Starting phenix.real_space_refine on Thu Jul 2 12:50:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fdv_31547/07_2026/7fdv_31547_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdv_31547/07_2026/7fdv_31547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fdv_31547/07_2026/7fdv_31547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdv_31547/07_2026/7fdv_31547.map" model { file = "/net/cci-nas-00/data/ceres_data/7fdv_31547/07_2026/7fdv_31547_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdv_31547/07_2026/7fdv_31547_neut.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 68 5.16 5 C 5556 2.51 5 N 1370 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8508 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4147 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 19, 'TRANS': 509} Chain breaks: 2 Chain: "D" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4147 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 19, 'TRANS': 509} Chain breaks: 2 Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'ATP': 1, 'CLR': 1, 'HWP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'ATP': 1, 'CLR': 1, 'HWP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.87, per 1000 atoms: 0.22 Number of scatterers: 8508 At special positions: 0 Unit cell: (71.71, 99.99, 122.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 8 15.00 O 1506 8.00 N 1370 7.00 C 5556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 184.2 milliseconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 50.1% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 123 through 133 removed outlier: 4.057A pdb=" N MET A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.991A pdb=" N SER A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.546A pdb=" N LEU A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.582A pdb=" N MET A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 4.253A pdb=" N LEU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 removed outlier: 3.558A pdb=" N TYR A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.558A pdb=" N GLU A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.534A pdb=" N LEU A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 433 through 441 removed outlier: 4.288A pdb=" N LEU A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 465 removed outlier: 3.918A pdb=" N PHE A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 477 through 488 removed outlier: 4.169A pdb=" N VAL A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 530 through 555 removed outlier: 3.637A pdb=" N LEU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 572 removed outlier: 4.062A pdb=" N PHE A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.647A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.687A pdb=" N ILE A 599 " --> pdb=" O TRP A 595 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER A 600 " --> pdb=" O MET A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 600' Processing helix chain 'A' and resid 601 through 614 removed outlier: 3.677A pdb=" N GLY A 605 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 608 " --> pdb=" O TYR A 604 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 614 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 664 removed outlier: 3.798A pdb=" N PHE A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 660 " --> pdb=" O GLY A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 673 Processing helix chain 'D' and resid 123 through 133 removed outlier: 4.057A pdb=" N MET D 128 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 185 removed outlier: 3.991A pdb=" N SER D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 221 through 230 removed outlier: 3.546A pdb=" N LEU D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.582A pdb=" N MET D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 264 " --> pdb=" O LYS D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 283 removed outlier: 4.253A pdb=" N LEU D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 311 removed outlier: 3.558A pdb=" N TYR D 307 " --> pdb=" O ASN D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 331 removed outlier: 3.558A pdb=" N GLU D 327 " --> pdb=" O ASP D 323 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 418 removed outlier: 3.534A pdb=" N LEU D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 433 Processing helix chain 'D' and resid 433 through 441 removed outlier: 4.288A pdb=" N LEU D 439 " --> pdb=" O LEU D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 465 removed outlier: 3.918A pdb=" N PHE D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 475 Processing helix chain 'D' and resid 477 through 488 removed outlier: 4.169A pdb=" N VAL D 483 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 486 " --> pdb=" O GLY D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 512 through 