Starting phenix.real_space_refine on Fri Mar 14 06:14:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xec_33155/03_2025/7xec_33155.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xec_33155/03_2025/7xec_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_2025/7xec_33155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xec_33155/03_2025/7xec_33155.map" model { file = "/net/cci-nas-00/data/ceres_data/7xec_33155/03_2025/7xec_33155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xec_33155/03_2025/7xec_33155.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.39, per 1000 atoms: 0.67 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.89 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: 2.52 Time building geometry restraints manager: 2.96 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.770 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- 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= 0.624 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (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 TRP 0.025 0.004 TRP B 339 HIS 0.014 0.003 HIS A 669 PHE 0.023 0.004 PHE A 295 TYR 0.043 0.005 TYR B 181 ARG 0.010 0.001 ARG B 401 *********************** 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 : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6196 (ttt180) cc_final: 0.5849 (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: 0.8026 (pm20) REVERT: A 566 MET cc_start: 0.8254 (tmm) cc_final: 0.7502 (ttt) 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: 0.8037 (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: 0.5358 (mtp) REVERT: B 561 ASP cc_start: 0.5338 (OUTLIER) cc_final: 0.4833 (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: 0.2501 time to fit residues: 51.6070 Evaluate side-chains 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0020 chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 0.0050 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.2202 ------------------------------------------------------------------------------- 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 = 0.4617 r_free = 0.4617 target = 0.243840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152324 restraints weight = 9360.097| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.04 r_work: 0.3463 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1848 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= 0.212 Angle : 0.694 10.350 13134 Z= 0.367 Chirality : 0.042 0.179 1465 Planarity : 0.005 0.044 1662 Dihedral : 10.028 87.799 1390 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.41 % Allowed : 12.25 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.22), residues: 1178 helix: -1.18 (0.18), residues: 769 sheet: -2.86 (0.60), residues: 46 loop : -3.22 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 326 HIS 0.005 0.001 HIS A 97 PHE 0.016 0.002 PHE B 265 TYR 0.019 0.002 TYR B 357 ARG 0.008 0.001 ARG A 568 *********************** 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 133 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.7392 (mmt180) cc_final: 0.7119 (mmt-90) REVERT: A 234 ARG cc_start: 0.6259 (ttt180) cc_final: 0.5567 (ttp-170) REVERT: A 281 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5864 (t80) REVERT: A 324 ARG cc_start: 0.6547 (tpp80) cc_final: 0.5667 (ptm160) REVERT: A 406 TYR cc_start: 0.7598 (t80) cc_final: 0.6607 (m-80) REVERT: A 501 MET cc_start: 0.8330 (mmm) cc_final: 0.8128 (mmm) REVERT: A 537 GLN cc_start: 0.8368 (pt0) cc_final: 0.8072 (pm20) REVERT: A 566 MET cc_start: 0.8357 (tmm) cc_final: 0.7988 (tmm) REVERT: B 96 LEU cc_start: 0.7822 (tp) cc_final: 0.7606 (tt) REVERT: B 278 GLU cc_start: 0.7662 (tt0) cc_final: 0.7367 (tt0) REVERT: B 321 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7227 (mt) REVERT: B 380 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: B 539 MET cc_start: 0.5504 (mtp) cc_final: 0.5172 (mtp) REVERT: B 610 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6455 (mmtp) REVERT: B 680 LYS cc_start: 0.5053 (OUTLIER) cc_final: 0.4788 (mptt) outliers start: 24 outliers final: 8 residues processed: 127 average time/residue: 0.2478 time to fit residues: 42.8816 Evaluate side-chains 108 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 55 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 99 optimal weight: 40.0000 chunk 17 optimal weight: 0.0030 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN B 433 HIS B 621 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.243789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173098 restraints weight = 9414.620| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.87 r_work: 0.3550 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2341 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= 0.210 Angle : 0.625 9.132 13134 Z= 0.326 