Starting phenix.real_space_refine on Fri Jul 3 08:26:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsi_36621/07_2026/8jsi_36621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsi_36621/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jsi_36621/07_2026/8jsi_36621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsi_36621/07_2026/8jsi_36621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jsi_36621/07_2026/8jsi_36621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsi_36621/07_2026/8jsi_36621.map" } 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-dev-6108/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: 2.67, per 1000 atoms: 0.20 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: 0.89 Conformation dependent library (CDL) restraints added in 389.3 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: 1.25 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: 2.44 Time building geometry restraints manager: 1.13 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: 18170 1.57 - 3.14: 622 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.380 Find NCS groups from input model: 0.170 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:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.470 ------------------------------------------------------------------------------- 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= 0.305 Angle : 0.644 7.842 18876 Z= 0.447 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 0.64407 / 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 : 0.292 Fit side-chains REVERT: A 169 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7166 (ttm-80) REVERT: A 348 THR cc_start: 0.7942 (p) cc_final: 0.7632 (t) REVERT: A 349 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7423 (mtp85) REVERT: A 574 MET cc_start: 0.8012 (ttm) cc_final: 0.7633 (ttt) REVERT: A 729 ARG cc_start: 0.6978 (tpt170) cc_final: 0.6469 (mpt180) REVERT: B 169 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7165 (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: 0.7600 (ttt) outliers start: 11 outliers final: 5 residues processed: 164 average time/residue: 0.5066 time to fit residues: 90.8947 Evaluate side-chains 140 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 10.0000 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 304 ASN B 639 HIS B 662 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.160211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.130635 restraints weight = 15784.535| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.98 r_work: 0.3398 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13772 Z= 0.168 Angle : 0.621 14.963 18876 Z= 0.338 Chirality : 0.048 0.420 2142 Planarity : 0.005 0.054 2156 Dihedral : 17.130 173.734 2318 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.24 % Allowed : 28.98 % Favored : 67.77 % 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: -0.20 (0.22), residues: 1458 helix: 1.17 (0.23), residues: 528 sheet: 0.52 (0.27), residues: 354 loop : -1.85 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 563 TYR 0.014 0.001 TYR A 650 PHE 0.013 0.001 PHE A 227 TRP 0.011 0.001 TRP B 735 HIS 0.007 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (13772) covalent geometry : angle 0.62096 / 0.34 (18876) hydrogen bonds : bond 0.05044 / 3.26 ( 580) hydrogen bonds : angle 4.58429 / 3.19 ( 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 192 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7429 (ttm-80) REVERT: A 348 THR cc_start: 0.7875 (p) cc_final: 0.7390 (t) REVERT: A 413 TRP cc_start: 0.6667 (m100) cc_final: 0.6215 (m100) REVERT: A 452 GLU cc_start: 0.7887 (tp30) cc_final: 0.7252 (tp30) REVERT: A 543 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6585 (tptp) REVERT: A 574 MET cc_start: 0.8127 (ttm) cc_final: 0.7595 (ttt) REVERT: B 169 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7504 (ttm-80) REVERT: B 348 THR cc_start: 0.7931 (p) cc_final: 0.7440 (t) REVERT: B 413 TRP cc_start: 0.6627 (m100) cc_final: 0.6145 (m100) REVERT: B 452 GLU cc_start: 0.7905 (tp30) cc_final: 0.7219 (tp30) REVERT: B 574 MET cc_start: 0.8105 (ttm) cc_final: 0.7570 (ttt) outliers start: 44 outliers final: 14 residues processed: 178 average time/residue: 0.4610 time to fit residues: 90.9389 Evaluate side-chains 141 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 562 ILE Chi-restraints excluded: chain A residue 664 ILE 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 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: 1.9990 chunk 126 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.159800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130174 restraints weight = 15969.811| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.00 r_work: 0.3408 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 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 0.051 13772 