Starting phenix.real_space_refine on Thu Aug 6 02:53:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsi_36621/08_2026/8jsi_36621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsi_36621/08_2026/8jsi_36621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jsi_36621/08_2026/8jsi_36621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsi_36621/08_2026/8jsi_36621.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsi_36621/08_2026/8jsi_36621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsi_36621/08_2026/8jsi_36621.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.111 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 64 5.49 5 Mg 6 5.21 5 S 26 5.16 5 C 8428 2.51 5 N 2292 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13377 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 6029 Classifications: {'peptide': 733} Link IDs: {'PTRANS': 29, 'TRANS': 703} Chain breaks: 1 Chain: "T" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 317 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "G" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 339 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "B" Number of atoms: 6029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 6029 Classifications: {'peptide': 733} Link IDs: {'PTRANS': 29, 'TRANS': 703} Chain breaks: 1 Chain: "U" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 317 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 339 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.19 Number of scatterers: 13377 At special positions: 0 Unit cell: (111.35, 89.25, 101.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 26 16.00 P 64 15.00 Mg 6 11.99 O 2560 8.00 N 2292 7.00 C 8428 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: 1.06 Conformation dependent library (CDL) restraints added in 414.5 milliseconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 38.2% alpha, 22.0% beta 26 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 94 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 202 through 218 removed outlier: 3.502A pdb=" N TYR A 217 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 232 Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.607A pdb=" N LEU A 271 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 286 through 303 Processing helix chain 'A' and resid 323 through 326 removed outlier: 3.561A pdb=" N ASP A 326 " --> pdb=" O ASP A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 326' Processing helix chain 'A' and resid 341 through 344 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.519A pdb=" N LYS A 355 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.698A pdb=" N LYS A 372 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 414 removed outlier: 3.809A pdb=" N ASN A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRP A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 448 removed outlier: 3.824A pdb=" N ILE A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 478 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 503 through 519 Processing helix chain 'A' and resid 579 through 595 removed outlier: 3.776A pdb=" N PHE A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 627 Processing helix chain 'A' and resid 693 through 704 Processing helix chain 'A' and resid 718 through 733 Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 202 through 218 removed outlier: 3.503A pdb=" N TYR B 217 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.594A pdb=" N LEU B 271 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 286 through 303 Processing helix chain 'B' and resid 323 through 326 removed outlier: 3.572A pdb=" N ASP B 326 " --> pdb=" O ASP B 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 323 through 326' Processing helix chain 'B' and resid 341 through 344 Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.518A pdb=" N LYS B 355 " --> pdb=" O THR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.698A pdb=" N LYS B 372 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 414 removed outlier: 3.809A pdb=" N ASN B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRP B 413 " --> pdb=" O SER B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 448 removed outlier: 3.823A pdb=" N ILE B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 478 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 503 through 519 Processing helix chain 'B' and resid 579 through 595 removed outlier: 3.776A pdb=" N PHE B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 627 Processing helix chain 'B' and resid 693 through 704 Processing helix chain 'B' and resid 718 through 733 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.942A pdb=" N GLU A 316 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG A 652 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU A 676 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL A 636 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU A 678 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 634 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 607 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 