Starting phenix.real_space_refine on Thu Jul 2 17:12:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x1w_32951/07_2026/7x1w_32951.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x1w_32951/07_2026/7x1w_32951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x1w_32951/07_2026/7x1w_32951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x1w_32951/07_2026/7x1w_32951.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7x1w_32951/07_2026/7x1w_32951.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x1w_32951/07_2026/7x1w_32951.cif" model { file = "/net/cci-nas-00/data/ceres_data/7x1w_32951/07_2026/7x1w_32951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x1w_32951/07_2026/7x1w_32951.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 6 5.49 5 S 44 5.16 5 C 5967 2.51 5 N 1641 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9315 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4624 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 557} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4629 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 558} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" 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: 1.49, per 1000 atoms: 0.16 Number of scatterers: 9315 At special positions: 0 Unit cell: (80.51, 83.83, 135.29, 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 44 16.00 P 6 15.00 O 1657 8.00 N 1641 7.00 C 5967 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: 0.76 Conformation dependent library (CDL) restraints added in 217.8 milliseconds 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 68.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.808A pdb=" N GLN A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 124 removed outlier: 3.649A pdb=" N TYR A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 140 Processing helix chain 'A' and resid 140 through 175 removed outlier: 3.537A pdb=" N ARG A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 removed outlier: 4.086A pdb=" N SER A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 236 removed outlier: 3.819A pdb=" N ASP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Proline residue: A 218 - end of helix removed outlier: 3.649A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 255 through 256 No H-bonds generated for 'chain 'A' and resid 255 through 256' Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.536A pdb=" N PHE A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A 262 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 289 removed outlier: 4.425A pdb=" N GLU A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.572A pdb=" N ALA A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 338 through 353 removed outlier: 3.872A pdb=" N LEU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 373 through 431 removed outlier: 3.926A pdb=" N SER A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 574 through 583 removed outlier: 4.069A pdb=" N VAL A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 4.273A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 590 " --> pdb=" O HIS A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 590' Processing helix chain 'A' and resid 606 through 622 removed outlier: 4.252A pdb=" N GLN A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A 612 " --> pdb=" O GLY A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 651 removed outlier: 3.542A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 667 removed outlier: 4.028A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 667 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 83 removed outlier: 3.712A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 124 removed outlier: 3.645A pdb=" N TYR B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 140 Processing helix chain 'B' and resid 140 through 175 removed outlier: 3.580A pdb=" N ARG B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 186 removed outlier: 4.049A pdb=" N SER B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 198 through 226 removed outlier: 3.623A pdb=" N VAL B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 226 through 236 removed outlier: 3.640A pdb=" N LEU B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 260 Processing helix chain 'B' and resid 263 through 289 removed outlier: 4.088A pdb=" N GLU B 267 " --> pdb=" O PRO B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 Processing helix chain 'B' and resid 298 through 337 Processing helix chain 'B' and resid 338 through 354 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 373 through 431 removed outlier: 3.931A pdb=" N SER B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 Processing helix chain 'B' and resid 572 through 583 removed outlier: 4.051A pdb=" N VAL