Starting phenix.real_space_refine on Thu Feb 13 18:46:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pru_13610/02_2025/7pru_13610.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pru_13610/02_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_13610/02_2025/7pru_13610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pru_13610/02_2025/7pru_13610.map" model { file = "/net/cci-nas-00/data/ceres_data/7pru_13610/02_2025/7pru_13610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pru_13610/02_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-5592/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: 5.95, 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 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: 0.99 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: 2.97 Time building geometry restraints manager: 2.71 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: 0.05 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: 1.700 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.870 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- 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 : 0.806 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: 0.2451 time to fit residues: 35.7073 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 : 1.052 ------------------------------------------------------------------------------- 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 = 0.203365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124622 restraints weight = 10453.001| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.05 r_work: 0.3357 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- 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 : 7.503 76.747 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 : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7578 (mmp-170) REVERT: A 485 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7682 (mtt90) REVERT: A 497 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8081 (mttm) REVERT: A 617 MET cc_start: 0.9162 (mmm) cc_final: 0.8838 (mtp) REVERT: B 497 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8225 (mttm) REVERT: B 537 TYR cc_start: 0.8541 (t80) cc_final: 0.8227 (t80) REVERT: B 599 LEU cc_start: 0.7782 (mp) cc_final: 0.7527 (mp) outliers start: 5 outliers final: 5 residues processed: 105 average time/residue: 0.2558 time to fit residues: 36.3333 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 : 1.073 ------------------------------------------------------------------------------- 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: 0.9990 chunk 115 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.202436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122489 restraints weight = 10687.587| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.06 r_work: 0.3333 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9282 Z= 0.225 Angle : 0.619 7.188 12584 Z= 0.320 Chirality : 0.042 0.155 1472 Planarity : 0.004 0.031 1598 Dihedral : 7.032 83.017 1306 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.35 % Allowed : 10.87 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.25), residues: 1160 helix: 0.64 (0.19), residues: 760 sheet: -0.83 (0.66), residues: 74 loop : -2.04 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.002 0.001 HIS A 636 PHE 0.022 0.002 PHE B 388 TYR 0.018 0.001 TYR A 232 ARG 0.004 0.000 ARG B 180 *********************** 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: 13 poor density : 96 time to evaluate : 0.911 Fit side-chains REVERT: A 194 ARG cc_start: 0.7630 (ptt90) cc_final: 0.7385 (mtm-85) REVERT: A 225 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7646 (mmp-170) REVERT: A 431 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7875 (mmtp) REVERT: A 497 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8075 (mttm) REVERT: A 617 MET cc_start: 0.9122 (mmm) cc_final: 0.8872 (mtp) REVERT: B 225 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7619 (mmp-170) REVERT: B 497 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8206 (mttp) REVERT: B 537 TYR cc_start: 0.8472 (t80) cc_final: 0.8126 (t80) outliers start: 13 outliers final: 12 residues processed: 106 average time/residue: 0.2491 time to fit residues: 35.9050 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 : 0.949 ------------------------------------------------------------------------------- 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 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 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 67 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.205583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124228 restraints weight = 10473.595| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.00 r_work: 0.3336 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2038 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= 0.210 Angle : 0.599 7.223 12584 Z= 0.308 Chirality : 0.042 0.154 1472 Planarity : 0.004 0.031 1598 Dihedral : 6.755 84.238 1306 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.48 % Allowed : 11.70 % Favored : 85.82 % 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: -0.00 (0.25), residues: 1160 helix: 0.90 (0.19), residues: 758 sheet: -0.75 (0.67), residues: 74 loop : -1.89 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.002 0.000 HIS B 636 PHE 0.020 0.002 PHE A 388 TYR 0.017 0.001 TYR A 232 ARG 0.006 0.000 ARG A 485 *********************** 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: 24 poor density : 89 time to evaluate : 1.081 Fit side-chains REVERT: A 497 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8225 (mttm) REVERT: A 617 MET cc_start: 0.9121 (mmm) cc_final: 0.8885 (mtp) REVERT: B 497 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8027 (mttm) REVERT: B 537 TYR cc_start: 0.8455 (t80) cc_final: 0.8107 (t80) REVERT: B 617 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8405 (mtt) REVERT: B 623 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8348 (p) outliers start: 24 outliers final: 14 residues processed: 110 average time/residue: 0.2387 time to fit residues: 36.3485 Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 B residue 174 VAL Chi-restraints excluded: chain B residue 195 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 617 MET 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: 0.4980 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.203313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124977 