Chirality : 0.041 0.144 1465 Planarity : 0.004 0.048 1662 Dihedral : 8.986 88.894 1377 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.81 % Allowed : 13.05 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.24), residues: 1178 helix: -0.49 (0.19), residues: 768 sheet: -2.32 (0.68), residues: 46 loop : -3.02 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.009 0.001 HIS B 420 PHE 0.014 0.001 PHE B 265 TYR 0.020 0.002 TYR B 357 ARG 0.006 0.000 ARG A 568 *********************** 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 135 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6282 (ttt180) cc_final: 0.5592 (ttp-170) REVERT: A 281 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.5647 (t80) REVERT: A 329 MET cc_start: 0.6494 (tmm) cc_final: 0.6289 (tmm) REVERT: A 537 GLN cc_start: 0.8389 (pt0) cc_final: 0.8148 (pm20) REVERT: A 566 MET cc_start: 0.8488 (tmm) cc_final: 0.8161 (tmm) REVERT: B 539 MET cc_start: 0.5495 (mtp) cc_final: 0.5101 (mtp) REVERT: B 548 MET cc_start: 0.5250 (mmp) cc_final: 0.2895 (tmm) REVERT: B 610 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6585 (mmtp) REVERT: B 680 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.5049 (mptt) outliers start: 28 outliers final: 15 residues processed: 129 average time/residue: 0.2796 time to fit residues: 50.2818 Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 A residue 649 ASP 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 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 34 optimal weight: 0.0010 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 = 0.4585 r_free = 0.4585 target = 0.240356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3952 r_free = 0.3952 target = 0.166965 restraints weight = 9406.208| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.77 r_work: 0.3464 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9693 Z= 0.254 Angle : 0.623 9.125 13134 Z= 0.322 Chirality : 0.042 0.159 1465 Planarity : 0.004 0.051 1662 Dihedral : 8.381 82.004 1375 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.31 % Allowed : 15.26 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1178 helix: -0.23 (0.19), residues: 773 sheet: -1.94 (0.75), residues: 46 loop : -2.79 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.007 0.001 HIS B 420 PHE 0.015 0.001 PHE B 265 TYR 0.021 0.002 TYR A 406 ARG 0.007 0.000 ARG A 568 *********************** 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 141 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6329 (ttt180) cc_final: 0.5574 (ttp-170) REVERT: A 537 GLN cc_start: 0.8429 (pt0) cc_final: 0.8200 (pm20) REVERT: A 566 MET cc_start: 0.8503 (tmm) cc_final: 0.8178 (tmm) REVERT: A 673 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.6701 (t80) REVERT: B 90 GLU cc_start: 0.7561 (mp0) cc_final: 0.7106 (mm-30) REVERT: B 539 MET cc_start: 0.5339 (mtp) cc_final: 0.4947 (mtp) REVERT: B 610 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.5996 (mmtp) REVERT: B 680 LYS cc_start: 0.5332 (OUTLIER) cc_final: 0.5073 (mptt) outliers start: 33 outliers final: 19 residues processed: 131 average time/residue: 0.2265 time to fit residues: 41.3868 Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 482 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 673 PHE 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 287 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 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 25 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4602 r_free = 0.4602 target = 0.242383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 138)---------------| | r_work = 0.3977 r_free = 0.3977 target = 0.169338 restraints weight = 9413.746| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.78 r_work: 0.3491 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9693 Z= 0.244 Angle : 0.595 7.708 13134 Z= 0.308 Chirality : 0.041 0.148 1465 Planarity : 0.004 0.052 1662 Dihedral : 7.983 77.931 1370 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.82 % Allowed : 17.37 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.24), residues: 1178 helix: -0.05 (0.19), residues: 774 sheet: -1.73 (0.80), residues: 46 loop : -2.68 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.005 0.001 HIS A 621 PHE 0.014 0.001 PHE B 265 TYR 0.021 0.002 TYR B 357 ARG 0.007 0.000 ARG A 568 *********************** 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 152 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8405 (mtp85) cc_final: 0.7992 (mmt90) REVERT: A 234 ARG cc_start: 0.6378 (ttt180) cc_final: 0.5570 (ttp-170) REVERT: A 537 GLN cc_start: 0.8403 (pt0) cc_final: 0.8136 (pm20) REVERT: A 673 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.6855 (t80) REVERT: B 90 GLU cc_start: 0.7360 (mp0) cc_final: 0.7110 (mm-30) REVERT: B 539 MET cc_start: 