518 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 530 through 555 removed outlier: 3.637A pdb=" N LEU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 545 " --> pdb=" O GLY D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 572 removed outlier: 4.062A pdb=" N PHE D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) Proline residue: D 570 - end of helix Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.647A pdb=" N LEU D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 594 Processing helix chain 'D' and resid 595 through 600 removed outlier: 3.687A pdb=" N ILE D 599 " --> pdb=" O TRP D 595 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER D 600 " --> pdb=" O MET D 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 595 through 600' Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.677A pdb=" N GLY D 605 " --> pdb=" O TYR D 601 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 607 " --> pdb=" O ARG D 603 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY D 608 " --> pdb=" O TYR D 604 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR D 614 " --> pdb=" O ILE D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 664 removed outlier: 3.798A pdb=" N PHE D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 660 " --> pdb=" O GLY D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 673 Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.537A pdb=" N LEU A 148 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 removed outlier: 6.598A pdb=" N TYR A 84 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 removed outlier: 4.068A pdb=" N ALA A 115 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU A 287 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG A 298 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL A 289 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA5, first strand: chain 'D' and resid 106 through 107 removed outlier: 3.537A pdb=" N LEU D 148 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 86 removed outlier: 6.598A pdb=" N TYR D 84 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 271 through 272 removed outlier: 4.068A pdb=" N ALA D 115 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU D 287 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG D 298 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL D 289 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 161 through 162 286 hydrogen bonds defined for protein. 822 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: 0.80 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1288 1.30 - 1.43: 2268 1.43 - 1.55: 5004 1.55 - 1.68: 24 1.68 - 1.81: 110 Bond restraints: 8694 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C4 ATP D 702 " pdb=" C5 ATP D 702 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C5 ATP D 702 " pdb=" C6 ATP D 702 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C16 HWP A 702 " pdb=" N18 HWP A 702 " ideal model delta sigma weight residual 1.381 1.482 -0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 8689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 11608 3.88 - 7.76: 128 7.76 - 11.64: 20 11.64 - 15.52: 4 15.52 - 19.39: 8 Bond angle restraints: 11768 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP D 702 " pdb=" O3B ATP D 702 " pdb=" PG ATP D 702 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PA ATP D 702 " pdb=" O3A ATP D 702 " pdb=" PB ATP D 702 " ideal model delta sigma weight residual 136.83 120.62 16.21 1.00e+00 1.00e+00 2.63e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 120.62 16.21 1.00e+00 1.00e+00 2.63e+02 angle pdb=" C GLU D 635 " pdb=" CA GLU D 635 " pdb=" CB GLU D 635 " ideal model delta sigma weight residual 110.04 93.03 17.01 1.51e+00 4.39e-01 1.27e+02 ... (remaining 11763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 4642 17.50 - 35.00: 548 35.00 - 52.50: 98 52.50 - 70.00: 26 70.00 - 87.50: 12 Dihedral angle restraints: 5326 sinusoidal: 2270 harmonic: 3056 Sorted by residual: dihedral pdb=" C GLU D 635 " pdb=" N GLU D 635 " pdb=" CA GLU D 635 " pdb=" CB GLU D 635 " ideal model delta harmonic sigma weight residual -122.60 -101.12 -21.48 0 2.50e+00 1.60e-01 7.39e+01 dihedral pdb=" C GLU A 635 " pdb=" N GLU A 635 " pdb=" CA GLU A 635 " pdb=" CB GLU A 635 " ideal model delta harmonic sigma weight residual -122.60 -102.25 -20.35 0 2.50e+00 1.60e-01 6.62e+01 dihedral pdb=" CA GLY A 615 " pdb=" C GLY A 615 " pdb=" N LEU A 616 " pdb=" CA LEU A 616 " ideal model delta harmonic sigma weight residual -180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 5323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1284 0.100 - 0.199: 54 0.199 - 0.298: 6 0.298 - 0.398: 4 0.398 - 0.497: 2 Chirality restraints: 1350 Sorted by residual: chirality pdb=" C13 CLR A 703 " pdb=" C12 CLR A 703 " pdb=" C14 CLR A 703 " pdb=" C17 CLR A 703 " both_signs ideal model delta