635 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR A 533 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU A 606 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 535 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP A 608 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE A 537 " --> pdb=" O ASP A 608 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 552 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.942A pdb=" N GLU A 316 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG A 652 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 11 Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.449A pdb=" N VAL A 47 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA A 56 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 71 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS A 25 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 69 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE A 27 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N PHE A 67 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 255 through 257 Processing sheet with id=AA6, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA7, first strand: chain 'A' and resid 421 through 429 removed outlier: 11.031A pdb=" N VAL A 379 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR A 425 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A 380 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ALA A 459 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 382 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY A 454 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLN A 484 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA A 456 " --> pdb=" O GLN A 484 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 486 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 removed outlier: 6.942A pdb=" N GLU B 316 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG B 652 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU B 676 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL B 636 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU B 678 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN B 634 " --> pdb=" O GLU B 678 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 607 " --> pdb=" O PHE B 633 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 635 " --> pdb=" O ARG B 607 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR B 533 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU B 606 " --> pdb=" O TYR B 533 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 535 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP B 608 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE B 537 " --> pdb=" O ASP B 608 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 552 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 6 removed outlier: 6.942A pdb=" N GLU B 316 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG B 652 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AB2, first strand: chain 'B' and resid 46 through 49 removed outlier: 5.449A pdb=" N VAL B 47 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA B 56 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 71 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS B 25 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE B 69 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B 27 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N PHE B 67 " --> pdb=" O PHE B 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 255 through 257 Processing sheet with id=AB4, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AB5, first strand: chain 'B' and resid 421 through 429 removed outlier: 11.031A pdb=" N VAL B 379 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TYR B 425 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B 380 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA B 459 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 382 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 454 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLN B 484 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 456 " --> pdb=" O GLN B 484 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL B 486 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE B 458 " --> pdb=" O VAL B 486 " (cutoff:3.500A) 542 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2483 1.33 - 1.45: 3505 1.45 - 1.57: 7608 1.57 - 1.69: 124 1.69 - 1.80: 52 Bond restraints: 13772 Sorted by residual: bond pdb=" C1' DC T 15 " pdb=" N1 DC T 15 " ideal model delta sigma weight residual 1.468 1.526 -0.058 1.40e-02 5.10e+03 1.70e+01 bond pdb=" C1' DC U 15 " pdb=" N1 DC U 15 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.67e+01 bond pdb=" C1' DT H 16 " pdb=" N1 DT H 16 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.16e+01 bond pdb=" C1' DT G 16 " pdb=" N1 DT G 16 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" C3' DG G 12 " pdb=" C2' DG G 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 13767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 18169 1.57 - 3.14: 623 3.14 - 4.71: 64 