Starting phenix.real_space_refine on Thu Jul 2 16:19:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pru_13610/07_2026/7pru_13610.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pru_13610/07_2026/7pru_13610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pru_13610/07_2026/7pru_13610.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pru_13610/07_2026/7pru_13610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pru_13610/07_2026/7pru_13610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pru_13610/07_2026/7pru_13610.map" model { file = "/net/cci-nas-00/data/ceres_data/7pru_13610/07_2026/7pru_13610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pru_13610/07_2026/7pru_13610.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.086 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 5836 2.51 5 N 1586 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 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: 9116 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4538 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 17, 'TRANS': 564} Chain: "B" Number of atoms: 4538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4538 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 17, 'TRANS': 564} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.92, per 1000 atoms: 0.21 Number of scatterers: 9116 At special positions: 0 Unit cell: (85.696, 89.856, 139.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1666 8.00 N 1586 7.00 C 5836 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: 0.92 Conformation dependent library (CDL) restraints added in 355.2 milliseconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 70.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.889A pdb=" N GLN A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 144 removed outlier: 3.766A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.812A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 206 removed outlier: 3.807A pdb=" N GLN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 215 through 240 Processing helix chain 'A' and resid 240 through 260 removed outlier: 3.524A pdb=" N ALA A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 309 removed outlier: 3.812A pdb=" N ALA A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 318 through 372 removed outlier: 3.750A pdb=" N GLU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 391 removed outlier: 3.962A pdb=" N VAL A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.548A pdb=" N LEU A 397 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 418 removed outlier: 3.712A pdb=" N ARG A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 removed outlier: 3.891A pdb=" N ARG A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.638A pdb=" N VAL A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 610 through 625 Processing helix chain 'A' and resid 660 through 665 Processing helix chain 'A' and resid 670 through 674 removed outlier: 4.443A pdb=" N GLU A 673 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 Processing helix chain 'B' and resid 109 through 144 removed outlier: 3.767A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.812A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 206 removed outlier: 3.807A pdb=" N GLN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 215 through 240 Processing helix chain 'B' and resid 240 through 260 removed outlier: 3.523A pdb=" N ALA B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 309 removed outlier: 3.811A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 318 through 372 removed outlier: 3.750A pdb=" N GLU B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 391 removed outlier: 3.962A pdb=" N VAL B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 3.549A pdb=" N LEU B 397 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 418 removed outlier: 3.712A pdb=" N ARG B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 removed outlier: 3.892A pdb=" N ARG B 485 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 530 through 537 Processing helix chain 'B' and resid 543 through 554 removed outlier: 3.638A pdb=" N VAL B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 562 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 579 through 595 Processing helix chain 'B' and resid 610 through 625 Processing helix chain 'B' and resid 660 through 665 Processing helix chain 'B' and resid 670 through 674 removed outlier: 4.444A pdb=" N GLU B 673 " --> pdb=" O VAL B 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 457 through 464 removed outlier: 4.862A pdb=" N ARG A 458 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE A 448 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A 462 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU A 444 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 464 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG A 442 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE A 443 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 499 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN A 445 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LYS A 497 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 520 removed outlier: 6.594A pdb=" N GLY A 518 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP A 602 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 520 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 599 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 634 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 601 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 470 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS A 469 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE A 648 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA A 471 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU A 650 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 473 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 647 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN A 658 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 649 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 457 through 464 removed outlier: 4.863A pdb=" N ARG B 458 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE B 448 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU B 462 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU B 444 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE B 464 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG B 442 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE B 443 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE B 499 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN B 445 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS B 497 " --> pdb=" O ASN B 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 517 through 520 removed outlier: 6.593A pdb=" N GLY B 518 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP B 602 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 520 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 599 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL B 634 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 601 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 470 " --> pdb=" O PHE B 633 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS B 469 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B 648 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA B 471 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU B 650 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 473 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE B 647 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN B 658 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 649 " --> pdb=" O VAL B 656 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1722 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: 1.36 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1484 1.30 - 1.43: 2404 1.43 - 1.56: 5344 1.56 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 9282 Sorted by residual: bond pdb=" CD1 GSH B 801 " pdb=" N2 GSH B 801 " ideal model delta sigma weight residual 1.336 1.453 -0.117 1.20e-02 6.94e+03 9.51e+01 bond pdb=" CD1 GSH A 801 " pdb=" N2 GSH A 801 " ideal model delta sigma weight residual 1.336 1.451 -0.115 1.20e-02 6.94e+03 9.15e+01 bond pdb=" C2 GSH A 801 " pdb=" N3 GSH A 801 " ideal model delta sigma weight residual 1.333 1.449 -0.116 1.30e-02 5.92e+03 7.92e+01 bond pdb=" C2 GSH B 801 " pdb=" N3 GSH B 801 " ideal model delta sigma weight residual 1.333 1.448 -0.115 1.30e-02 5.92e+03 7.86e+01 bond pdb=" C2 GSH A 801 " pdb=" O2 GSH A 801 " ideal model delta sigma weight residual 1.227 1.181 0.046 1.00e-02 1.00e+04 2.13e+01 ... (remaining 9277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11738 1.90 - 3.80: 698 3.80 - 5.70: 111 5.70 - 7.60: 26 7.60 - 9.50: 11 Bond angle restraints: 12584 Sorted by residual: angle pdb=" CG1 GSH B 801 " pdb=" CD1 GSH B 801 " pdb=" N2 GSH B 801 " ideal model delta sigma weight residual 115.92 121.70 -5.78 1.00e+00 1.00e+00 3.35e+01 angle pdb=" CG1 GSH A 801 " pdb=" CD1 GSH A 801 " pdb=" N2 GSH A 801 " ideal model delta sigma weight residual 115.92 121.06 -5.14 1.00e+00 1.00e+00 2.64e+01 angle pdb=" SG2 GSH B 801 " pdb=" CB2 GSH B 801 " pdb=" CA2 GSH B 801 " ideal model delta sigma weight residual 114.04 109.81 4.23 1.00e+00 1.00e+00 1.79e+01 angle pdb=" N PHE B 355 " pdb=" CA PHE B 355 " pdb=" CB PHE B 355 " ideal model delta sigma weight residual 110.22 115.78 -5.56 1.54e+00 4.22e-01 1.30e+01 angle pdb=" CA3 GSH A 801 " pdb=" C3 GSH A 801 " pdb=" O32 GSH A 801 " ideal model delta sigma weight residual 111.89 120.66 -8.77 2.43e+00 1.69e-01 1.30e+01 ... (remaining 12579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4983 17.42 - 34.84: 449 34.84 - 52.27: 88 52.27 - 69.69: 14 69.69 - 87.11: 12 Dihedral angle restraints: 5546 sinusoidal: 2174 harmonic: 3372 Sorted by residual: dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N VAL A 422 " pdb=" CA VAL A 422 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASN B 421 " pdb=" C ASN B 421 " pdb=" N VAL B 422 " pdb=" CA VAL B 422 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ARG B 102 " pdb=" C ARG B 102 " pdb=" N TYR B 103 " pdb=" CA TYR B 103 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1147 0.068 - 0.136: 280 0.136 - 0.203: 34 0.203 - 0.271: 9 0.271 - 0.339: 2 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CA PHE A 355 " pdb=" N PHE A 355 " pdb=" C PHE A 355 " pdb=" CB PHE A 355 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA PHE B 355 " pdb=" N PHE B 355 " pdb=" C PHE B 355 " pdb=" CB PHE B 355 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL B 571 " pdb=" CA VAL B 571 " pdb=" CG1 VAL B 571 " pdb=" CG2 VAL B 571 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1469 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 431 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.94e+00 pdb=" N PRO A 432 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 432 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 432 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 431 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO B 432 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 388 " 0.026 2.00e-02 2.50e+03 1.82e-02 5.83e+00 pdb=" CG PHE B 388 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 388 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 388 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 388 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 388 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 388 " 0.007 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 246 2.68 - 3.24: 9396 3.24 - 3.79: 14982 3.79 - 4.35: 18834 4.35 - 4.90: 31789 Nonbonded interactions: 75247 Sorted by model distance: nonbonded pdb=" OD1 ASP A 327 " pdb=" OG1 THR B 197 " model vdw 2.128 3.040 nonbonded pdb=" O ARG A 637 " pdb=" OG1 THR A 640 " model vdw 2.169 3.040 nonbonded pdb=" O ARG B 637 " pdb=" OG1 THR B 640 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR B 274 " pdb=" O LEU B 394 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 274 " pdb=" O LEU A 394 " model vdw 2.215 3.040 ... (remaining 75242 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.240 Find NCS groups from input model: 0.070 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.010 0.117 9282 Z= 0.450 Angle : 1.051 9.502 12584 Z= 0.594 Chirality : 0.060 0.339 1472 Planarity : 0.007 0.066 1598 Dihedral : 14.414 87.110 3374 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -2.01 (0.23), residues: 1160 helix: -0.88 (0.17), residues: 756 sheet: -1.02 (0.60), residues: 74 loop : -2.13 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 180 TYR 0.028 0.003 TYR A 274 PHE 0.035 0.004 PHE A 388 TRP 0.016 0.003 TRP A 110 HIS 0.005 0.002 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00970 / 0.45 ( 9282) covalent geometry : angle 1.05143 / 0.59 (12584) hydrogen bonds : bond 0.13881 / 9.68 ( 592) hydrogen bonds : angle 6.19364 / 4.48 ( 1722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 SER cc_start: 0.8669 (t) cc_final: 0.8425 (p) REVERT: A 546 GLN cc_start: 0.7373 (mp10) cc_final: 0.7125 (mp10) REVERT: B 537 TYR cc_start: 0.8556 (t80) cc_final: 0.8257 (t80) REVERT: B 599 LEU cc_start: 0.7591 (mp) cc_final: 0.7373 (mp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1060 time to fit residues: 15.5258 Evaluate side-chains 92 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 GLN B 584 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.202628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123256 restraints weight = 10626.094| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.05 r_work: 0.3339 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9282 Z= 0.156 Angle : 0.659 7.348 12584 Z= 0.343 Chirality : 0.043 0.165 1472 Planarity : 0.005 0.038 1598 Dihedral : 5.877 50.638 1278 