sigma weight residual False -2.93 -2.43 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C13 CLR D 701 " pdb=" C12 CLR D 701 " pdb=" C14 CLR D 701 " pdb=" C17 CLR D 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.43 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C10 CLR A 703 " pdb=" C1 CLR A 703 " pdb=" C5 CLR A 703 " pdb=" C9 CLR A 703 " both_signs ideal model delta sigma weight residual False -2.85 -2.45 -0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 1347 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 634 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C SER D 634 " -0.052 2.00e-02 2.50e+03 pdb=" O SER D 634 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU D 635 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 634 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C SER A 634 " 0.052 2.00e-02 2.50e+03 pdb=" O SER A 634 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 635 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 471 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO D 472 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 472 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 472 " 0.019 5.00e-02 4.00e+02 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 85 2.58 - 3.16: 7001 3.16 - 3.74: 11891 3.74 - 4.32: 17353 4.32 - 4.90: 28967 Nonbonded interactions: 65297 Sorted by model distance: nonbonded pdb=" O GLU D 635 " pdb=" CG GLU D 635 " model vdw 2.001 3.440 nonbonded pdb=" O GLU A 635 " pdb=" CG GLU A 635 " model vdw 2.059 3.440 nonbonded pdb=" OG SER A 120 " pdb=" O3G ATP A 701 " model vdw 2.199 3.040 nonbonded pdb=" OG SER D 120 " pdb=" O3G ATP D 702 " model vdw 2.199 3.040 nonbonded pdb=" O SER A 634 " pdb=" CB GLU A 635 " model vdw 2.231 3.440 ... (remaining 65292 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 72 through 675) selection = (chain 'D' and resid 72 through 675) } 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: 0.830 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.160 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.008 0.101 8694 Z= 0.431 Angle : 1.120 19.395 11768 Z= 0.663 Chirality : 0.056 0.497 1350 Planarity : 0.004 0.034 1432 Dihedral : 15.627 87.499 3370 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.66 % Allowed : 9.69 % Favored : 89.65 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.08 (0.17), residues: 1046 helix: -3.89 (0.14), residues: 554 sheet: -4.92 (0.35), residues: 64 loop : -3.92 (0.21), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 486 TYR 0.010 0.001 TYR A 441 PHE 0.013 0.001 PHE A 281 TRP 0.004 0.001 TRP A 492 HIS 0.003 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.43 ( 8694) covalent geometry : angle 1.12048 / 0.66 (11768) hydrogen bonds : bond 0.23045 / 15.09 ( 286) hydrogen bonds : angle 8.66769 / 5.89 ( 822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.228 Fit side-chains REVERT: A 326 MET cc_start: 0.8136 (tpp) cc_final: 0.7754 (mmm) REVERT: A 580 SER cc_start: 0.8732 (m) cc_final: 0.8415 (m) REVERT: D 326 MET cc_start: 0.8136 (tpp) cc_final: 0.7754 (mmm) REVERT: D 580 SER cc_start: 0.8731 (m) cc_final: 0.8415 (m) outliers start: 6 outliers final: 4 residues processed: 134 average time/residue: 0.0846 time to fit residues: 15.8723 Evaluate side-chains 98 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 635 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN A 630 HIS D 254 GLN D 630 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098673 restraints weight = 12900.266| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.72 r_work: 0.3097 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8694 Z= 0.172 Angle : 0.683 6.850 11768 Z= 0.332 Chirality : 0.044 0.136 1350 Planarity : 0.004 0.028 1432 Dihedral : 13.300 89.080 1456 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.98 % Allowed : 15.20 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.94 (0.20), residues: 1046 helix: -2.87 (0.17), residues: 562 sheet: -4.61 (0.36), residues: 64 loop : -3.48 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 194 TYR 0.008 0.001 TYR A 667 PHE 0.010 0.001 PHE A 405 TRP 0.004 0.001 TRP A 492 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 8694) covalent geometry : angle 0.68331 / 0.33 (11768) hydrogen bonds : bond 0.03641 / 2.33 ( 286) hydrogen bonds : angle 4.85819 / 3.30 ( 822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.529 Fit side-chains REVERT: A 196 MET cc_start: 0.8053 (mtt) cc_final: 0.7615 (mtt) REVERT: A 258 LEU cc_start: 0.8316 (pp) cc_final: 0.7709 (mt) REVERT: A 425 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8075 (tt) REVERT: D 196 MET cc_start: 0.8051 (mtt) cc_final: 0.7616 (mtt) REVERT: D 258 LEU cc_start: 0.8315 (pp) cc_final: 0.7709 (mt) REVERT: D 425 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8080 (tt) outliers start: 18 outliers final: 8 