Starting phenix.real_space_refine on Thu Mar 13 21:56:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pru_13610/03_2025/7pru_13610.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pru_13610/03_2025/7pru_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pru_13610/03_2025/7pru_13610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pru_13610/03_2025/7pru_13610.map" model { file = "/net/cci-nas-00/data/ceres_data/7pru_13610/03_2025/7pru_13610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pru_13610/03_2025/7pru_13610.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.92, per 1000 atoms: 0.65 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: 2.35 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.94 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: 2.48 Time building geometry restraints manager: 2.76 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: 4988 17.42 - 34.84: 456 34.84 - 52.27: 96 52.27 - 69.69: 21 69.69 - 87.11: 13 Dihedral angle restraints: 5574 sinusoidal: 2202 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 5571 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: 0.04 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.130 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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= 0.615 Angle : 1.051 9.502 12584 Z= 0.594 Chirality : 0.060 0.339 1472 Planarity : 0.007 0.066 1598 Dihedral : 14.865 87.110 3402 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (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 TRP 0.016 0.003 TRP A 110 HIS 0.005 0.002 HIS B 202 PHE 0.035 0.004 PHE A 388 TYR 0.028 0.003 TYR A 274 ARG 0.020 0.001 ARG A 180 *********************** 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 : 0.904 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: 0.2446 time to fit residues: 35.8213 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 : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4357 r_free = 0.4357 target = 0.203367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124667 restraints weight = 10452.863| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.03 r_work: 0.3360 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1461 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= 0.205 Angle : 0.648 7.446 12584 Z= 0.337 Chirality : 0.042 0.164 1472 Planarity : 0.005 0.038 1598 Dihedral : 7.504 76.746 1306 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1160 helix: 0.26 (0.18), residues: 756 sheet: -0.91 (0.64), residues: 74 loop : -2.09 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.002 0.001 HIS A 611 PHE 0.025 0.002 PHE A 388 TYR 0.021 0.002 TYR A 232 ARG 0.004 0.000 ARG A 485 *********************** 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 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7571 (mmp-170) REVERT: A 485 ARG cc_start: 0.7909 (mtt-85) cc_final: 0.7675 (mtt90) REVERT: A 497 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8078 (mttm) REVERT: A 617 MET cc_start: 0.9163 (mmm) cc_final: 0.8838 (mtp) REVERT: B 497 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8226 (mttm) REVERT: B 537 TYR cc_start: 0.8542 (t80) cc_final: 0.8228 (t80) REVERT: B 599 LEU cc_start: 0.7778 (mp) cc_final: 0.7522 (mp) outliers start: 5 outliers final: 5 residues processed: 105 average time/residue: 0.2492 time to fit residues: 35.7408 Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.0070 chunk 115 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4378 r_free = 0.4378 target = 0.205667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.127661 restraints weight = 10626.803| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.00 r_work: 0.3405 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9282 Z= 0.169 Angle : 0.591 7.118 12584 Z= 0.305 Chirality : 0.041 0.150 1472 Planarity : 0.004 0.031 1598 Dihedral : 6.918 84.793 1306 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.72 % Allowed : 11.28 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1160 helix: 0.80 (0.19), residues: 762 sheet: -0.79 (0.65), residues: 74 loop : -1.97 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.003 0.000 HIS A 636 PHE 0.017 0.002 PHE A 388 TYR 0.017 0.001 TYR A 232 ARG 0.003 0.000 ARG B 514 *********************** 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 104 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.944 Fit side-chains REVERT: A 194 ARG cc_start: 0.7506 (ptt90) cc_final: 0.7289 (mtm-85) REVERT: A 225 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7425 (mmp-170) REVERT: A 485 ARG cc_start: 0.7858 (mtt-85) cc_final: 0.7604 (mtt90) REVERT: A 497 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8128 (mttm) REVERT: A 617 MET cc_start: 0.9146 (mmm) cc_final: 0.8894 (mtp) REVERT: B 225 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7507 (mmp-170) REVERT: B 497 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8167 (mttm) REVERT: B 537 TYR cc_start: 0.8428 (t80) cc_final: 0.8083 (t80) REVERT: B 546 GLN cc_start: 0.7689 (mp10) cc_final: 0.7315 (mp10) REVERT: B 599 LEU cc_start: 0.7792 (mp) cc_final: 0.7588 (mp) outliers start: 7 outliers