0.5301 (mtp) cc_final: 0.4890 (mtp) REVERT: B 548 MET cc_start: 0.4902 (mmp) cc_final: 0.3805 (tpp) REVERT: B 610 LYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6133 (mmtp) REVERT: B 618 MET cc_start: 0.6843 (ptt) cc_final: 0.6582 (ptt) REVERT: B 680 LYS cc_start: 0.5367 (OUTLIER) cc_final: 0.5108 (mptt) outliers start: 38 outliers final: 20 residues processed: 142 average time/residue: 0.2808 time to fit residues: 53.4412 Evaluate side-chains 126 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 340 SER 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 588 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 96 LEU 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 322 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 378 VAL 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 82 optimal weight: 0.8980 chunk 20 optimal weight: 0.0370 chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.4606 r_free = 0.4606 target = 0.243148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.171192 restraints weight = 9357.554| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.87 r_work: 0.3517 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9693 Z= 0.227 Angle : 0.589 9.569 13134 Z= 0.301 Chirality : 0.040 0.146 1465 Planarity : 0.004 0.054 1662 Dihedral : 7.738 75.007 1370 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.31 % Allowed : 18.17 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1178 helix: 0.12 (0.19), residues: 771 sheet: -1.53 (0.82), residues: 46 loop : -2.65 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 595 HIS 0.006 0.001 HIS A 621 PHE 0.013 0.001 PHE B 265 TYR 0.018 0.001 TYR B 357 ARG 0.008 0.000 ARG A 568 *********************** 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 139 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8146 (mmm) cc_final: 0.7849 (mmm) REVERT: A 191 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8049 (mmt90) REVERT: A 234 ARG cc_start: 0.6328 (ttt180) cc_final: 0.5483 (ttp-170) REVERT: A 389 ARG cc_start: 0.7348 (ttm170) cc_final: 0.7129 (ttp-170) REVERT: A 537 GLN cc_start: 0.8410 (pt0) cc_final: 0.8156 (pm20) REVERT: A 673 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.6870 (t80) REVERT: B 126 ASP cc_start: 0.7250 (t0) cc_final: 0.7047 (m-30) REVERT: B 379 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.7890 (m) REVERT: B 539 MET cc_start: 0.5371 (mtp) cc_final: 0.4952 (mtp) REVERT: B 548 MET cc_start: 0.4992 (mmp) cc_final: 0.4094 (tpp) REVERT: B 610 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6061 (mmtp) REVERT: B 680 LYS cc_start: 0.5350 (OUTLIER) cc_final: 0.5125 (mptt) outliers start: 33 outliers final: 19 residues processed: 128 average time/residue: 0.2467 time to fit residues: 42.9629 Evaluate side-chains 125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 271 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 340 SER Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 96 LEU 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 322 LEU Chi-restraints excluded: chain B residue 378 VAL 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 67 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 102 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 94 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 37 optimal weight: 0.0040 chunk 92 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4601 r_free = 0.4601 target = 0.242457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 149)---------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152478 restraints weight = 9412.473| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.66 r_work: 0.3392 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3339 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= 0.209 Angle : 0.578 8.284 13134 Z= 0.296 Chirality : 0.040 0.171 1465 Planarity : 0.004 0.054 1662 Dihedral : 7.529 71.702 1370 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.21 % Allowed : 18.78 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.25), residues: 1178 helix: 0.26 (0.19), residues: 772 sheet: -1.26 (0.84), residues: 46 loop : -2.54 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 595 HIS 0.005 0.001 HIS A 621 PHE 0.015 0.001 PHE B 434 TYR 0.020 0.001 TYR B 357 ARG 0.008 0.000 ARG A 568 *********************** 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 143 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8110 (mmm) cc_final: 0.7853 (mmm) REVERT: A 191 ARG cc_start: 0.8367 (mtp85) cc_final: 0.7971 (mmt90) REVERT: A 234 ARG cc_start: 0.6239 (ttt180) cc_final: 0.5376 (ttp-170) REVERT: A 431 ARG cc_start: 0.8098 (ttp-110) cc_final: 0.7575 (ttp80) REVERT: A 537 GLN cc_start: 0.8387 (pt0) cc_final: 0.8086 (pm20) REVERT: A 673 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6825 (t80) REVERT: B 90 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6781 (mm-30) REVERT: B 539 MET cc_start: 0.5308 (mtp) cc_final: 0.4909 (mtp) REVERT: B 548 MET cc_start: 0.5158 (mmp) cc_final: 0.4407 (tpp) REVERT: B 680 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.5280 (mptt) outliers start: 32 outliers final: 18 residues processed: 131 average time/residue: 0.2337 time to fit residues: 42.4719 Evaluate side-chains 122 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 271 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 340 SER Chi-restraints excluded: chain A residue 347 VAL 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 588 ILE Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 96 LEU 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 322 LEU Chi-restraints excluded: chain B residue 550 VAL 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 50 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 0.0570 chunk 109 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 101 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.0270 chunk 86 optimal weight: 1.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 = 0.4629 r_free = 0.4629 target = 0.245694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.178769 restraints weight = 9472.120| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.07 r_work: 0.3573 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9693 Z= 0.182 Angle : 0.564 8.460 13134 Z= 0.288 Chirality : 0.040 0.151 1465 Planarity : 0.004 0.054 1662 Dihedral : 7.093 67.987 1366 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.81 % Allowed : 19.38 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.25), residues: 1178 helix: 0.39 (0.19), residues: 778 sheet: -1.07 (0.85), residues: 46 loop : -2.57 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 595 HIS 0.006 0.001 HIS A 621 PHE 0.014 0.001 PHE B 434 TYR 0.021 0.001 TYR B 357 ARG 0.009 0.000 ARG A 568 *********************** 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 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.899 Fit side-chains REVERT: A 67 MET cc_start: 0.8147 (mmm) cc_final: 0.7907 (mmm) REVERT: A 191 ARG cc_start: 0.8370 (mtp85) cc_final: 0.8027 (mmt90) REVERT: A 234 ARG cc_start: 0.6319 (ttt180) cc_final: 0.5519 (ttp-170) REVERT: A 389 ARG cc_start: 0.7324 (ttm170) cc_final: 0.7096 (ttp-170) REVERT: A 517 PHE cc_start: 0.7719 (m-10) cc_final: 0.7504 (m-80) REVERT: A 537 GLN cc_start: 0.8384 (pt0) cc_final: 0.8181 (pm20) REVERT: A 673 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6951 (t80) REVERT: B 90 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6790 (mm-30) REVERT: B 126 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6865 (m-30) REVERT: B 278 GLU cc_start: 0.7856 (tt0) cc_final: 0.7267 (tt0) REVERT: B 321 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7400 (mt) REVERT: B 539 MET cc_start: 0.5332 (mtp) cc_final: 0.4906 (mtp) REVERT: B 615 MET cc_start: 0.8451 (ptt) cc_final: 0.7987 (ppp) outliers start: 28 outliers final: 17 residues processed: 118 average time/residue: 0.2426 time to fit residues: 39.1532 Evaluate side-chains 121 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 340 SER 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 588 ILE Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 126 ASP 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 322 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 79 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 80 optimal weight: 0.4980 chunk 96 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 100 optimal weight: 0.0670 overall best weight: 0.2318 ------------------------------------------------------------------------------- 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 = 0.4642 r_free = 0.4642 target = 0.247421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180807 restraints weight = 9355.240| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.06 r_work: 0.3552 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9693 Z= 0.164 Angle : 0.559 9.219 13134 Z= 0.283 Chirality : 0.039 0.139 1465 Planarity : 0.004 0.055 1662 Dihedral : 6.624 63.742 1359 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.61 % Allowed : 19.