B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 590 removed outlier: 4.231A pdb=" N LEU B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 590 " --> pdb=" O HIS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 590' Processing helix chain 'B' and resid 606 through 622 removed outlier: 4.129A pdb=" N GLN B 611 " --> pdb=" O GLY B 607 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 651 removed outlier: 3.855A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 667 removed outlier: 4.219A pdb=" N LYS B 665 " --> pdb=" O SER B 662 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS B 667 " --> pdb=" O TRP B 664 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469 Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 482 Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA4, first strand: chain 'B' and resid 466 through 469 Processing sheet with id=AA5, first strand: chain 'B' and resid 481 through 482 removed outlier: 6.659A pdb=" N ILE B 481 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 539 through 540 586 hydrogen bonds defined for protein. 1716 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: 1.03 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3033 1.34 - 1.46: 1597 1.46 - 1.57: 4807 1.57 - 1.69: 12 1.69 - 1.81: 74 Bond restraints: 9523 Sorted by residual: bond pdb=" C2' ATP B 801 " pdb=" C3' ATP B 801 " ideal model delta sigma weight residual 1.531 1.306 0.225 1.20e-02 6.94e+03 3.51e+02 bond pdb=" C2' ATP A 801 " pdb=" C3' ATP A 801 " ideal model delta sigma weight residual 1.531 1.307 0.224 1.20e-02 6.94e+03 3.50e+02 bond pdb=" C4' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.444 1.302 0.142 1.10e-02 8.26e+03 1.67e+02 bond pdb=" C4' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.444 1.302 0.142 1.10e-02 8.26e+03 1.67e+02 bond pdb=" C6 ATP B 801 " pdb=" N6 ATP B 801 " ideal model delta sigma weight residual 1.337 1.465 -0.128 1.10e-02 8.26e+03 1.35e+02 ... (remaining 9518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 12764 2.89 - 5.79: 116 5.79 - 8.68: 18 8.68 - 11.57: 5 11.57 - 14.46: 4 Bond angle restraints: 12907 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 125.41 14.46 1.00e+00 1.00e+00 2.09e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 125.44 14.43 1.00e+00 1.00e+00 2.08e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 124.21 12.62 1.00e+00 1.00e+00 1.59e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 124.29 12.54 1.00e+00 1.00e+00 1.57e+02 angle pdb=" C5 ATP B 801 " pdb=" C4 ATP B 801 " pdb=" N3 ATP B 801 " ideal model delta sigma weight residual 126.80 117.87 8.93 1.00e+00 1.00e+00 7.98e+01 ... (remaining 12902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5009 17.73 - 35.46: 528 35.46 - 53.19: 93 53.19 - 70.91: 9 70.91 - 88.64: 10 Dihedral angle restraints: 5649 sinusoidal: 2286 harmonic: 3363 Sorted by residual: dihedral pdb=" CA LYS A 533 " pdb=" C LYS A 533 " pdb=" N PRO A 534 " pdb=" CA PRO A 534 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LYS B 533 " pdb=" C LYS B 533 " pdb=" N PRO B 534 " pdb=" CA PRO B 534 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA SER A 572 " pdb=" C SER A 572 " pdb=" N GLU A 573 " pdb=" CA GLU A 573 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1207 0.054 - 0.107: 193 0.107 - 0.161: 31 0.161 - 0.214: 2 0.214 - 0.268: 2 Chirality restraints: 1435 Sorted by residual: chirality pdb=" C2' ATP A 801 " pdb=" C1' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" O2' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C2' ATP B 801 " pdb=" C1' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" O2' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.41 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3' ATP B 801 " pdb=" C2' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" O3' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1432 not shown) Planarity restraints: 1625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 479 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 480 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 507 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO B 508 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 508 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 508 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 507 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 508 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " -0.023 5.00e-02 4.00e+02 ... (remaining 1622 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 238 2.71 - 3.26: 9413 3.26 - 3.81: 14904 3.81 - 4.35: 18596 4.35 - 4.90: 32484 Nonbonded interactions: 75635 Sorted by model distance: nonbonded pdb=" OG1 THR B 506 " pdb=" OE1 GLN B 672 " model vdw 2.163 3.040 nonbonded pdb=" O PRO B 508 " pdb=" NZ LYS B 513 " model vdw 2.253 3.120 