residues processed: 122 average time/residue: 0.0749 time to fit residues: 13.3585 Evaluate side-chains 104 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097069 restraints weight = 12901.571| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.67 r_work: 0.3072 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8694 Z= 0.190 Angle : 0.674 7.916 11768 Z= 0.323 Chirality : 0.044 0.139 1350 Planarity : 0.004 0.029 1432 Dihedral : 11.913 81.013 1456 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.30 % Allowed : 18.61 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.22), residues: 1046 helix: -2.20 (0.20), residues: 556 sheet: -4.30 (0.39), residues: 64 loop : -3.13 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 224 TYR 0.008 0.001 TYR A 667 PHE 0.013 0.001 PHE D 281 TRP 0.012 0.001 TRP A 523 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 ( 8694) covalent geometry : angle 0.67361 / 0.32 (11768) hydrogen bonds : bond 0.03482 / 2.23 ( 286) hydrogen bonds : angle 4.43509 / 3.01 ( 822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.315 Fit side-chains REVERT: A 258 LEU cc_start: 0.8354 (pp) cc_final: 0.7643 (mt) REVERT: A 425 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8146 (tt) REVERT: D 258 LEU cc_start: 0.8353 (pp) cc_final: 0.7644 (mt) REVERT: D 425 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8149 (tt) outliers start: 30 outliers final: 18 residues processed: 122 average time/residue: 0.0727 time to fit residues: 13.2956 Evaluate side-chains 120 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099543 restraints weight = 12816.169| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.68 r_work: 0.3107 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8694 Z= 0.138 Angle : 0.632 9.356 11768 Z= 0.300 Chirality : 0.042 0.130 1350 Planarity : 0.003 0.029 1432 Dihedral : 10.857 79.217 1456 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.96 % Allowed : 20.37 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.23), residues: 1046 helix: -1.77 (0.21), residues: 558 sheet: -4.13 (0.40), residues: 64 loop : -3.02 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 224 TYR 0.007 0.001 TYR D 307 PHE 0.011 0.001 PHE A 281 TRP 0.007 0.001 TRP A 523 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 8694) covalent geometry : angle 0.63177 / 0.30 (11768) hydrogen bonds : bond 0.02943 / 1.90 ( 286) hydrogen bonds : angle 4.08595 / 2.78 ( 822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.284 Fit side-chains REVERT: A 179 MET cc_start: 0.8997 (mmm) cc_final: 0.8749 (mmm) REVERT: A 258 LEU cc_start: 0.8262 (pp) cc_final: 0.7679 (mt) REVERT: A 326 MET cc_start: 0.8141 (mmm) cc_final: 0.7714 (mmm) REVERT: A 425 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8353 (tp) REVERT: A 563 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8320 (mp10) REVERT: D 179 MET cc_start: 0.9003 (mmm) cc_final: 0.8751 (mmm) REVERT: D 258 LEU cc_start: 0.8262 (pp) cc_final: 0.7678 (mt) REVERT: D 326 MET cc_start: 0.8132 (mmm) cc_final: 0.7709 (mmm) REVERT: D 425 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8360 (tp) REVERT: D 563 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8315 (mp10) outliers start: 36 outliers final: 20 residues processed: 134 average time/residue: 0.0742 time to fit residues: 14.6482 Evaluate side-chains 124 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095305 restraints weight = 13107.732| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.71 r_work: 0.3042 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 8694 Z= 0.289 Angle : 0.760 8.995 11768 Z= 0.364 Chirality : 0.047 0.162 1350 Planarity : 0.004 0.031 1432 Dihedral : 11.088 75.481 1456 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 3.74 % Allowed : 20.93 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.23), residues: 1046 helix: -1.83 (0.20), residues: 556 sheet: -4.21 (0.39), residues: 64 loop : -3.02 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.013 0.002 TYR A 672 PHE 0.015 0.002 PHE D 281 TRP 0.007 0.001 TRP D 523 HIS 0.003 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.29 ( 8694) covalent geometry : angle 0.76033 / 0.36 (11768) hydrogen bonds : bond 0.03725 / 2.43 ( 286) hydrogen bonds : angle 4.46703 / 3.03 ( 822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.204 Fit side-chains REVERT: A 258 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7536 (mt) REVERT: A 425 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8243 (tt) REVERT: D 425 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8243 (tt) outliers start: 34 outliers final: 24 residues processed: 124 average time/residue: 0.0601 time to fit residues: 11.1376 Evaluate side-chains 125 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101321 restraints weight = 12825.823| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.68 