4.71 - 6.27: 9 6.27 - 7.84: 11 Bond angle restraints: 18876 Sorted by residual: angle pdb=" N ARG B 247 " pdb=" CA ARG B 247 " pdb=" C ARG B 247 " ideal model delta sigma weight residual 110.43 103.46 6.97 1.31e+00 5.83e-01 2.83e+01 angle pdb=" C ALA A 654 " pdb=" CA ALA A 654 " pdb=" CB ALA A 654 " ideal model delta sigma weight residual 117.23 110.75 6.48 1.36e+00 5.41e-01 2.27e+01 angle pdb=" C ALA B 654 " pdb=" CA ALA B 654 " pdb=" CB ALA B 654 " ideal model delta sigma weight residual 117.23 110.76 6.47 1.36e+00 5.41e-01 2.27e+01 angle pdb=" N3 DT G 13 " pdb=" C4 DT G 13 " pdb=" O4 DT G 13 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT U 13 " pdb=" C4 DT U 13 " pdb=" O4 DT U 13 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 18871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.54: 7609 33.54 - 67.08: 593 67.08 - 100.63: 14 100.63 - 134.17: 0 134.17 - 167.71: 4 Dihedral angle restraints: 8220 sinusoidal: 3878 harmonic: 4342 Sorted by residual: dihedral pdb=" C4' DA U 2 " pdb=" C3' DA U 2 " pdb=" O3' DA U 2 " pdb=" P DA U 3 " ideal model delta sinusoidal sigma weight residual 220.00 52.29 167.71 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA T 2 " pdb=" C3' DA T 2 " pdb=" O3' DA T 2 " pdb=" P DA T 3 " ideal model delta sinusoidal sigma weight residual 220.00 52.34 167.66 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA PHE B 556 " pdb=" C PHE B 556 " pdb=" N ASP B 557 " pdb=" CA ASP B 557 " ideal model delta harmonic sigma weight residual -180.00 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 8217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1477 0.041 - 0.083: 433 0.083 - 0.124: 213 0.124 - 0.166: 17 0.166 - 0.207: 2 Chirality restraints: 2142 Sorted by residual: chirality pdb=" C3' DA T 2 " pdb=" C4' DA T 2 " pdb=" O3' DA T 2 " pdb=" C2' DA T 2 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' DA U 2 " pdb=" C4' DA U 2 " pdb=" O3' DA U 2 " pdb=" C2' DA U 2 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL A 568 " pdb=" CA VAL A 568 " pdb=" CG1 VAL A 568 " pdb=" CG2 VAL A 568 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 2139 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 566 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 567 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 567 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 567 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 566 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO A 567 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 567 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 567 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 638 " 0.191 9.50e-02 1.11e+02 8.59e-02 4.79e+00 pdb=" NE ARG B 638 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 638 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 638 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 638 " 0.004 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 63 2.46 - 3.07: 8085 3.07 - 3.68: 18959 3.68 - 4.29: 29630 4.29 - 4.90: 50150 Nonbonded interactions: 106887 Sorted by model distance: nonbonded pdb=" OP1 DT U 6 " pdb="MG MG B 801 " model vdw 1.846 2.170 nonbonded pdb=" OD2 ASP A 538 " pdb="MG MG A 802 " model vdw 1.858 2.170 nonbonded pdb=" OP1 DT T 6 " pdb="MG MG A 802 " model vdw 1.924 2.170 nonbonded pdb=" ND1 HIS B 546 " pdb="ZN ZN A 801 " model vdw 1.935 2.310 nonbonded pdb=" ND1 HIS A 546 " pdb="ZN ZN A 801 " model vdw 1.936 2.310 ... (remaining 106882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 736) selection = (chain 'B' and resid 1 through 736) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'T' selection = chain 'U' } 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: 0.850 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.180 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.004 0.058 13772 Z= 0.307 Angle : 0.645 7.842 18876 Z= 0.449 Chirality : 0.047 0.207 2142 Planarity : 0.005 0.086 2156 Dihedral : 20.291 167.708 5408 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.81 % Allowed : 31.19 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.22), residues: 1458 helix: 0.71 (0.23), residues: 518 sheet: 0.43 (0.27), residues: 334 loop : -2.00 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 638 TYR 0.010 0.001 TYR A 723 PHE 0.018 0.002 PHE A 529 TRP 0.018 0.001 TRP B 735 HIS 0.009 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.31 (13772) covalent geometry : angle 0.64546 / 0.45 (18876) hydrogen bonds : bond 0.14405 / 9.08 ( 580) hydrogen bonds : angle 5.82042 / 4.06 ( 1626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.444 Fit side-chains REVERT: A 169 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7167 (ttm-80) REVERT: A 348 THR cc_start: 0.7942 (p) cc_final: 0.7631 (t) REVERT: A 349 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7424 (mtp85) REVERT: A 574 MET cc_start: 0.8012 (ttm) cc_final: 0.7635 (ttt) REVERT: B 169 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7166 (ttm-80) REVERT: B 348 THR cc_start: 0.7971 (p) cc_final: 0.7651 (t) REVERT: B 574 MET cc_start: 0.7992 (ttm) cc_final: 0.7593 (ttt) outliers start: 11 outliers final: 5 residues processed: 164 average time/residue: 0.5333 time to fit residues: 95.5388 Evaluate side-chains 141 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 562 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 10.