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.52 % Allowed : 7.25 % Favored : 92.24 % 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: -0.80 (0.24), residues: 1160 helix: 0.22 (0.18), residues: 754 sheet: -0.93 (0.64), residues: 74 loop : -2.02 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 180 TYR 0.020 0.002 TYR A 232 PHE 0.026 0.002 PHE A 388 TRP 0.012 0.001 TRP A 110 HIS 0.002 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 9282) covalent geometry : angle 0.65879 / 0.34 (12584) hydrogen bonds : bond 0.04888 / 3.25 ( 592) hydrogen bonds : angle 4.42538 / 3.19 ( 1722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7626 (mmp-170) REVERT: A 431 LYS cc_start: 0.8368 (mmtm) cc_final: 0.7894 (mmtp) REVERT: A 485 ARG cc_start: 0.7949 (mtt-85) cc_final: 0.7683 (mtt90) REVERT: A 497 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8083 (mttm) REVERT: B 497 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8209 (mttm) REVERT: B 537 TYR cc_start: 0.8552 (t80) cc_final: 0.8244 (t80) REVERT: B 599 LEU cc_start: 0.7797 (mp) cc_final: 0.7524 (mp) outliers start: 5 outliers final: 5 residues processed: 104 average time/residue: 0.0993 time to fit residues: 14.1281 Evaluate side-chains 95 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN A 603 GLN B 539 ASN B 603 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.202960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.123919 restraints weight = 10565.240| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.02 r_work: 0.3342 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9282 Z= 0.146 Angle : 0.610 7.179 12584 Z= 0.316 Chirality : 0.042 0.170 1472 Planarity : 0.004 0.031 1598 Dihedral : 5.414 51.283 1278 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.24 % Allowed : 10.56 % Favored : 88.20 % 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: -0.28 (0.25), residues: 1160 helix: 0.66 (0.19), residues: 758 sheet: -0.80 (0.66), residues: 74 loop : -1.96 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 180 TYR 0.018 0.001 TYR A 232 PHE 0.021 0.002 PHE B 388 TRP 0.011 0.001 TRP A 284 HIS 0.002 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 9282) covalent geometry : angle 0.61048 / 0.32 (12584) hydrogen bonds : bond 0.04596 / 3.05 ( 592) hydrogen bonds : angle 4.10951 / 2.96 ( 1722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.355 Fit side-chains REVERT: A 194 ARG cc_start: 0.7609 (ptt90) cc_final: 0.7378 (mtm-85) REVERT: A 497 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8081 (mttm) REVERT: A 617 MET cc_start: 0.9122 (mmm) cc_final: 0.8873 (mtp) REVERT: B 225 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7615 (mmp-170) REVERT: B 497 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8188 (mttp) REVERT: B 537 TYR cc_start: 0.8454 (t80) cc_final: 0.8107 (t80) outliers start: 12 outliers final: 10 residues processed: 106 average time/residue: 0.0977 time to fit residues: 14.1812 Evaluate side-chains 103 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 5 optimal weight: 0.0020 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.204289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126428 restraints weight = 10543.429| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.92 r_work: 0.3365 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9282 Z= 0.134 Angle : 0.581 7.187 12584 Z= 0.299 Chirality : 0.041 0.171 1472 Planarity : 0.004 0.031 1598 Dihedral : 5.144 49.304 1278 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.17 % Allowed : 11.59 % Favored : 86.23 % 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: 0.12 (0.25), residues: 1160 helix: 0.96 (0.19), residues: 760 sheet: -0.46 (0.67), residues: 76 loop : -1.85 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 485 TYR 0.017 0.001 TYR A 232 PHE 0.018 0.001 PHE A 388 TRP 0.010 0.001 TRP A 284 HIS 0.002 0.000 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9282) covalent geometry : angle 0.58070 / 0.30 (12584) hydrogen bonds : bond 0.04331 / 2.87 ( 592) hydrogen bonds : angle 3.93873 / 2.85 ( 1722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.291 Fit side-chains REVERT: A 130 ASN cc_start: 0.8393 (t0) cc_final: 0.7904 (t0) REVERT: A 194 ARG cc_start: 0.7621 (ptt90) cc_final: 0.7399 (mtm-85) REVERT: A 362 MET cc_start: 0.8443 (mtt) cc_final: 0.8242 (mtt) REVERT: A 497 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8250 (mttm) REVERT: A 600 PHE cc_start: 0.7185 (m-80) cc_final: 0.6870 (m-80) REVERT: A 617 MET cc_start: 0.9094 (mmm) cc_final: 0.8877 (mtp) REVERT: B 130 ASN cc_start: 0.8411 (t0) cc_final: 0.8008 (t0) REVERT: B 537 TYR cc_start: 0.8477 (t80) cc_final: 