluded: chain A residue 550 VAL 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 140 ILE Chi-restraints excluded: chain B residue 155 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 550 VAL Chi-restraints excluded: chain B residue 610 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 55 optimal weight: 0.3980 chunk 65 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4606 r_free = 0.4606 target = 0.243099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171916 restraints weight = 9386.689| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.95 r_work: 0.3535 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9693 Z= 0.136 Angle : 0.613 10.628 13134 Z= 0.306 Chirality : 0.042 0.224 1465 Planarity : 0.004 0.054 1662 Dihedral : 7.381 71.449 1366 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.71 % Allowed : 19.08 % Favored : 78.21 % 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: -1.01 (0.25), residues: 1178 helix: 0.24 (0.19), residues: 777 sheet: -1.06 (0.86), residues: 46 loop : -2.59 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 568 TYR 0.020 0.002 TYR B 357 PHE 0.013 0.001 PHE B 265 TRP 0.020 0.001 TRP A 595 HIS 0.005 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9693) covalent geometry : angle 0.61277 (13134) hydrogen bonds : bond 0.04035 ( 498) hydrogen bonds : angle 4.67248 ( 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 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8433 (mtp85) cc_final: 0.8036 (mmt90) REVERT: A 211 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7713 (tp) REVERT: A 234 ARG cc_start: 0.6352 (ttt180) cc_final: 0.5484 (ttp-170) REVERT: A 295 PHE cc_start: 0.3928 (OUTLIER) cc_final: 0.2445 (p90) REVERT: A 431 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7883 (ttp80) REVERT: A 517 PHE cc_start: 0.7587 (m-10) cc_final: 0.7258 (m-80) REVERT: A 537 GLN cc_start: 0.8405 (pt0) cc_final: 0.8170 (pm20) REVERT: A 622 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8310 (mtt-85) REVERT: B 126 ASP cc_start: 0.7430 (t0) cc_final: 0.6988 (t0) REVERT: B 321 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7447 (mt) REVERT: B 539 MET cc_start: 0.4865 (mtp) cc_final: 0.4633 (mtp) REVERT: B 548 MET cc_start: 0.4592 (mmp) cc_final: 0.3761 (tpp) outliers start: 27 outliers final: 17 residues processed: 119 average time/residue: 0.1064 time to fit residues: 17.2363 Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 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 295 PHE 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 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.242258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169747 restraints weight = 9451.661| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.91 r_work: 0.3525 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3605 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= 0.143 Angle : 0.608 10.131 13134 Z= 0.304 Chirality : 0.042 0.231 1465 Planarity : 0.004 0.055 1662 Dihedral : 7.085 71.668 1362 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.81 % Allowed : 18.57 % 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: -0.91 (0.25), residues: 1178 helix: 0.32 (0.19), residues: 775 sheet: -0.89 (0.88), residues: 46 loop : -2.60 (0.30), residues: 357 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 0.017 0.001 TRP A 595 HIS 0.006 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9693) covalent geometry : angle 0.60802 (13134) hydrogen bonds : bond 0.04071 ( 498) hydrogen bonds : angle 4.64372 ( 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 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8019 (mmt90) REVERT: A 211 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7714 (tp) REVERT: A 389 ARG cc_start: 0.7269 (ttm170) cc_final: 0.7055 (ttp-170) REVERT: A 431 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7893 (ttp80) REVERT: A 517 PHE cc_start: 0.7571 (m-10) cc_final: 0.7251 (m-80) REVERT: A 537 GLN cc_start: 0.8390 (pt0) cc_final: 0.8147 (pm20) REVERT: A 622 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8329 (mtt-85) REVERT: B 321 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7436 (mt) REVERT: B 539 MET cc_start: 0.5053 (mtp) cc_final: 0.4724 (mtp) outliers start: 28 outliers final: 23 residues processed: 120 average time/residue: 0.0947 time to fit residues: 15.8553 Evaluate side-chains 123 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 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 334 LEU 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 583 VAL Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 155 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 502 HIS Chi-restraints excluded: chain B residue 550 VAL 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 28 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 53 optimal weight: 0.0870 chunk 46 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.245223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151305 restraints weight = 9287.447| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.34 r_work: 0.3446 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9693 Z= 0.125 Angle : 0.603 13.490 13134 Z= 0.298 Chirality : 0.041 0.206 1465 Planarity : 0.004 0.055 1662 Dihedral : 6.883 67.424 1362 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.41 % Allowed : 19.68 % 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: -0.80 (0.25), residues: 1178 helix: 0.45 (0.20), residues: 772 sheet: -1.71 (0.75), residues: 59 loop : -2.50 (0.30), residues: 347 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 0.014 0.001 TRP A 595 HIS 0.006 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9693) covalent geometry : angle 0.60252 (13134) hydrogen bonds : bond 0.03888 ( 498) hydrogen bonds : angle 4.59330 ( 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 120 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8483 (mtp85) cc_final: 0.7942 (mmt90) REVERT: A 211 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7622 (tp) REVERT: A 389 ARG cc_start: 0.7346 (ttm170) cc_final: 0.7122 (ttp-170) REVERT: A 431 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.7922 (ttp80) REVERT: A 517 PHE cc_start: 0.7463 (m-10) cc_final: 0.7179 (m-80) REVERT: A 537 GLN cc_start: 0.8397 (pt0) cc_final: 0.8067 (pm20) REVERT: A 622 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8369 (mtt-85) REVERT: B 321 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7363 (mt) REVERT: B 539 MET cc_start: 0.5191 (mtp) cc_final: 0.4844 (mtp) REVERT: B 548 MET cc_start: 0.4616 (mmp) cc_final: 0.3794 (tpp) REVERT: B 609 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6437 (pt0) outliers start: 24 outliers final: 19 residues processed: 114 average time/residue: 0.1149 time to fit residues: 17.5135 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 : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 271 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 583 VAL Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 321 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: 0.9980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 3 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 100 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4614 r_free = 0.4614 target = 0.243905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.174558 restraints weight = 9345.862| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.05 r_work: 0.3570 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9693 Z= 0.126 Angle : 0.598 12.011 13134 Z= 0.296 Chirality : 0.041 0.194 1465 Planarity : 0.004 0.055 1662 Dihedral : 6.803 67.970 1362 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.51 % Allowed : 19.08 % Favored : 78.41 % 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: -0.76 (0.25), residues: 1178 helix: 0.52 (0.20), residues: 768 sheet: -1.72 (0.74), residues: 59 loop : -2.55 (0.30), residues: 351 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 0.012 0.001 TRP A 595 HIS 0.005 0.001 HIS A 621 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9693) covalent geometry : angle 0.59805 (13134) hydrogen bonds : bond 0.03838 ( 498) hydrogen bonds : angle 4.56154 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3391.87 seconds wall clock time: 58 minutes 24.70 seconds (3504.70 seconds total)