restraints weight = 10440.955| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.94 r_work: 0.3359 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2313 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= 0.198 Angle : 0.586 7.094 12584 Z= 0.300 Chirality : 0.042 0.162 1472 Planarity : 0.003 0.030 1598 Dihedral : 6.626 85.630 1306 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % 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 (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: 0.27 (0.25), residues: 1160 helix: 1.12 (0.19), residues: 758 sheet: -0.42 (0.67), residues: 76 loop : -1.86 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS B 636 PHE 0.018 0.002 PHE A 388 TYR 0.017 0.001 TYR B 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 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.994 Fit side-chains REVERT: A 225 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7589 (mmp-170) REVERT: A 352 ASN cc_start: 0.8652 (t0) cc_final: 0.8202 (t0) REVERT: A 497 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8245 (mttm) REVERT: A 617 MET cc_start: 0.9097 (mmm) cc_final: 0.8866 (mtp) REVERT: B 100 MET cc_start: 0.5496 (mtt) cc_final: 0.5288 (mtt) REVERT: B 130 ASN cc_start: 0.8448 (t0) cc_final: 0.8012 (t0) REVERT: B 352 ASN cc_start: 0.8663 (t0) cc_final: 0.8188 (t0) REVERT: B 355 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8044 (t80) REVERT: B 537 TYR cc_start: 0.8485 (t80) cc_final: 0.8148 (t80) REVERT: B 664 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6268 (mm) outliers start: 23 outliers final: 18 residues processed: 108 average time/residue: 0.2441 time to fit residues: 36.3340 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 : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 195 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 35 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 48 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.202512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124171 restraints weight = 10482.958| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.51 r_work: 0.3298 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9282 Z= 0.225 Angle : 0.592 7.181 12584 Z= 0.302 Chirality : 0.042 0.164 1472 Planarity : 0.003 0.029 1598 Dihedral : 6.614 86.675 1306 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.59 % Allowed : 13.46 % Favored : 83.95 % 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: 0.32 (0.25), residues: 1160 helix: 1.07 (0.19), residues: 772 sheet: -0.43 (0.66), residues: 76 loop : -1.73 (0.34), residues: 312 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 0.017 0.002 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 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8472 (t0) cc_final: 0.7921 (t0) REVERT: A 225 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.7518 (mmp-170) REVERT: A 355 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8038 (t80) REVERT: A 497 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8165 (mttm) REVERT: A 617 MET cc_start: 0.9159 (mmm) cc_final: 0.8894 (mtp) REVERT: B 355 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8039 (t80) REVERT: B 537 TYR cc_start: 0.8490 (t80) cc_final: 0.8139 (t80) REVERT: B 664 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6262 (mm) outliers start: 25 outliers final: 20 residues processed: 109 average time/residue: 0.2330 time to fit residues: 35.0144 Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 174 VAL Chi-restraints excluded: chain B residue 195 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4356 r_free = 0.4356 target = 0.203461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124246 restraints weight = 10550.767| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.02 r_work: 0.3352 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2582 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= 0.192 Angle : 0.577 6.999 12584 Z= 0.294 Chirality : 0.041 0.167 1472 Planarity : 0.003 0.029 1598 Dihedral : 6.526 87.336 1306 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.69 % Allowed : 13.46 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.25), residues: 1160 helix: 1.26 (0.19), residues: 760 sheet: -0.29 (0.66), residues: 76 loop : -1.75 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 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 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 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8448 (t0) cc_final: 0.7970 (t0) REVERT: A 225 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7575 (mmp-170) REVERT: A 352 ASN cc_start: 0.8670 (t0) cc_final: 0.8226 (t0) REVERT: A 355 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.8003 (t80) REVERT: A 497 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8161 (mttp) REVERT: A 584 GLN cc_start: 0.9225 (mm-40) cc_final: 0.9002 (mm-40) REVERT: A 617 MET cc_start: 0.9124 (mmm) cc_final: 0.8881 (mtp) REVERT: B 130 ASN cc_start: 0.8422 (t0) cc_final: 0.8110 (t0) REVERT: B 225 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7633 (mmp-170) REVERT: B 352 ASN cc_start: 0.8675 (t0) cc_final: 0.8219 (t0) REVERT: B 355 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8024 (t80) REVERT: B 362 MET cc_start: 0.8522 (mtt) cc_final: 0.8319 (mtt) REVERT: B 484 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8182 (pp) REVERT: B 537 TYR cc_start: 0.8509 (t80) cc_final: 0.8103 (t80) REVERT: B 664 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6191 (mm) outliers start: 26 outliers final: 17 residues processed: 112 average time/residue: 0.2308 time to fit residues: 35.8239 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 : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU 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 195 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.202225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123232 restraints weight = 10583.248| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.93 r_work: 0.3331 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9282 Z= 0.240 Angle : 0.597 7.688 12584 Z= 0.305 Chirality : 0.043 0.176 1472 Planarity : 0.003 0.030 1598 Dihedral : 6.578 88.100 1306 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.59 % Allowed : 14.70 % 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 (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: 0.45 (0.25), residues: 1160 helix: 1.15 (0.19), residues: 