nonbonded pdb=" O TYR B 547 " pdb=" NH2 ARG B 617 " model vdw 2.290 3.120 nonbonded pdb=" O GLN B 472 " pdb=" OH TYR B 625 " model vdw 2.294 3.040 nonbonded pdb=" O TYR A 547 " pdb=" NH2 ARG A 617 " model vdw 2.295 3.120 ... (remaining 75630 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' selection = (chain 'B' and (resid 64 through 353 or resid 371 through 801)) } 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.120 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.007 0.225 9523 Z= 0.512 Angle : 0.764 14.464 12907 Z= 0.506 Chirality : 0.042 0.268 1435 Planarity : 0.004 0.045 1625 Dihedral : 14.720 88.644 3487 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.25), residues: 1147 helix: 0.80 (0.20), residues: 746 sheet: -2.70 (0.84), residues: 32 loop : -3.15 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 152 TYR 0.018 0.002 TYR B 541 PHE 0.026 0.001 PHE B 540 TRP 0.019 0.001 TRP B 326 HIS 0.003 0.001 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.51 ( 9523) covalent geometry : angle 0.76366 / 0.51 (12907) hydrogen bonds : bond 0.13226 / 8.83 ( 586) hydrogen bonds : angle 5.70325 / 4.39 ( 1716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.340 Fit side-chains REVERT: A 466 GLN cc_start: 0.7903 (mt0) cc_final: 0.6817 (tt0) REVERT: B 466 GLN cc_start: 0.7863 (mt0) cc_final: 0.6880 (tt0) REVERT: B 498 GLU cc_start: 0.7795 (pt0) cc_final: 0.7468 (pt0) REVERT: B 502 HIS cc_start: 0.8669 (m90) cc_final: 0.8351 (m170) REVERT: B 524 TRP cc_start: 0.8488 (m-10) cc_final: 0.8163 (m-10) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0972 time to fit residues: 14.6797 Evaluate side-chains 90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS A 289 ASN A 420 HIS A 433 HIS A 659 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.167933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130292 restraints weight = 9171.942| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.54 r_work: 0.3205 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9523 Z= 0.167 Angle : 0.597 8.370 12907 Z= 0.303 Chirality : 0.041 0.148 1435 Planarity : 0.004 0.043 1625 Dihedral : 5.247 53.111 1299 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.72 % Allowed : 6.78 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1147 helix: 1.03 (0.19), residues: 757 sheet: -2.43 (0.69), residues: 48 loop : -3.32 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.016 0.002 TYR A 296 PHE 0.017 0.001 PHE B 540 TRP 0.014 0.001 TRP B 326 HIS 0.005 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 9523) covalent geometry : angle 0.59651 / 0.30 (12907) hydrogen bonds : bond 0.04539 / 3.14 ( 586) hydrogen bonds : angle 4.32150 / 3.22 ( 1716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.271 Fit side-chains REVERT: A 615 MET cc_start: 0.8376 (mmm) cc_final: 0.7924 (mmt) REVERT: B 200 ASP cc_start: 0.6614 (m-30) cc_final: 0.6336 (m-30) REVERT: B 466 GLN cc_start: 0.7797 (mt0) cc_final: 0.6605 (tt0) REVERT: B 498 GLU cc_start: 0.7923 (pt0) cc_final: 0.7588 (pt0) REVERT: B 502 HIS cc_start: 0.8825 (m90) cc_final: 0.8310 (m170) outliers start: 7 outliers final: 5 residues processed: 98 average time/residue: 0.0943 time to fit residues: 12.6919 Evaluate side-chains 90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 16 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN ** B 169 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 = 0.3881 r_free = 0.3881 target = 0.171945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128595 restraints weight = 9163.488| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.71 r_work: 0.3276 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9523 Z= 0.163 Angle : 0.568 8.442 12907 Z= 0.290 Chirality : 0.040 0.148 1435 Planarity : 0.004 0.046 1625 Dihedral : 5.185 54.772 1299 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.64 % Allowed : 8.83 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.25), residues: 1147 helix: 1.12 (0.19), residues: 764 sheet: -2.42 (0.69), residues: 48 loop : -3.34 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.015 0.001 TYR A 296 PHE 0.015 0.001 PHE B 540 TRP 0.013 0.001 TRP B 326 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 9523) covalent geometry : angle 0.56769 / 0.29 (12907) hydrogen bonds : bond 0.04385 / 3.04 ( 586) hydrogen bonds : angle 4.13642 / 3.07 ( 1716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.260 Fit side-chains REVERT: A 411 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 466 GLN cc_start: 0.7901 (mt0) cc_final: 0.6708 (tt0) REVERT: B 498 GLU cc_start: 0.7876 (pt0) cc_final: 0.7525 (pt0) REVERT: B 502 HIS cc_start: 0.8895 (m90) cc_final: 0.8435 (m170) outliers start: 16 outliers final: 8 residues processed: 102 average time/residue: 0.0807 time to fit residues: 