r_work: 0.3138 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8694 Z= 0.104 Angle : 0.615 8.850 11768 Z= 0.290 Chirality : 0.041 0.132 1350 Planarity : 0.003 0.029 1432 Dihedral : 10.060 69.706 1456 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.52 % Allowed : 21.26 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.24), residues: 1046 helix: -1.23 (0.22), residues: 546 sheet: -3.94 (0.49), residues: 54 loop : -2.86 (0.25), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 224 TYR 0.011 0.001 TYR A 672 PHE 0.009 0.001 PHE D 281 TRP 0.011 0.001 TRP D 492 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 8694) covalent geometry : angle 0.61466 / 0.29 (11768) hydrogen bonds : bond 0.02521 / 1.63 ( 286) hydrogen bonds : angle 3.89533 / 2.66 ( 822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.272 Fit side-chains REVERT: A 258 LEU cc_start: 0.8228 (pp) cc_final: 0.7656 (mt) REVERT: A 326 MET cc_start: 0.7947 (mmm) cc_final: 0.7536 (mmm) REVERT: A 425 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 534 PHE cc_start: 0.9099 (t80) cc_final: 0.8835 (t80) REVERT: A 563 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8329 (mp10) REVERT: D 326 MET cc_start: 0.7940 (mmm) cc_final: 0.7528 (mmm) REVERT: D 425 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8328 (tp) REVERT: D 534 PHE cc_start: 0.9099 (t80) cc_final: 0.8835 (t80) REVERT: D 563 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8319 (mp10) outliers start: 32 outliers final: 22 residues processed: 135 average time/residue: 0.0668 time to fit residues: 13.3193 Evaluate side-chains 121 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101052 restraints weight = 13058.827| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.71 r_work: 0.3131 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8694 Z= 0.113 Angle : 0.629 10.706 11768 Z= 0.291 Chirality : 0.041 0.126 1350 Planarity : 0.003 0.028 1432 Dihedral : 9.455 68.610 1456 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.85 % Allowed : 21.81 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.24), residues: 1046 helix: -1.04 (0.22), residues: 552 sheet: -3.71 (0.55), residues: 54 loop : -2.63 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 224 TYR 0.008 0.001 TYR A 307 PHE 0.011 0.001 PHE D 281 TRP 0.009 0.001 TRP D 492 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 ( 8694) covalent geometry : angle 0.62895 / 0.29 (11768) hydrogen bonds : bond 0.02523 / 1.62 ( 286) hydrogen bonds : angle 3.76920 / 2.58 ( 822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.253 Fit side-chains REVERT: A 179 MET cc_start: 0.9006 (mmm) cc_final: 0.8770 (mmm) REVERT: A 258 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7619 (mt) REVERT: A 326 MET cc_start: 0.7998 (mmm) cc_final: 0.7608 (mmm) REVERT: A 425 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8345 (tp) REVERT: A 534 PHE cc_start: 0.9145 (t80) cc_final: 0.8903 (t80) REVERT: A 563 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8251 (mp10) REVERT: D 179 MET cc_start: 0.9007 (mmm) cc_final: 0.8773 (mmm) REVERT: D 326 MET cc_start: 0.7988 (mmm) cc_final: 0.7599 (mmm) REVERT: D 425 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8345 (tp) REVERT: D 534 PHE cc_start: 0.9140 (t80) cc_final: 0.8899 (t80) REVERT: D 563 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8240 (mp10) outliers start: 35 outliers final: 20 residues processed: 125 average time/residue: 0.0718 time to fit residues: 12.8037 Evaluate side-chains 120 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.095077 restraints weight = 13008.096| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.70 r_work: 0.3019 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 8694 Z= 0.327 Angle : 0.808 10.212 11768 Z= 0.384 Chirality : 0.049 0.175 1350 Planarity : 0.004 0.036 1432 Dihedral : 10.206 88.339 1456 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.41 % Allowed : 20.93 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.23), residues: 1046 helix: -1.49 (0.21), residues: 556 sheet: -3.73 (0.49), residues: 64 loop : -2.81 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 486 TYR 0.015 0.002 TYR D 672 PHE 0.015 0.002 PHE A 457 TRP 0.006 0.001 TRP D 523 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00804 / 0.33 ( 8694) covalent geometry : angle 0.80821 / 0.38 (11768) hydrogen bonds : bond 0.03833 / 2.51 ( 286) hydrogen bonds : angle 4.49130 / 3.03 ( 822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.287 Fit side-chains REVERT: A 425 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 534 PHE cc_start: 0.9187 (t80) cc_final: 0.8945 (t80) REVERT: A 563 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8339 (mp10) REVERT: D 425 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8240 (tt) REVERT: D 534 PHE cc_start: 0.9192 (t80) cc_final: 0.8952 (t80) REVERT: D 