772 sheet: -0.24 (0.66), residues: 76 loop : -1.66 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS B 636 PHE 0.017 0.001 PHE A 388 TYR 0.017 0.001 TYR A 232 ARG 0.005 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: 25 poor density : 88 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7600 (mmp-170) REVERT: A 352 ASN cc_start: 0.8704 (t0) cc_final: 0.8276 (t0) REVERT: A 355 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8034 (t80) REVERT: A 497 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8190 (mttm) REVERT: A 617 MET cc_start: 0.9108 (mmm) cc_final: 0.8860 (mtp) REVERT: B 130 ASN cc_start: 0.8475 (t0) cc_final: 0.8091 (t0) REVERT: B 225 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7666 (mmp-170) REVERT: B 352 ASN cc_start: 0.8712 (t0) cc_final: 0.8283 (t0) REVERT: B 355 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.8047 (t80) REVERT: B 484 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8189 (pp) REVERT: B 537 TYR cc_start: 0.8516 (t80) cc_final: 0.8107 (t80) REVERT: B 664 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6210 (mm) outliers start: 25 outliers final: 17 residues processed: 109 average time/residue: 0.2415 time to fit residues: 36.2704 Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 524 THR Chi-restraints excluded: chain A residue 603 GLN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 195 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.202529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122504 restraints weight = 10422.372| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.00 r_work: 0.3329 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9282 Z= 0.226 Angle : 0.613 9.305 12584 Z= 0.310 Chirality : 0.043 0.195 1472 Planarity : 0.003 0.029 1598 Dihedral : 6.555 88.024 1306 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.90 % Allowed : 15.01 % Favored : 82.09 % 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: 0.51 (0.25), residues: 1160 helix: 1.26 (0.19), residues: 760 sheet: -0.30 (0.65), residues: 76 loop : -1.69 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.001 HIS B 636 PHE 0.018 0.001 PHE A 388 TYR 0.018 0.001 TYR A 232 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 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8517 (t0) cc_final: 0.7854 (t0) REVERT: A 225 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7578 (mmp-170) REVERT: A 355 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8058 (t80) REVERT: A 389 GLN cc_start: 0.7804 (mt0) cc_final: 0.7576 (mt0) REVERT: A 555 HIS cc_start: 0.8410 (m90) cc_final: 0.8204 (m90) REVERT: A 617 MET cc_start: 0.9115 (mmm) cc_final: 0.8867 (mtp) REVERT: B 130 ASN cc_start: 0.8479 (t0) cc_final: 0.8118 (t0) REVERT: B 225 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7611 (mmp-170) REVERT: B 355 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7989 (t80) REVERT: B 484 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8207 (pp) REVERT: B 537 TYR cc_start: 0.8484 (t80) cc_final: 0.8140 (t80) REVERT: B 647 ILE cc_start: 0.6694 (mm) cc_final: 0.6295 (mm) REVERT: B 664 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6202 (mm) outliers start: 28 outliers final: 20 residues processed: 114 average time/residue: 0.2331 time to fit residues: 36.8441 Evaluate side-chains 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 203 LEU 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 174 VAL Chi-restraints excluded: chain B residue 195 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.202702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124801 restraints weight = 10600.370| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.88 r_work: 0.3329 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9282 Z= 0.205 Angle : 0.621 14.256 12584 Z= 0.310 Chirality : 0.042 0.168 1472 Planarity : 0.003 0.032 1598 Dihedral : 6.515 88.707 1306 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.48 % Allowed : 15.63 % Favored : 81.88 % 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: 0.61 (0.25), residues: 1160 helix: 1.33 (0.19), residues: 768 sheet: -0.39 (0.65), residues: 76 loop : -1.66 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS B 636 PHE 0.012 0.001 PHE A 601 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 115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8519 (t0) cc_final: 0.8112 (t0) REVERT: A 225 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7433 (mmp-170) REVERT: A 355 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8020 (t80) REVERT: A 555 HIS cc_start: 0.8432 (m90) cc_final: 0.8226 (m90) REVERT: A 617 MET cc_start: 0.9103 (mmm) cc_final: 0.8865 (mtp) REVERT: B 130 ASN cc_start: 0.8482 (t0) cc_final: 0.8133 (t0) REVERT: B 225 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7474 (mmp-170) REVERT: B 355 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8011 (t80) REVERT: B 537 TYR cc_start: 0.8440 (t80) cc_final: 0.8009 (t80) REVERT: B 647 ILE cc_start: 0.6691 (mm) cc_final: 0.6297 (mm) REVERT: B 664 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6200 (mm) outliers start: 24 outliers final: 19 residues processed: 111 average time/residue: 0.2333 time to fit residues: 35.6894 Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 203 LEU 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 195 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 chunk 1 optimal weight: 0.0050 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.3772 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.205055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129917 restraints weight = 10445.340| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.36 r_work: 0.3314 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3076 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= 0.158 Angle : 0.585 9.897 12584 Z= 0.289 Chirality : 0.041 0.166 1472 Planarity : 0.003 0.031 1598 Dihedral : 6.406 89.746 1306 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.76 % Allowed : 16.36 % Favored : 81.88 % 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: 0.84 (0.25), residues: 1160 helix: 1.54 (0.19), residues: 768 sheet: -0.38 (0.66), residues: 76 loop : -1.67 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.002 0.000 HIS A 636 PHE 0.014 0.001 PHE A 601 TYR 0.018 0.001 TYR A 232 ARG 0.008 0.000 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5847.00 seconds wall clock time: 104 minutes 2.49 seconds (6242.49 seconds total)