11.4727 Evaluate side-chains 96 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.176166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133203 restraints weight = 9113.734| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.68 r_work: 0.3339 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9523 Z= 0.145 Angle : 0.542 7.980 12907 Z= 0.277 Chirality : 0.039 0.148 1435 Planarity : 0.004 0.044 1625 Dihedral : 4.999 52.796 1299 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.05 % Allowed : 11.60 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.26), residues: 1147 helix: 1.28 (0.19), residues: 765 sheet: -2.34 (0.70), residues: 48 loop : -3.28 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.017 0.001 TYR A 296 PHE 0.008 0.001 PHE B 265 TRP 0.012 0.001 TRP B 326 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 9523) covalent geometry : angle 0.54193 / 0.28 (12907) hydrogen bonds : bond 0.04171 / 2.89 ( 586) hydrogen bonds : angle 4.00868 / 2.98 ( 1716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.288 Fit side-chains REVERT: A 163 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7804 (ttt180) REVERT: A 177 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.6533 (mm-40) REVERT: A 200 ASP cc_start: 0.6748 (m-30) cc_final: 0.6518 (m-30) REVERT: A 411 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 615 MET cc_start: 0.8144 (mmm) cc_final: 0.7933 (mmt) REVERT: A 618 MET cc_start: 0.8198 (tmm) cc_final: 0.7756 (ttt) REVERT: B 73 GLN cc_start: 0.7193 (tt0) cc_final: 0.6978 (mt0) REVERT: B 177 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.6518 (mm-40) REVERT: B 200 ASP cc_start: 0.6703 (m-30) cc_final: 0.6467 (m-30) REVERT: B 466 GLN cc_start: 0.7896 (mt0) cc_final: 0.6738 (tt0) REVERT: B 498 GLU cc_start: 0.7882 (pt0) cc_final: 0.7535 (pt0) REVERT: B 615 MET cc_start: 0.8457 (mmm) cc_final: 0.8026 (mmp) outliers start: 20 outliers final: 13 residues processed: 106 average time/residue: 0.0766 time to fit residues: 11.5011 Evaluate side-chains 97 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 78 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN ** B 169 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 = 0.3880 r_free = 0.3880 target = 0.172071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128371 restraints weight = 9195.263| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.70 r_work: 0.3233 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9523 Z= 0.145 Angle : 0.551 10.422 12907 Z= 0.277 Chirality : 0.040 0.249 1435 Planarity : 0.004 0.043 1625 Dihedral : 4.941 50.245 1299 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.36 % Allowed : 13.04 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.26), residues: 1147 helix: 1.38 (0.19), residues: 764 sheet: -2.15 (0.73), residues: 46 loop : -3.19 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.016 0.001 TYR A 296 PHE 0.007 0.001 PHE A 385 TRP 0.012 0.001 TRP B 326 HIS 0.004 0.001 HIS B 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9523) covalent geometry : angle 0.55086 / 0.28 (12907) hydrogen bonds : bond 0.04134 / 2.87 ( 586) hydrogen bonds : angle 3.96650 / 2.94 ( 1716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.267 Fit side-chains REVERT: A 163 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7833 (ttt180) REVERT: A 177 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.6573 (mm-40) REVERT: A 178 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: A 411 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7558 (tm-30) REVERT: A 618 MET cc_start: 0.8187 (tmm) cc_final: 0.7773 (ttt) REVERT: B 73 GLN cc_start: 0.7129 (tt0) cc_final: 0.6912 (mt0) REVERT: B 177 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: B 178 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: B 200 ASP cc_start: 0.6696 (m-30) cc_final: 0.6436 (m-30) REVERT: B 466 GLN cc_start: 0.7859 (mt0) cc_final: 0.6700 (tt0) REVERT: B 498 GLU cc_start: 0.7815 (pt0) cc_final: 0.7456 (pt0) REVERT: B 615 MET cc_start: 0.8433 (mmm) cc_final: 0.8073 (mmm) outliers start: 23 outliers final: 15 residues processed: 106 average time/residue: 0.0764 time to fit residues: 11.3772 Evaluate side-chains 105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 105 optimal weight: 0.0670 chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.174243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130876 restraints weight = 9120.415| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.69 r_work: 0.3249 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9523 Z= 0.131 Angle : 0.532 9.053 12907 Z= 0.268 Chirality : 0.039 0.235 1435 Planarity : 0.004 0.042 1625 Dihedral : 4.799 48.512 1299 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.87 % Allowed : 13.35 