563 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8338 (mp10) outliers start: 40 outliers final: 28 residues processed: 131 average time/residue: 0.0727 time to fit residues: 13.9891 Evaluate side-chains 130 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 68 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101963 restraints weight = 12762.089| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.68 r_work: 0.3134 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8694 Z= 0.105 Angle : 0.656 10.339 11768 Z= 0.299 Chirality : 0.041 0.131 1350 Planarity : 0.003 0.029 1432 Dihedral : 8.848 80.987 1456 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.86 % Allowed : 21.59 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.24), residues: 1046 helix: -0.91 (0.22), residues: 548 sheet: -3.58 (0.58), residues: 54 loop : -2.69 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 418 TYR 0.012 0.001 TYR A 672 PHE 0.011 0.001 PHE A 281 TRP 0.007 0.001 TRP D 492 HIS 0.002 0.000 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.10 ( 8694) covalent geometry : angle 0.65613 / 0.30 (11768) hydrogen bonds : bond 0.02458 / 1.60 ( 286) hydrogen bonds : angle 3.81737 / 2.61 ( 822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.326 Fit side-chains REVERT: A 178 MET cc_start: 0.8928 (mmm) cc_final: 0.8518 (mmm) REVERT: A 326 MET cc_start: 0.7844 (mmm) cc_final: 0.7489 (mmm) REVERT: A 425 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8301 (tp) REVERT: A 563 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8358 (mp10) REVERT: D 178 MET cc_start: 0.8943 (mmm) cc_final: 0.8536 (mmm) REVERT: D 258 LEU cc_start: 0.8348 (pp) cc_final: 0.7655 (mt) REVERT: D 326 MET cc_start: 0.7846 (mmm) cc_final: 0.7491 (mmm) REVERT: D 425 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8304 (tp) REVERT: D 563 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8350 (mp10) outliers start: 26 outliers final: 20 residues processed: 121 average time/residue: 0.0769 time to fit residues: 13.5622 Evaluate side-chains 125 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 83 optimal weight: 3.9990 chunk 86 optimal weight: 0.0010 chunk 90 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099128 restraints weight = 12963.331| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.68 r_work: 0.3096 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8694 Z= 0.166 Angle : 0.689 10.223 11768 Z= 0.316 Chirality : 0.043 0.129 1350 Planarity : 0.003 0.030 1432 Dihedral : 8.846 72.594 1456 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.08 % Allowed : 21.70 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.24), residues: 1046 helix: -0.95 (0.22), residues: 556 sheet: -3.27 (0.56), residues: 64 loop : -2.59 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 418 TYR 0.008 0.001 TYR A 667 PHE 0.011 0.001 PHE A 281 TRP 0.006 0.001 TRP A 523 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 8694) covalent geometry : angle 0.68946 / 0.32 (11768) hydrogen bonds : bond 0.02873 / 1.87 ( 286) hydrogen bonds : angle 3.94603 / 2.69 ( 822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.238 Fit side-chains REVERT: A 326 MET cc_start: 0.8073 (mmm) cc_final: 0.7712 (mmm) REVERT: A 425 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8336 (tp) REVERT: A 563 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8355 (mp10) REVERT: D 326 MET cc_start: 0.8064 (mmm) cc_final: 0.7704 (mmm) REVERT: D 425 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8334 (tp) REVERT: D 563 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8351 (mp10) outliers start: 28 outliers final: 22 residues processed: 116 average time/residue: 0.0693 time to fit residues: 11.7227 Evaluate side-chains 122 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.0030 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101927 restraints weight = 12704.473| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.70 r_work: 0.3132 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8694 Z= 0.109 Angle : 0.638 10.178 11768 Z= 0.292 Chirality : 0.041 0.130 1350 Planarity : 0.003 0.028 1432 Dihedral : 8.415 70.930 1456 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.64 % Allowed : 22.25 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.24), residues: 1046 helix: -0.76 (0.22), residues: 566 sheet: -3.36 (0.62), residues: 54 loop : -2.57 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 224 TYR 0.014 0.001 TYR A 672 PHE 0.010 0.001 PHE A 281 TRP 0.006 0.001 TRP D 492 HIS 0.002 0.000 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 8694) covalent geometry : angle 0.63832 / 0.29 (11768) hydrogen bonds : bond 0.02430 / 1.57 ( 286) hydrogen bonds : angle 3.70145 / 2.53 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1385.74 seconds wall clock time: 24 minutes 30.62 seconds (1470.62 seconds total)