0.8154 (t80) REVERT: B 617 MET cc_start: 0.9095 (mmm) cc_final: 0.8697 (tpp) REVERT: B 623 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8352 (p) outliers start: 21 outliers final: 15 residues processed: 110 average time/residue: 0.0816 time to fit residues: 12.5611 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 630 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 8 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 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 = 0.4360 r_free = 0.4360 target = 0.204035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124506 restraints weight = 10575.843| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.04 r_work: 0.3356 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9282 Z= 0.132 Angle : 0.572 6.996 12584 Z= 0.293 Chirality : 0.041 0.171 1472 Planarity : 0.003 0.030 1598 Dihedral : 4.937 46.340 1278 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.17 % Allowed : 13.25 % Favored : 84.58 % 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: 0.43 (0.25), residues: 1160 helix: 1.24 (0.19), residues: 756 sheet: -0.25 (0.69), residues: 76 loop : -1.81 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 485 TYR 0.017 0.001 TYR B 232 PHE 0.015 0.001 PHE A 388 TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9282) covalent geometry : angle 0.57193 / 0.29 (12584) hydrogen bonds : bond 0.04329 / 2.88 ( 592) hydrogen bonds : angle 3.84313 / 2.78 ( 1722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.370 Fit side-chains REVERT: A 130 ASN cc_start: 0.8402 (t0) cc_final: 0.7935 (t0) REVERT: A 225 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7558 (mmp-170) REVERT: A 352 ASN cc_start: 0.8611 (t0) cc_final: 0.8210 (t0) REVERT: A 497 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8145 (mttm) REVERT: A 617 MET cc_start: 0.9128 (mmm) cc_final: 0.8883 (mtp) REVERT: B 130 ASN cc_start: 0.8398 (t0) cc_final: 0.7956 (t0) REVERT: B 352 ASN cc_start: 0.8639 (t0) cc_final: 0.8204 (t0) REVERT: B 355 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8028 (t80) REVERT: B 497 LYS cc_start: 0.8582 (mttm) cc_final: 0.8321 (mttp) REVERT: B 537 TYR cc_start: 0.8493 (t80) cc_final: 0.8092 (t80) REVERT: B 664 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6196 (mm) outliers start: 21 outliers final: 16 residues processed: 111 average time/residue: 0.0907 time to fit residues: 14.0569 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.200295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118940 restraints weight = 10613.236| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.01 r_work: 0.3291 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9282 Z= 0.201 Angle : 0.626 7.809 12584 Z= 0.320 Chirality : 0.044 0.163 1472 Planarity : 0.004 0.030 1598 Dihedral : 4.929 38.793 1278 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.38 % Allowed : 13.35 % Favored : 84.27 % 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: 0.21 (0.25), residues: 1160 helix: 1.02 (0.19), residues: 758 sheet: -0.40 (0.66), residues: 76 loop : -1.79 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 485 TYR 0.018 0.002 TYR A 232 PHE 0.021 0.002 PHE A 388 TRP 0.008 0.001 TRP B 284 HIS 0.002 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 9282) covalent geometry : angle 0.62559 / 0.32 (12584) hydrogen bonds : bond 0.04882 / 3.25 ( 592) hydrogen bonds : angle 4.01487 / 2.92 ( 1722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 225 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7663 (mmp-170) REVERT: A 355 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8020 (t80) REVERT: A 497 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8152 (mttp) REVERT: A 600 PHE cc_start: 0.7382 (m-80) cc_final: 0.7085 (m-80) REVERT: A 617 MET cc_start: 0.9122 (mmm) cc_final: 0.8867 (mtp) REVERT: B 225 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7700 (mmp-170) REVERT: B 355 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8003 (t80) REVERT: B 537 TYR cc_start: 0.8482 (t80) cc_final: 0.8128 (t80) REVERT: B 617 MET cc_start: 0.9173 (mmm) cc_final: 0.8890 (mtt) REVERT: B 664 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6206 (mm) outliers start: 23 outliers final: 20 residues processed: 106 average time/residue: 0.1023 time to fit residues: 15.0219 Evaluate side-chains 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 557 HIS Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 37 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 53 optimal weight: 0.2980 chunk 108 optimal weight: 0.0000 chunk 92 optimal weight: 4.9990 chunk 111 optimal weight: 0.0870 overall