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.26), residues: 1147 helix: 1.53 (0.19), residues: 764 sheet: -2.10 (0.76), residues: 44 loop : -3.14 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.015 0.001 TYR A 296 PHE 0.007 0.001 PHE A 385 TRP 0.012 0.001 TRP B 326 HIS 0.003 0.001 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 9523) covalent geometry : angle 0.53189 / 0.27 (12907) hydrogen bonds : bond 0.03994 / 2.76 ( 586) hydrogen bonds : angle 3.89786 / 2.89 ( 1716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.520 Fit side-chains REVERT: A 163 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7806 (ttt180) REVERT: A 178 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: A 411 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7536 (tm-30) REVERT: A 660 ARG cc_start: 0.7051 (mtm180) cc_final: 0.6844 (mtm180) REVERT: B 73 GLN cc_start: 0.7148 (tt0) cc_final: 0.6937 (mt0) REVERT: B 200 ASP cc_start: 0.6646 (m-30) cc_final: 0.6374 (m-30) REVERT: B 466 GLN cc_start: 0.7843 (mt0) cc_final: 0.6683 (tt0) REVERT: B 498 GLU cc_start: 0.7840 (pt0) cc_final: 0.7480 (pt0) REVERT: B 615 MET cc_start: 0.8390 (mmm) cc_final: 0.7985 (mmm) outliers start: 28 outliers final: 17 residues processed: 112 average time/residue: 0.0792 time to fit residues: 12.4669 Evaluate side-chains 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 657 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 66 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.172085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128639 restraints weight = 9180.500| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.66 r_work: 0.3356 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9523 Z= 0.135 Angle : 0.537 8.158 12907 Z= 0.270 Chirality : 0.040 0.223 1435 Planarity : 0.004 0.042 1625 Dihedral : 4.743 47.352 1299 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.46 % Allowed : 14.07 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1147 helix: 1.56 (0.19), residues: 766 sheet: -2.02 (0.77), residues: 44 loop : -3.12 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 381 TYR 0.015 0.001 TYR A 296 PHE 0.007 0.001 PHE A 385 TRP 0.011 0.001 TRP B 326 HIS 0.003 0.001 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9523) covalent geometry : angle 0.53726 / 0.27 (12907) hydrogen bonds : bond 0.04008 / 2.77 ( 586) hydrogen bonds : angle 3.90735 / 2.89 ( 1716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.226 Fit side-chains REVERT: A 163 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7829 (ttt180) REVERT: A 411 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7648 (tm-30) REVERT: B 200 ASP cc_start: 0.6675 (m-30) cc_final: 0.6411 (m-30) REVERT: B 376 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7475 (tt0) REVERT: B 466 GLN cc_start: 0.7889 (mt0) cc_final: 0.6767 (tt0) REVERT: B 498 GLU cc_start: 0.7847 (pt0) cc_final: 0.7616 (pt0) REVERT: B 615 MET cc_start: 0.8453 (mmm) cc_final: 0.8039 (mmp) outliers start: 24 outliers final: 17 residues processed: 112 average time/residue: 0.0760 time to fit residues: 11.9091 Evaluate side-chains 99 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.178041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135594 restraints weight = 9034.895| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.63 r_work: 0.3368 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9523 Z= 0.154 Angle : 0.556 7.863 12907 Z= 0.279 Chirality : 0.040 0.203 1435 Planarity : 0.004 0.042 1625 Dihedral : 4.778 47.081 1299 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.16 % Allowed : 14.27 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.26), residues: 1147 helix: 1.52 (0.19), residues: 765 sheet: -2.07 (0.74), residues: 46 loop : -3.10 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.015 0.001 TYR A 296 PHE 0.007 0.001 PHE B 265 TRP 0.010 0.001 TRP B 326 HIS 0.004 0.001 HIS A 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.15 ( 9523) covalent geometry : angle 0.55631 / 0.28 (12907) hydrogen bonds : bond 0.04154 / 2.88 ( 586) hydrogen bonds : angle 3.95048 / 2.93 ( 1716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.283 Fit side-chains REVERT: A 163 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7870 (ttt180) REVERT: A 411 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 615 MET cc_start: 0.8463 (mmm) cc_final: 0.8142 (mmt) REVERT: B 376 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7472 (tt0) REVERT: B 466 GLN cc_start: 0.7895 (mt0) cc_final: 0.6757 (tt0) REVERT: B 498 GLU cc_start: 0.8003 (pt0) cc_final: 0.7661 (pt0) REVERT: B 615 MET cc_start: 0.8435 (mmm) cc_final: 0.8007 (mmp) outliers start: 21 outliers final: 18 residues processed: 98 average time/residue: 0.0718 time to fit residues: 10.0599 Evaluate side-chains 100 