final: 6 residues processed: 103 average time/residue: 0.2417 time to fit residues: 34.0818 Evaluate side-chains 98 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 603 GLN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 524 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 92 optimal weight: 0.0570 chunk 64 optimal weight: 0.0980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.206666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128581 restraints weight = 10458.526| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.02 r_work: 0.3407 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9282 Z= 0.155 Angle : 0.558 7.037 12584 Z= 0.286 Chirality : 0.040 0.152 1472 Planarity : 0.003 0.029 1598 Dihedral : 6.564 86.996 1306 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.07 % Allowed : 11.90 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1160 helix: 1.16 (0.19), residues: 758 sheet: -0.61 (0.67), residues: 74 loop : -1.96 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS A 636 PHE 0.012 0.001 PHE A 388 TYR 0.016 0.001 TYR B 232 ARG 0.003 0.000 ARG B 514 *********************** 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 115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.624 Fit side-chains REVERT: A 130 ASN cc_start: 0.8348 (t0) cc_final: 0.7979 (t0) REVERT: A 225 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.7453 (mmp-170) REVERT: A 497 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8241 (mttm) REVERT: A 617 MET cc_start: 0.9105 (mmm) cc_final: 0.8880 (mtp) REVERT: B 130 ASN cc_start: 0.8355 (t0) cc_final: 0.7964 (t0) REVERT: B 237 MET cc_start: 0.8303 (tpt) cc_final: 0.8062 (tpp) REVERT: B 537 TYR cc_start: 0.8486 (t80) cc_final: 0.8098 (t80) REVERT: B 569 THR cc_start: 0.7399 (t) cc_final: 0.7184 (p) REVERT: B 617 MET cc_start: 0.9077 (mmm) cc_final: 0.8790 (mtp) REVERT: B 623 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8388 (p) outliers start: 20 outliers final: 9 residues processed: 115 average time/residue: 0.2715 time to fit residues: 43.4247 Evaluate side-chains 101 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 377 VAL 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 110 optimal weight: 6.9990 chunk 87 optimal weight: 0.0020 chunk 40 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.0870 chunk 56 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.206126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128418 restraints weight = 10495.588| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.96 r_work: 0.3411 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9282 Z= 0.166 Angle : 0.555 6.880 12584 Z= 0.282 Chirality : 0.041 0.160 1472 Planarity : 0.003 0.029 1598 Dihedral : 6.471 88.446 1306 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.14 % Allowed : 13.98 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1160 helix: 1.36 (0.19), residues: 758 sheet: -0.25 (0.68), residues: 76 loop : -1.91 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 284 HIS 0.002 0.000 HIS A 636 PHE 0.011 0.001 PHE A 388 TYR 0.017 0.001 TYR A 232 ARG 0.006 0.000 ARG A 485 *********************** 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 104 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.5629 (mtt) cc_final: 0.5403 (mtt) REVERT: A 130 ASN cc_start: 0.8419 (t0) cc_final: 0.7948 (t0) REVERT: A 225 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7325 (mmp-170) REVERT: A 497 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8195 (mttm) REVERT: A 617 MET cc_start: 0.9105 (mmm) cc_final: 0.8878 (mtp) REVERT: B 130 ASN cc_start: 0.8434 (t0) cc_final: 0.7907 (t0) REVERT: B 225 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7514 (mmp-170) REVERT: B 237 MET cc_start: 0.8288 (tpt) cc_final: 0.8035 (tpp) REVERT: B 426 GLU cc_start: 0.7914 (pm20) cc_final: 0.6896 (tt0) REVERT: B 537 TYR cc_start: 0.8462 (t80) cc_final: 0.8073 (t80) REVERT: B 569 THR cc_start: 0.7302 (t) cc_final: 0.7095 (p) REVERT: B 617 MET cc_start: 0.9064 (mmm) cc_final: 0.8802 (mtp) outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 0.2351 time to fit residues: 34.5843 Evaluate side-chains 101 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 203 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.203355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125093 restraints weight = 10332.906| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.81 r_work: 0.3339 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9282 Z= 0.215 Angle : 0.572 6.992 12584 Z= 0.291 Chirality : 0.042 0.162 1472 Planarity : 0.003 0.030 1598 Dihedral : 6.494 89.040 1306 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.24 % Allowed : 14.