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN A 267 ASN A 639 HIS A 662 HIS B 639 HIS B 662 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.160179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130595 restraints weight = 15792.422| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.98 r_work: 0.3413 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13772 Z= 0.166 Angle : 0.628 16.254 18876 Z= 0.340 Chirality : 0.048 0.448 2142 Planarity : 0.005 0.054 2156 Dihedral : 17.104 172.295 2318 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.47 % Allowed : 28.54 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1458 helix: 1.18 (0.23), residues: 528 sheet: 0.53 (0.27), residues: 354 loop : -1.84 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 563 TYR 0.014 0.001 TYR A 650 PHE 0.013 0.001 PHE A 227 TRP 0.012 0.001 TRP B 735 HIS 0.007 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (13772) covalent geometry : angle 0.62758 / 0.34 (18876) hydrogen bonds : bond 0.04895 / 3.18 ( 580) hydrogen bonds : angle 4.55661 / 3.17 ( 1626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ARG cc_start: 0.7946 (ttm110) cc_final: 0.7437 (ttm-80) REVERT: A 348 THR cc_start: 0.7887 (p) cc_final: 0.7401 (t) REVERT: A 413 TRP cc_start: 0.6645 (m100) cc_final: 0.6177 (m100) REVERT: A 452 GLU cc_start: 0.7875 (tp30) cc_final: 0.7239 (tp30) REVERT: A 543 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6592 (tptp) REVERT: A 574 MET cc_start: 0.8131 (ttm) cc_final: 0.7597 (ttt) REVERT: B 169 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7514 (ttm-80) REVERT: B 348 THR cc_start: 0.7946 (p) cc_final: 0.7456 (t) REVERT: B 413 TRP cc_start: 0.6621 (m100) cc_final: 0.6137 (m100) REVERT: B 452 GLU cc_start: 0.7884 (tp30) cc_final: 0.7183 (tp30) REVERT: B 574 MET cc_start: 0.8119 (ttm) cc_final: 0.7575 (ttt) outliers start: 47 outliers final: 17 residues processed: 182 average time/residue: 0.4896 time to fit residues: 98.6309 Evaluate side-chains 142 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 728 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 7 optimal weight: 0.0570 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 1.6902 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.159768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130547 restraints weight = 15956.207| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.97 r_work: 0.3408 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13772 Z= 0.154 Angle : 0.642 16.752 18876 Z= 0.334 Chirality : 0.048 0.423 2142 Planarity : 0.005 0.052 2156 Dihedral : 17.036 170.784 2316 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.73 % Allowed : 29.06 % Favored : 68.22 % 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: 0.09 (0.22), residues: 1458 helix: 1.40 (0.23), residues: 526 sheet: 0.67 (0.28), residues: 354 loop : -1.65 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 729 TYR 0.012 0.001 TYR A 650 PHE 0.018 0.001 PHE B 591 TRP 0.012 0.001 TRP A 735 HIS 0.005 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (13772) covalent geometry : angle 0.64237 / 0.33 (18876) hydrogen bonds : bond 0.04594 / 3.00 ( 580) hydrogen bonds : angle 4.36168 / 3.04 ( 1626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.440 Fit side-chains REVERT: A 169 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7630 (ttm-80) REVERT: A 413 TRP cc_start: 0.6623 (m100) cc_final: 0.6198 (m100) REVERT: A 452 GLU cc_start: 0.7888 (tp30) cc_final: 0.7185 (tp30) REVERT: A 563 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7183 (ptp90) REVERT: A 574 MET cc_start: 0.8061 (ttm) cc_final: 0.7522 (ttt) REVERT: A 594 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6823 (t80) REVERT: B 169 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7530 (ttm-80) REVERT: B 316 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: B 413 TRP cc_start: 0.6627 (m100) cc_final: 0.6138 (m100) REVERT: B 563 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7199 (ptm160) REVERT: B 574 MET cc_start: 0.8081 (ttm) cc_final: 0.7536 (ttt) REVERT: B 594 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6864 (t80) outliers start: 37 outliers final: 17 residues processed: 174 average time/residue: 0.4778 time to fit residues: 92.2008 Evaluate side-chains 147 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.152185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124773 restraints weight = 16029.155| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.21 r_work: 0.3301 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 13772 Z= 0.283 Angle : 0.783 17.129 18876 Z= 0.401 Chirality : 0.054 0.521 2142 Planarity : 0.006 0.063 2156 Dihedral : 16.987 169.472 2314 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.98 % Allowed : 29.57 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.22), residues: 