best weight: 0.2762 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.209310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.139378 restraints weight = 10517.560| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.68 r_work: 0.3516 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9282 Z= 0.108 Angle : 0.551 6.872 12584 Z= 0.280 Chirality : 0.040 0.165 1472 Planarity : 0.003 0.028 1598 Dihedral : 4.706 48.004 1278 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.45 % Allowed : 15.32 % Favored : 83.23 % 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: 0.70 (0.26), residues: 1160 helix: 1.46 (0.19), residues: 758 sheet: -0.13 (0.67), residues: 76 loop : -1.79 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 485 TYR 0.018 0.001 TYR A 232 PHE 0.009 0.001 PHE B 488 TRP 0.013 0.001 TRP B 284 HIS 0.002 0.000 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 9282) covalent geometry : angle 0.55147 / 0.28 (12584) hydrogen bonds : bond 0.03973 / 2.64 ( 592) hydrogen bonds : angle 3.70050 / 2.67 ( 1722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.335 Fit side-chains REVERT: A 130 ASN cc_start: 0.8322 (t0) cc_final: 0.7931 (t0) REVERT: A 194 ARG cc_start: 0.7729 (tmm160) cc_final: 0.7257 (mtm110) REVERT: A 225 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7425 (mmp-170) REVERT: A 555 HIS cc_start: 0.8457 (m90) cc_final: 0.8243 (m90) REVERT: A 584 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8969 (mm-40) REVERT: A 600 PHE cc_start: 0.7331 (m-80) cc_final: 0.7057 (m-80) REVERT: A 617 MET cc_start: 0.9140 (mmm) cc_final: 0.8877 (mtp) REVERT: B 130 ASN cc_start: 0.8301 (t0) cc_final: 0.7910 (t0) REVERT: B 225 ARG cc_start: 0.8207 (mtm-85) cc_final: 0.7517 (mmp-170) REVERT: B 537 TYR cc_start: 0.8455 (t80) cc_final: 0.8036 (t80) REVERT: B 617 MET cc_start: 0.9201 (mmm) cc_final: 0.8907 (mtt) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.0955 time to fit residues: 13.8048 Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.0020 chunk 74 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.204424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.130073 restraints weight = 10410.226| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.42 r_work: 0.3294 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9282 Z= 0.127 Angle : 0.575 8.198 12584 Z= 0.286 Chirality : 0.041 0.227 1472 Planarity : 0.003 0.029 1598 Dihedral : 4.548 43.496 1278 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.76 % Allowed : 15.53 % Favored : 82.71 % 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: 0.80 (0.25), residues: 1160 helix: 1.47 (0.19), residues: 770 sheet: 0.02 (0.68), residues: 76 loop : -1.71 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 485 TYR 0.018 0.001 TYR A 232 PHE 0.011 0.001 PHE B 388 TRP 0.008 0.001 TRP B 284 HIS 0.002 0.000 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9282) covalent geometry : angle 0.57493 / 0.29 (12584) hydrogen bonds : bond 0.04198 / 2.77 ( 592) hydrogen bonds : angle 3.69323 / 2.67 ( 1722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8567 (t0) cc_final: 0.7917 (t0) REVERT: A 225 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7293 (mmp-170) REVERT: A 237 MET cc_start: 0.8268 (tpt) cc_final: 0.7981 (tpp) REVERT: A 389 GLN cc_start: 0.7598 (mt0) cc_final: 0.7355 (mt0) REVERT: A 555 HIS cc_start: 0.8463 (m90) cc_final: 0.8250 (m90) REVERT: A 600 PHE cc_start: 0.7325 (m-80) cc_final: 0.7033 (m-80) REVERT: A 617 MET cc_start: 0.9115 (mmm) cc_final: 0.8871 (mtp) REVERT: B 130 ASN cc_start: 0.8484 (t0) cc_final: 0.7913 (t0) REVERT: B 225 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7368 (mmp-170) REVERT: B 537 TYR cc_start: 0.8499 (t80) cc_final: 0.8097 (t80) REVERT: B 617 MET cc_start: 0.9203 (mmm) cc_final: 0.8915 (mtt) REVERT: B 664 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6137 (mm) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.0840 time to fit residues: 12.6208 Evaluate side-chains 103 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 111 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 58 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.203142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124895 restraints weight = 10416.747| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.86 r_work: 0.3327 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9282 Z= 0.144 Angle : 0.592 8.274 12584 Z= 0.297 Chirality : 0.042 0.273 1472 Planarity : 0.003 0.029 1598 Dihedral : 4.582 42.646 1278 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.28 % Allowed : 15.42 % Favored : 82.30 % 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: 