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1160 helix: 1.28 (0.19), residues: 772 sheet: -0.35 (0.67), residues: 76 loop : -1.78 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 284 HIS 0.002 0.000 HIS B 636 PHE 0.015 0.001 PHE A 388 TYR 0.017 0.001 TYR A 232 ARG 0.006 0.000 ARG A 485 *********************** 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 102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 1.179 Fit side-chains REVERT: A 130 ASN cc_start: 0.8495 (t0) cc_final: 0.7947 (t0) REVERT: A 225 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7411 (mmp-170) REVERT: A 497 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8183 (mttp) REVERT: A 617 MET cc_start: 0.9092 (mmm) cc_final: 0.8873 (mtp) REVERT: B 130 ASN cc_start: 0.8475 (t0) cc_final: 0.8003 (t0) REVERT: B 225 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7538 (mmp-170) REVERT: B 537 TYR cc_start: 0.8484 (t80) cc_final: 0.8084 (t80) REVERT: B 617 MET cc_start: 0.9060 (mmm) cc_final: 0.8796 (mtp) REVERT: B 664 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6225 (mm) outliers start: 12 outliers final: 11 residues processed: 102 average time/residue: 0.2905 time to fit residues: 42.0640 Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 203 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 524 THR 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 62 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 56 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.204172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128524 restraints weight = 10421.595| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.34 r_work: 0.3308 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2694 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= 0.181 Angle : 0.563 7.009 12584 Z= 0.284 Chirality : 0.041 0.165 1472 Planarity : 0.003 0.030 1598 Dihedral : 6.436 89.114 1306 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.86 % Allowed : 14.49 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1160 helix: 1.47 (0.19), residues: 760 sheet: -0.13 (0.67), residues: 76 loop : -1.83 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 284 HIS 0.002 0.000 HIS B 636 PHE 0.013 0.001 PHE A 388 TYR 0.017 0.001 TYR A 232 ARG 0.007 0.000 ARG A 485 *********************** 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 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.911 Fit side-chains REVERT: A 130 ASN cc_start: 0.8519 (t0) cc_final: 0.7976 (t0) REVERT: A 225 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7303 (mmp-170) REVERT: A 355 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.8043 (t80) REVERT: A 497 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8206 (mttm) REVERT: A 584 GLN cc_start: 0.9247 (mm-40) cc_final: 0.9034 (mm-40) REVERT: A 617 MET cc_start: 0.9143 (mmm) cc_final: 0.8903 (mtp) REVERT: B 130 ASN cc_start: 0.8488 (t0) cc_final: 0.7955 (t0) REVERT: B 225 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7456 (mmp-170) REVERT: B 355 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8077 (t80) REVERT: B 497 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8445 (mttm) REVERT: B 537 TYR cc_start: 0.8483 (t80) cc_final: 0.8077 (t80) REVERT: B 617 MET cc_start: 0.9106 (mmm) cc_final: 0.8815 (mtp) REVERT: B 664 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6222 (mm) outliers start: 18 outliers final: 13 residues processed: 105 average time/residue: 0.2333 time to fit residues: 34.0875 Evaluate side-chains 104 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 203 LEU 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 497 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.203208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124591 restraints weight = 10543.528| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.90 r_work: 0.3320 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9282 Z= 0.209 Angle : 0.579 7.960 12584 Z= 0.292 Chirality : 0.042 0.177 1472 Planarity : 0.003 0.030 1598 Dihedral : 6.464 89.827 1306 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.38 % Allowed : 14.18 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1160 helix: 1.38 (0.19), residues: 772 sheet: -0.03 (0.67), residues: 76 loop : -1.71 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 284 HIS 0.002 0.000 HIS B 636 PHE 0.015 0.001 PHE A 388 TYR 0.017 0.001 TYR A 232 ARG 0.008 0.000 ARG A 485 *********************** 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 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8508 (t0) cc_final: 0.7975 (t0) REVERT: A 225 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7321 (mmp-170) REVERT: A 355 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7995 (t80) REVERT: A 497 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8158 (mttm) REVERT: A 584 GLN cc_start: 0.9245 (mm-40) cc_final: 0.9040 (mm-40) REVERT: A 617 MET cc_start: 0.9128 (mmm) cc_final: 0.8897 (mtp) REVERT: B 130 ASN cc_start: 0.8460 (t0) cc_final: 0.7944 (t0) REVERT: B 225 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7434 (mmp-170) REVERT: B 355 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8073 (t80) REVERT: B 497 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8425 (mttm) REVERT: B 537 TYR cc_start: 0.8444 (t80) cc_final: 0.8036 (t80) REVERT: B 617 MET cc_start: 0.9098 (mmm) cc_final: 0.8804 (mtp) REVERT: B 664 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6210 (mm) outliers start: 23 outliers final: 17 residues processed: 107 average time/residue: 0.2395 time to fit residues: 36.0289 