1458 helix: 1.21 (0.23), residues: 530 sheet: 0.59 (0.27), residues: 352 loop : -1.75 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 729 TYR 0.013 0.002 TYR B 650 PHE 0.023 0.002 PHE B 556 TRP 0.011 0.002 TRP A 735 HIS 0.008 0.002 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.28 (13772) covalent geometry : angle 0.78311 / 0.40 (18876) hydrogen bonds : bond 0.06424 / 4.13 ( 580) hydrogen bonds : angle 4.52909 / 3.16 ( 1626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 0.451 Fit side-chains REVERT: A 205 ASP cc_start: 0.8715 (m-30) cc_final: 0.8493 (m-30) REVERT: A 247 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7237 (mpt90) REVERT: A 376 LYS cc_start: 0.7287 (mttp) cc_final: 0.6988 (mtmt) REVERT: A 413 TRP cc_start: 0.6642 (m100) cc_final: 0.6300 (m100) REVERT: A 452 GLU cc_start: 0.7938 (tp30) cc_final: 0.7159 (tp30) REVERT: A 455 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7487 (tp) REVERT: A 563 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7035 (ptp-170) REVERT: A 574 MET cc_start: 0.8144 (ttm) cc_final: 0.7549 (ttt) REVERT: A 593 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7600 (ptpt) REVERT: A 599 GLU cc_start: 0.8462 (tt0) cc_final: 0.8171 (tt0) REVERT: B 247 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7173 (mpt90) REVERT: B 376 LYS cc_start: 0.7343 (mttp) cc_final: 0.7035 (mtmt) REVERT: B 413 TRP cc_start: 0.6639 (m100) cc_final: 0.6241 (m100) REVERT: B 452 GLU cc_start: 0.7834 (tp30) cc_final: 0.7139 (tp30) REVERT: B 455 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7470 (tp) REVERT: B 574 MET cc_start: 0.8159 (ttm) cc_final: 0.7557 (ttt) REVERT: B 593 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7569 (ptpt) REVERT: B 594 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6922 (t80) REVERT: B 599 GLU cc_start: 0.8469 (tt0) cc_final: 0.8209 (tt0) outliers start: 54 outliers final: 24 residues processed: 178 average time/residue: 0.4756 time to fit residues: 93.8126 Evaluate side-chains 158 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 728 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.157345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127964 restraints weight = 15901.686| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.01 r_work: 0.3379 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13772 Z= 0.134 Angle : 0.643 16.793 18876 Z= 0.334 Chirality : 0.048 0.403 2142 Planarity : 0.005 0.059 2156 Dihedral : 17.039 170.586 2312 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.10 % Allowed : 30.38 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.23), residues: 1458 helix: 1.46 (0.23), residues: 534 sheet: 0.82 (0.28), residues: 344 loop : -1.58 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 729 TYR 0.011 0.001 TYR A 650 PHE 0.022 0.001 PHE B 556 TRP 0.012 0.001 TRP A 735 HIS 0.007 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (13772) covalent geometry : angle 0.64263 / 0.33 (18876) hydrogen bonds : bond 0.04475 / 2.98 ( 580) hydrogen bonds : angle 4.32398 / 3.02 ( 1626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.374 Fit side-chains REVERT: A 316 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8061 (tp30) REVERT: A 574 MET cc_start: 0.8091 (ttm) cc_final: 0.7491 (ttt) REVERT: B 413 TRP cc_start: 0.6684 (m100) cc_final: 0.6239 (m100) REVERT: B 556 PHE cc_start: 0.7915 (t80) cc_final: 0.7700 (t80) REVERT: B 574 MET cc_start: 0.8115 (ttm) cc_final: 0.7510 (ttt) REVERT: B 594 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6917 (t80) outliers start: 42 outliers final: 12 residues processed: 171 average time/residue: 0.4932 time to fit residues: 92.7329 Evaluate side-chains 135 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 728 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 93 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.156078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127089 restraints weight = 15861.619| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.94 r_work: 0.3348 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13772 Z= 0.168 Angle : 0.666 16.772 18876 Z= 0.342 Chirality : 0.049 0.447 2142 Planarity : 0.005 0.058 2156 Dihedral : 16.907 170.431 2304 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.17 % Allowed : 30.68 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.23), residues: 1458 helix: 1.51 (0.23), residues: 532 sheet: 0.89 (0.28), residues: 344 loop : -1.57 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 501 TYR 0.012 0.001 TYR A 650 PHE 0.026 0.001 PHE B 591 TRP 0.012 0.001 TRP A 735 HIS 0.007 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (13772) covalent geometry : angle 0.66616 / 0.34 (18876) hydrogen bonds : bond 0.04730 / 3.08 ( 580) hydrogen bonds : angle 4.27266 / 2.98 ( 1626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.498 Fit side-chains REVERT: A 350 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7178 (pp) REVERT: A 376 LYS cc_start: 0.7229 (mttp) cc_final: 0.6927 (mtmt) REVERT: A 549 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.5949 (mt) REVERT: A 574 MET cc_start: 0.8104 (ttm) cc_final: 0.7456 (ttt) REVERT: B 350 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7191 (pp) REVERT: B 376 LYS cc_start: 0.7252 (mttp) cc_final: 0.6946 (mtmt) REVERT: B 413 TRP cc_start: 0.6545 (m100) cc_final: 0.6139 (m100) REVERT: B 543 LYS cc_start: 0.6958 (ttpt) cc_final: 0.6558 (tptp) REVERT: B 563 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7260 (ptp-170) REVERT: B 574 MET cc_start: 0.8142 (ttm) cc_final: 0.7490 (ttt) REVERT: B 594 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6889 (t80) outliers start: 43 outliers final: 19 residues processed: 173 average time/residue: 0.4701 time to fit residues: 90.4201 Evaluate side-chains 149 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 728 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 0.0970 chunk 64 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.156358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127389 restraints weight = 15933.393| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.94 r_work: 0.3366 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13772 Z= 0.161 Angle : 0.658 17.161 18876 Z= 0.338 Chirality : 0.048 0.433 2142 Planarity : 0.005 0.057 2156 Dihedral : 16.899 170.607 2304 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.24 % Allowed : 31.19 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.23), residues: 1458 helix: 1.51 (0.23), residues: 534 sheet: 0.90 (0.29), residues: 344 loop : -1.47 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 501 TYR 0.012 0.001 TYR B 650 PHE 0.028 0.001 PHE A 591 TRP 0.015 0.001 TRP A 735 HIS 0.008 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (13772) covalent geometry : angle 0.65768 / 0.34 (18876) hydrogen bonds : bond 0.04549 / 2.98 ( 580) hydrogen bonds : angle 4.24733 / 2.96 ( 1626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.499 Fit side-chains REVERT: A 350 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7204 (pp) REVERT: A 376 LYS cc_start: 0.7310 (mttp) cc_final: 0.7004 (mtmt) REVERT: A 549 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6006 (mt) REVERT: A 574 MET cc_start: 0.8115 (ttm) cc_final: 0.7460 (ttt) REVERT: B 350 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7176 (pp) REVERT: B 376 LYS cc_start: 0.7329 (mttp) cc_final: 0.7014 (mtmt) REVERT: B 543 LYS cc_start: 0.6979 (ttpt) cc_final: 0.6613 (tptp) REVERT: B 549 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6053 (mt) REVERT: B 574 MET cc_start: 0.8136 (ttm) cc_final: 0.7485 (ttt) REVERT: B 594 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6894 (t80) outliers start: 44 outliers final: 24 residues processed: 168 average time/residue: 0.5524 time to fit residues: 102.2476 Evaluate side-chains 154 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 728 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.154824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126195 restraints weight = 15873.931| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.92 r_work: 0.3350 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13772 Z= 0.187 Angle : 0.680 17.089 18876 Z= 0.348 Chirality : 0.049 0.456 2142 Planarity : 0.005 0.058 2156 Dihedral : 16.880 170.496 2304 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.17 % Allowed : 31.12 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1458 helix: 1.51 (0.23), residues: 532 sheet: 0.88 (0.28), residues: 344 loop : -1.47 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 501 TYR 0.012 0.001 TYR A 650 PHE 0.017 0.001 PHE B 556 TRP 0.019 0.002 TRP A 735 HIS 0.010 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (13772) covalent geometry : angle 0.67978 / 0.35 (18876) hydrogen bonds : bond 0.04873 / 3.17 ( 580) hydrogen bonds : angle 4.28016 / 2.99 ( 1626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7265 (pp) REVERT: A 376 LYS cc_start: 0.7311 (mttp) cc_final: 0.7020 (mtmt) REVERT: A 543 LYS cc_start: 0.7043 (ttpt) cc_final: 0.6573 (tptt) REVERT: A 549 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6433 (mt) REVERT: A 574 MET cc_start: 0.8099 (ttm) cc_final: 0.7465 (ttt) REVERT: B 350 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7223 (pp) REVERT: B 376 LYS cc_start: 0.7332 (mttp) cc_final: 0.7021 (mtmt) REVERT: B 543 LYS cc_start: 0.6956 (ttpt) cc_final: 0.6496 (tptt) REVERT: B 549 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6091 (mt) REVERT: B 563 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7321 (ptp-170) REVERT: B 574 MET cc_start: 0.8167 (ttm) cc_final: 0.7512 (ttt) REVERT: B 594 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6871 (t80) outliers start: 43 outliers final: 25 residues processed: 163 average time/residue: 0.4290 time to fit residues: 77.7695 Evaluate side-chains 152 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 728 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 149 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 18 optimal weight: 0.0570 chunk 69 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.154878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126213 