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 92 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 101 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.171636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.128209 restraints weight = 9143.339| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.65 r_work: 0.3371 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9523 Z= 0.145 Angle : 0.550 7.566 12907 Z= 0.277 Chirality : 0.040 0.200 1435 Planarity : 0.004 0.042 1625 Dihedral : 4.738 46.274 1299 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.46 % Allowed : 14.27 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 1147 helix: 1.54 (0.19), residues: 765 sheet: -2.06 (0.75), residues: 46 loop : -3.09 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.014 0.001 TYR A 296 PHE 0.007 0.001 PHE A 385 TRP 0.011 0.001 TRP B 326 HIS 0.004 0.001 HIS A 669 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9523) covalent geometry : angle 0.54971 / 0.28 (12907) hydrogen bonds : bond 0.04094 / 2.84 ( 586) hydrogen bonds : angle 3.92644 / 2.91 ( 1716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.239 Fit side-chains REVERT: A 163 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7829 (ttt180) REVERT: A 411 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 615 MET cc_start: 0.8470 (mmm) cc_final: 0.8118 (mmt) REVERT: B 376 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7466 (tt0) REVERT: B 466 GLN cc_start: 0.7887 (mt0) cc_final: 0.6753 (tt0) REVERT: B 498 GLU cc_start: 0.8024 (pt0) cc_final: 0.7730 (pt0) outliers start: 24 outliers final: 21 residues processed: 99 average time/residue: 0.0793 time to fit residues: 11.3897 Evaluate side-chains 100 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 502 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 = 0.3952 r_free = 0.3952 target = 0.177783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135264 restraints weight = 8973.794| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.63 r_work: 0.3295 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9523 Z= 0.157 Angle : 0.561 7.609 12907 Z= 0.282 Chirality : 0.041 0.190 1435 Planarity : 0.004 0.042 1625 Dihedral : 4.768 45.990 1299 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.26 % Allowed : 14.89 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.26), residues: 1147 helix: 1.48 (0.19), residues: 765 sheet: -2.05 (0.74), residues: 46 loop : -3.03 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.014 0.001 TYR A 296 PHE 0.007 0.001 PHE A 265 TRP 0.010 0.001 TRP B 326 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 9523) covalent geometry : angle 0.56092 / 0.28 (12907) hydrogen bonds : bond 0.04191 / 2.90 ( 586) hydrogen bonds : angle 3.96673 / 2.94 ( 1716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2294 Ramachandran restraints generated. 1147 Oldfield, 0 Emsley, 1147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.254 Fit side-chains REVERT: A 163 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7896 (ttt180) REVERT: A 411 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 615 MET cc_start: 0.8522 (mmm) cc_final: 0.8186 (mmt) REVERT: B 376 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7508 (tt0) REVERT: B 466 GLN cc_start: 0.7895 (mt0) cc_final: 0.6749 (tt0) REVERT: B 498 GLU cc_start: 0.8009 (pt0) cc_final: 0.7697 (pt0) outliers start: 22 outliers final: 21 residues processed: 99 average time/residue: 0.0819 time to fit residues: 11.6314 Evaluate side-chains 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 112 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.0470 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 502 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 = 0.3856 r_free = 0.3856 target = 0.170313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126687 restraints weight = 9097.187| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.66 r_work: 0.3350 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9523 Z= 0.150 Angle : 0.555 7.603 12907 Z= 0.279 Chirality : 0.040 0.189 1435 Planarity : 0.004 0.041 1625 Dihedral : 4.727 45.417 1299 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.26 % Allowed : 14.99 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1147 helix: 1.51 (0.19), residues: 765 sheet: -1.98 (0.77), residues: 44 loop : -2.98 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.014 0.001 TYR A 296 PHE 0.007 0.001 PHE A 385 TRP 0.011 0.001 TRP B 326 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 9523) covalent geometry : angle 0.55488 / 0.28 (12907) hydrogen bonds : bond 0.04127 / 2.86 ( 586) hydrogen bonds : angle 3.93782 / 2.92 ( 1716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1973.66 seconds wall clock time: 34 minutes 29.80 seconds (2069.80 seconds total)