Evaluate side-chains 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 524 THR Chi-restraints excluded: chain A residue 603 GLN 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 497 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.200775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121732 restraints weight = 10358.908| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.87 r_work: 0.3278 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9282 Z= 0.280 Angle : 0.633 10.280 12584 Z= 0.317 Chirality : 0.044 0.169 1472 Planarity : 0.004 0.030 1598 Dihedral : 6.579 89.354 1306 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.38 % Allowed : 14.60 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1160 helix: 1.19 (0.19), residues: 776 sheet: -0.05 (0.67), residues: 76 loop : -1.63 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.002 0.001 HIS B 636 PHE 0.021 0.002 PHE A 388 TYR 0.018 0.001 TYR A 274 ARG 0.007 0.000 ARG A 485 *********************** 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: 23 poor density : 90 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7382 (mmp-170) REVERT: A 355 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7993 (t80) REVERT: A 362 MET cc_start: 0.8410 (mtt) cc_final: 0.8136 (mtm) REVERT: A 497 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8158 (mttm) REVERT: A 617 MET cc_start: 0.9115 (mmm) cc_final: 0.8869 (mtp) REVERT: B 225 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7471 (mmp-170) REVERT: B 355 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8078 (t80) REVERT: B 362 MET cc_start: 0.8481 (mtt) cc_final: 0.8201 (mtt) REVERT: B 537 TYR cc_start: 0.8443 (t80) cc_final: 0.8015 (t80) REVERT: B 617 MET cc_start: 0.9084 (mmm) cc_final: 0.8795 (mtp) REVERT: B 664 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6262 (mm) outliers start: 23 outliers final: 17 residues processed: 107 average time/residue: 0.2234 time to fit residues: 33.3894 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 524 THR Chi-restraints excluded: chain A residue 603 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 112 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.203227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125900 restraints weight = 10545.355| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.85 r_work: 0.3340 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.003 0.041 9282 Z= 0.195 Angle : 0.616 14.983 12584 Z= 0.304 Chirality : 0.042 0.186 1472 Planarity : 0.003 0.030 1598 Dihedral : 6.515 89.395 1306 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.28 % Allowed : 15.32 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1160 helix: 1.34 (0.19), residues: 772 sheet: 0.00 (0.68), residues: 76 loop : -1.66 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.002 0.000 HIS A 636 PHE 0.012 0.001 PHE A 388 TYR 0.018 0.001 TYR A 232 ARG 0.008 0.000 ARG A 485 ********************** 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: 22 poor density : 87 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8507 (t0) cc_final: 0.7912 (t0) REVERT: A 225 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7416 (mmp-170) REVERT: A 355 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8040 (t80) REVERT: A 362 MET cc_start: 0.8297 (mtt) cc_final: 0.8064 (mtt) REVERT: A 617 MET cc_start: 0.9085 (mmm) cc_final: 0.8859 (mtp) REVERT: B 130 ASN cc_start: 0.8511 (t0) cc_final: 0.7850 (t0) REVERT: B 225 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7478 (mmp-170) REVERT: B 355 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8066 (t80) REVERT: B 362 MET cc_start: 0.8369 (mtt) cc_final: 0.8074 (mtm) REVERT: B 389 GLN cc_start: 0.7776 (mt0) cc_final: 0.7408 (mt0) REVERT: B 537 TYR cc_start: 0.8402 (t80) cc_final: 0.8052 (t80) REVERT: B 617 MET cc_start: 0.9077 (mmm) cc_final: 0.8804 (mtp) REVERT: B 664 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6201 (mm) outliers start: 22 outliers final: 16 residues processed: 105 average time/residue: 0.2189 time to fit residues: 32.6752 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 : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 0.0050 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.207945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131504 restraints weight = 10483.614| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.00 r_work: 0.3502 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3073 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= 0.176 Angle : 0.582 8.552 12584 Z= 0.290 Chirality : 0.041 0.168 1472 Planarity : 0.003 0.031 1598 Dihedral : 6.474 88.356 1306 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.76 % Allowed : 15.63 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.25), residues: 1160 helix: 1.45 (0.19), residues: 772 sheet: 0.09 (0.68), residues: 76 loop : -1.59 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.003 0.001 HIS A 555 PHE 0.008 0.001 PHE B 448 TYR 0.018 0.001 TYR B 232 ARG 0.007 0.000 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6139.44 seconds wall clock time: 108 minutes 15.36 seconds (6495.36 seconds total)