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1178 helix: 0.57 (0.20), residues: 779 sheet: -1.80 (0.73), residues: 59 loop : -2.58 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 595 HIS 0.006 0.001 HIS A 621 PHE 0.012 0.001 PHE B 540 TYR 0.021 0.001 TYR B 357 ARG 0.010 0.000 ARG A 568 *********************** 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: 26 poor density : 102 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8388 (mtp85) cc_final: 0.7997 (mmt90) REVERT: A 211 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7695 (tp) REVERT: A 431 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7752 (ttp80) REVERT: A 517 PHE cc_start: 0.7647 (m-10) cc_final: 0.7416 (m-80) REVERT: A 673 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.6909 (t80) REVERT: B 126 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6847 (m-30) REVERT: B 278 GLU cc_start: 0.7796 (tt0) cc_final: 0.7224 (tt0) REVERT: B 321 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7300 (mt) REVERT: B 324 ARG cc_start: 0.7804 (mmt90) cc_final: 0.6909 (mmm160) REVERT: B 539 MET cc_start: 0.5359 (mtp) cc_final: 0.4919 (mtp) REVERT: B 609 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6453 (pt0) REVERT: B 618 MET cc_start: 0.6870 (ptt) cc_final: 0.6642 (ptt) outliers start: 26 outliers final: 15 residues processed: 119 average time/residue: 0.2425 time to fit residues: 39.6893 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 : 0.913 ------------------------------------------------------------------------------- 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 271 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 340 SER 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 588 ILE Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 155 GLU 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 38 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** ** A 586 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 = 0.242983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.173680 restraints weight = 9363.932| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.99 r_work: 0.3534 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9693 Z= 0.270 Angle : 0.621 13.501 13134 Z= 0.311 Chirality : 0.043 0.304 1465 Planarity : 0.004 0.054 1662 Dihedral : 6.906 73.391 1359 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.51 % Allowed : 20.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1178 helix: 0.39 (0.19), residues: 783 sheet: -1.87 (0.72), residues: 59 loop : -2.50 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 595 HIS 0.005 0.001 HIS B 420 PHE 0.018 0.001 PHE B 434 TYR 0.020 0.002 TYR B 357 ARG 0.010 0.000 ARG A 568 ********************** 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 119 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8425 (mmm) cc_final: 0.8197 (mmm) REVERT: A 191 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8033 (mmt90) REVERT: A 211 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7761 (tp) REVERT: A 431 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7881 (ttp80) REVERT: A 673 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.6981 (t80) REVERT: B 126 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6853 (m-30) REVERT: B 278 GLU cc_start: 0.7810 (tt0) cc_final: 0.7518 (tt0) REVERT: B 321 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7472 (mt) REVERT: B 539 MET cc_start: 0.5277 (mtp) cc_final: 0.4834 (mtp) REVERT: B 609 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6582 (pt0) REVERT: B 618 MET cc_start: 0.6884 (ptt) cc_final: 0.6669 (ptt) outliers start: 25 outliers final: 17 residues processed: 112 average time/residue: 0.2396 time to fit residues: 36.9491 Evaluate side-chains 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU 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 317 ILE Chi-restraints excluded: chain A residue 340 SER 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 588 ILE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 673 PHE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 155 GLU 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 658 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0670 chunk 22 optimal weight: 0.0040 chunk 12 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 overall best weight: 0.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 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 = 0.4626 r_free = 0.4626 target = 0.245775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.179253 restraints weight = 9287.382| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.20 r_work: 0.3559 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4002 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= 0.167 Angle : 0.583 15.719 13134 Z= 0.290 Chirality : 0.040 0.291 1465 Planarity : 0.004 0.054 1662 Dihedral : 6.608 65.352 1359 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.21 % Allowed : 20.78 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1178 helix: 0.59 (0.20), residues: 778 sheet: -1.83 (0.73), residues: 59 loop : -2.47 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 595 HIS 0.006 0.001 HIS B 420 PHE 0.013 0.001 PHE B 434 TYR 0.021 0.001 TYR B 357 ARG 0.009 0.000 ARG A 568 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6746.66 seconds wall clock time: 116 minutes 57.74 seconds (7017.74 seconds total)