0.79 (0.25), residues: 1160 helix: 1.49 (0.19), residues: 762 sheet: -0.00 (0.68), residues: 76 loop : -1.70 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 485 TYR 0.017 0.001 TYR A 232 PHE 0.013 0.001 PHE A 388 TRP 0.008 0.001 TRP A 284 HIS 0.002 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9282) covalent geometry : angle 0.59168 / 0.30 (12584) hydrogen bonds : bond 0.04375 / 2.89 ( 592) hydrogen bonds : angle 3.75041 / 2.71 ( 1722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 ARG cc_start: 0.7582 (tmm160) cc_final: 0.7121 (mtm110) REVERT: A 225 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7339 (mmp-170) REVERT: A 355 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8045 (t80) REVERT: A 600 PHE cc_start: 0.7254 (m-80) cc_final: 0.6967 (m-80) REVERT: A 617 MET cc_start: 0.9075 (mmm) cc_final: 0.8820 (mtp) REVERT: B 225 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7384 (mmp-170) REVERT: B 355 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8024 (t80) REVERT: B 537 TYR cc_start: 0.8440 (t80) cc_final: 0.8031 (t80) REVERT: B 617 MET cc_start: 0.9156 (mmm) cc_final: 0.8890 (mtt) REVERT: B 664 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6132 (mm) outliers start: 22 outliers final: 16 residues processed: 110 average time/residue: 0.0995 time to fit residues: 15.2970 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.203605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128322 restraints weight = 10360.949| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.63 r_work: 0.3297 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9282 Z= 0.138 Angle : 0.601 12.217 12584 Z= 0.298 Chirality : 0.042 0.165 1472 Planarity : 0.003 0.029 1598 Dihedral : 4.586 43.271 1278 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.17 % Allowed : 15.53 % Favored : 82.30 % 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: 0.83 (0.25), residues: 1160 helix: 1.45 (0.19), residues: 772 sheet: -0.09 (0.67), residues: 76 loop : -1.56 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 485 TYR 0.017 0.001 TYR A 232 PHE 0.012 0.001 PHE A 388 TRP 0.009 0.001 TRP B 284 HIS 0.002 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9282) covalent geometry : angle 0.60066 / 0.30 (12584) hydrogen bonds : bond 0.04312 / 2.85 ( 592) hydrogen bonds : angle 3.75833 / 2.73 ( 1722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8569 (t0) cc_final: 0.8047 (t0) REVERT: A 194 ARG cc_start: 0.7655 (tmm160) cc_final: 0.7229 (mtm110) REVERT: A 225 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7437 (mmp-170) REVERT: A 355 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8011 (t80) REVERT: A 600 PHE cc_start: 0.7300 (m-80) cc_final: 0.6976 (m-80) REVERT: A 617 MET cc_start: 0.9063 (mmm) cc_final: 0.8822 (mtp) REVERT: B 130 ASN cc_start: 0.8510 (t0) cc_final: 0.8059 (t0) REVERT: B 225 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7444 (mmp-170) REVERT: B 355 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8030 (t80) REVERT: B 497 LYS cc_start: 0.8499 (mttm) cc_final: 0.8227 (mttp) REVERT: B 537 TYR cc_start: 0.8450 (t80) cc_final: 0.8038 (t80) REVERT: B 617 MET cc_start: 0.9196 (mmm) cc_final: 0.8903 (mtt) REVERT: B 664 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6135 (mm) outliers start: 21 outliers final: 17 residues processed: 105 average time/residue: 0.0866 time to fit residues: 12.6353 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 355 PHE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.204469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127869 restraints weight = 10348.602| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.52 r_work: 0.3300 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9282 Z= 0.141 Angle : 0.598 10.830 12584 Z= 0.297 Chirality : 0.042 0.153 1472 Planarity : 0.003 0.029 1598 Dihedral : 4.579 42.330 1278 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.38 % Allowed : 15.63 % Favored : 81.99 % 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: 0.80 (0.25), residues: 1160 helix: 1.49 (0.19), residues: 760 sheet: -0.11 (0.68), residues: 76 loop : -1.62 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 485 TYR 0.017 0.001 TYR A 232 PHE 0.014 0.001 PHE A 388 TRP 0.009 0.001 TRP B 284 HIS 0.002 0.001 HIS B 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9282) covalent geometry : angle 0.59833 / 0.30 (12584) hydrogen bonds : bond 0.04353 / 2.87 ( 592) hydrogen bonds : angle 3.76799 / 2.73 ( 1722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2629.40 seconds wall clock time: 45 minutes 32.78 seconds (2732.78 seconds total)