restraints weight = 16021.531| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.93 r_work: 0.3334 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13772 Z= 0.187 Angle : 0.684 17.063 18876 Z= 0.350 Chirality : 0.049 0.453 2142 Planarity : 0.005 0.058 2156 Dihedral : 16.922 170.487 2304 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.73 % Allowed : 31.93 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1458 helix: 1.53 (0.23), residues: 528 sheet: 0.88 (0.28), residues: 344 loop : -1.44 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 501 TYR 0.012 0.001 TYR A 650 PHE 0.022 0.001 PHE A 591 TRP 0.022 0.002 TRP A 735 HIS 0.011 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (13772) covalent geometry : angle 0.68422 / 0.35 (18876) hydrogen bonds : bond 0.04866 / 3.17 ( 580) hydrogen bonds : angle 4.30212 / 3.00 ( 1626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7247 (pp) REVERT: A 376 LYS cc_start: 0.7244 (mttp) cc_final: 0.6949 (mtmt) REVERT: A 396 LYS cc_start: 0.6812 (mtmm) cc_final: 0.6599 (mtmm) REVERT: A 549 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6427 (mt) REVERT: A 574 MET cc_start: 0.8112 (ttm) cc_final: 0.7481 (ttt) REVERT: B 350 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7239 (pp) REVERT: B 376 LYS cc_start: 0.7298 (mttp) cc_final: 0.6994 (mtmt) REVERT: B 543 LYS cc_start: 0.6957 (ttpt) cc_final: 0.6489 (tptt) REVERT: B 549 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6439 (mt) REVERT: B 574 MET cc_start: 0.8127 (ttm) cc_final: 0.7498 (ttt) REVERT: B 594 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6944 (t80) outliers start: 37 outliers final: 23 residues processed: 154 average time/residue: 0.4720 time to fit residues: 81.1175 Evaluate side-chains 149 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 66 optimal weight: 0.0010 chunk 25 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN B 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131044 restraints weight = 15855.012| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.93 r_work: 0.3426 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 13772 Z= 0.120 Angle : 0.625 16.570 18876 Z= 0.324 Chirality : 0.047 0.386 2142 Planarity : 0.004 0.055 2156 Dihedral : 17.012 171.169 2304 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.51 % Allowed : 32.15 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1458 helix: 1.66 (0.23), residues: 528 sheet: 0.95 (0.29), residues: 344 loop : -1.34 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 663 TYR 0.012 0.001 TYR A 650 PHE 0.022 0.001 PHE B 591 TRP 0.019 0.001 TRP A 735 HIS 0.014 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (13772) covalent geometry : angle 0.62512 / 0.32 (18876) hydrogen bonds : bond 0.03997 / 2.67 ( 580) hydrogen bonds : angle 4.17211 / 2.91 ( 1626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 44 HIS cc_start: 0.8256 (m-70) cc_final: 0.7604 (m90) REVERT: A 350 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7283 (pp) REVERT: A 376 LYS cc_start: 0.7237 (mttp) cc_final: 0.6959 (mtmt) REVERT: A 543 LYS cc_start: 0.7015 (ttpt) cc_final: 0.6535 (tptt) REVERT: A 574 MET cc_start: 0.8110 (ttm) cc_final: 0.7468 (ttt) REVERT: B 44 HIS cc_start: 0.8265 (m-70) cc_final: 0.7607 (m90) REVERT: B 350 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7253 (pp) REVERT: B 376 LYS cc_start: 0.7259 (mttp) cc_final: 0.7052 (mtmt) REVERT: B 543 LYS cc_start: 0.6950 (ttpt) cc_final: 0.6523 (tptt) REVERT: B 549 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.5981 (mt) REVERT: B 563 ARG cc_start: 0.7739 (ttp-110) cc_final: 0.7311 (ptp-170) REVERT: B 574 MET cc_start: 0.8186 (ttm) cc_final: 0.7519 (ttt) outliers start: 34 outliers final: 19 residues processed: 156 average time/residue: 0.4817 time to fit residues: 84.0217 Evaluate side-chains 148 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 1 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 141 optimal weight: 0.0070 chunk 101 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.157438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128729 restraints weight = 15992.493| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.93 r_work: 0.3369 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13772 Z= 0.154 Angle : 0.663 16.877 18876 Z= 0.336 Chirality : 0.048 0.430 2142 Planarity : 0.004 0.056 2156 Dihedral : 16.832 170.840 2304 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.06 % Allowed : 32.82 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1458 helix: 1.67 (0.23), residues: 524 sheet: 0.92 (0.28), residues: 344 loop : -1.31 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 501 TYR 0.012 0.001 TYR B 650 PHE 0.015 0.001 PHE B 556 TRP 0.024 0.002 TRP A 735 HIS 0.016 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (13772) covalent geometry : angle 0.66261 / 0.34 (18876) hydrogen bonds : bond 0.04321 / 2.81 ( 580) hydrogen bonds : angle 4.16752 / 2.90 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3673.57 seconds wall clock time: 63 minutes 18.20 seconds (3798.20 seconds total)