Z= 0.155 Angle : 0.636 16.613 18876 Z= 0.333 Chirality : 0.048 0.394 2142 Planarity : 0.005 0.052 2156 Dihedral : 17.057 172.288 2316 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.95 % Allowed : 28.98 % Favored : 68.07 % 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: 0.07 (0.22), residues: 1458 helix: 1.40 (0.23), residues: 526 sheet: 0.67 (0.28), residues: 352 loop : -1.66 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 563 TYR 0.012 0.001 TYR A 650 PHE 0.017 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 0.00329 / 0.16 (13772) covalent geometry : angle 0.63609 / 0.33 (18876) hydrogen bonds : bond 0.04580 / 2.98 ( 580) hydrogen bonds : angle 4.34368 / 3.02 ( 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 187 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.432 Fit side-chains REVERT: A 169 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7636 (ttm-80) REVERT: A 452 GLU cc_start: 0.7860 (tp30) cc_final: 0.7172 (tp30) REVERT: A 563 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7177 (ptp90) REVERT: A 574 MET cc_start: 0.8068 (ttm) cc_final: 0.7534 (ttt) REVERT: A 594 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6815 (t80) REVERT: B 169 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7541 (ttm-80) REVERT: B 316 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: B 413 TRP cc_start: 0.6615 (m100) cc_final: 0.6128 (m100) REVERT: B 455 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7458 (tp) REVERT: B 563 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7206 (ptm160) REVERT: B 574 MET cc_start: 0.8096 (ttm) cc_final: 0.7556 (ttt) REVERT: B 594 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6870 (t80) outliers start: 40 outliers final: 19 residues processed: 181 average time/residue: 0.4608 time to fit residues: 92.1826 Evaluate side-chains 149 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 A residue 728 VAL 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 316 GLU Chi-restraints excluded: chain B residue 455 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 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: 0.3980 chunk 96 optimal weight: 4.9990 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: 10.0000 chunk 119 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.154996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125786 restraints weight = 15966.653| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.96 r_work: 0.3334 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13772 Z= 0.230 Angle : 0.712 17.228 18876 Z= 0.365 Chirality : 0.050 0.453 2142 Planarity : 0.005 0.059 2156 Dihedral : 16.984 172.402 2314 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.17 % Allowed : 29.79 % Favored : 67.04 % 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: 1.43 (0.23), residues: 524 sheet: 0.68 (0.28), residues: 352 loop : -1.65 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 563 TYR 0.014 0.002 TYR B 650 PHE 0.032 0.002 PHE B 556 TRP 0.014 0.001 TRP A 735 HIS 0.007 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (13772) covalent geometry : angle 0.71233 / 0.36 (18876) hydrogen bonds : bond 0.05457 / 3.52 ( 580) hydrogen bonds : angle 4.39156 / 3.06 ( 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 177 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.414 Fit side-chains REVERT: A 2 LEU cc_start: 0.8799 (tp) cc_final: 0.8453 (tm) REVERT: A 169 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7666 (ttm-80) REVERT: A 376 LYS cc_start: 0.7247 (mttp) cc_final: 0.6943 (mtmt) REVERT: A 452 GLU cc_start: 0.7927 (tp30) cc_final: 0.7149 (tp30) REVERT: A 455 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7439 (tp) REVERT: A 563 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7171 (ptp90) REVERT: A 574 MET cc_start: 0.8127 (ttm) cc_final: 0.7503 (ttt) REVERT: A 593 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7611 (ptpt) REVERT: A 594 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6818 (t80) REVERT: B 169 ARG cc_start: 0.8143 (ttm110) cc_final: 0.7669 (ttm-80) REVERT: B 247 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7075 (mpt90) REVERT: B 376 LYS cc_start: 0.7254 (mttp) cc_final: 0.6939 (mtmt) REVERT: B 413 TRP cc_start: 0.6623 (m100) cc_final: 0.6209 (m100) REVERT: B 455 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7441 (tp) REVERT: B 574 MET cc_start: 0.8157 (ttm) cc_final: 0.7524 (ttt) REVERT: B 591 PHE cc_start: 0.7631 (m-80) cc_final: 0.7431 (m-80) REVERT: B 593 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7472 (ptpt) REVERT: B 594 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6909 (t80) outliers start: 43 outliers final: 20 residues processed: 172 average time/residue: 0.4507 time to fit residues: 85.6878 Evaluate side-chains 150 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU 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 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 594 PHE 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 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 455 LEU Chi-restraints excluded: chain B residue 477 PHE 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: 4.9990 chunk 136 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.154560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.125490 restraints weight = 16008.834| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.96 r_work: 0.3326 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13772 Z= 0.206 Angle : 0.674 16.990 18876 Z= 0.349 Chirality : 0.049 0.433 2142 Planarity : 0.005 0.061 2156 Dihedral : 16.968 172.320 2308 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.24 % Allowed : 30.90 % Favored : 65.86 % 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: 0.11 (0.22), residues: 1458 helix: 1.39 (0.23), residues: 532 sheet: 0.71 (0.28), residues: 346 loop : -1.62 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 729 TYR 0.013 0.001 TYR A 650 PHE 0.018 0.002 PHE B 556 TRP 0.014 0.002 TRP A 735 HIS 0.006 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (13772) covalent geometry : angle 0.67413 / 0.35 (18876) hydrogen bonds : bond 0.05142 / 3.35 ( 580) hydrogen bonds : angle 4.35032 / 3.03 ( 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 179 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 LYS cc_start: 0.7245 (mttp) cc_final: 0.6874 (mtmt) REVERT: A 455 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7440 (tp) REVERT: A 563 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7141 (ptp-170) REVERT: A 574 MET cc_start: 0.8089 (ttm) cc_final: 0.7470 (ttt) REVERT: A 594 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6835 (t80) REVERT: B 316 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8052 (tp30) REVERT: B 376 LYS cc_start: 0.7272 (mttp) cc_final: 0.6875 (mtmt) REVERT: B 413 TRP cc_start: 0.6643 (m100) cc_final: 0.6260 (m100) REVERT: B 543 LYS cc_start: 0.7045 (ttpt) cc_final: 0.6630 (tptp) REVERT: B 574 MET cc_start: 0.8104 (ttm) cc_final: 0.7470 (ttt) REVERT: B 594 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6952 (t80) outliers start: 44 outliers final: 18 residues processed: 173 average time/residue: 0.4690 time to fit residues: 90.0475 Evaluate side-chains 144 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU 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 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 594 PHE 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 195 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 303 THR 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 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: 0.0970 chunk 148 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.157841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128571 restraints weight = 15870.140| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.98 r_work: 0.3400 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13772 Z= 0.134 Angle : 0.632 16.879 18876 Z= 0.326 Chirality : 0.047 0.380 2142 Planarity : 0.005 0.056 2156 Dihedral : 16.985 172.198 2304 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.10 % Allowed : 31.64 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1458 helix: 1.55 (0.23), residues: 534 sheet: 0.83 (0.28), residues: 346 loop : -1.49 (0.25), residues: 578 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 0.022 0.001 PHE B 556 TRP 0.011 0.001 TRP A 735 HIS 0.008 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (13772) covalent geometry : angle 0.63224 / 0.33 (18876) hydrogen bonds : bond 0.04229 / 2.81 ( 580) hydrogen bonds : angle 4.21828 / 2.94 ( 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: 42 poor density : 137 time to evaluate : 0.428 Fit side-chains REVERT: A 4 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8527 (mmtt) REVERT: A 42 ARG cc_start: 0.7209 (mtm110) cc_final: 0.6841 (mtp180) REVERT: A 316 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 350 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7236 (pp) REVERT: A 376 LYS cc_start: 0.7213 (mttp) cc_final: 0.6862 (mtmt) REVERT: A 455 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7465 (tp) REVERT: A 543 LYS cc_start: 0.7108 (ttpt) cc_final: 0.6664 (tptt) REVERT: A 563 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7153 (ptp-170) REVERT: A 574 MET cc_start: 0.8088 (ttm) cc_final: 0.7461 (ttt) REVERT: A 594 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6864 (t80) REVERT: B 44 HIS cc_start: 0.8244 (m-70) cc_final: 0.7711 (m-70) REVERT: B 350 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7228 (pp) REVERT: B 376 LYS cc_start: 0.7259 (mttp) cc_final: 0.6902 (mtmt) REVERT: B 455 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7459 (tp) REVERT: B 481 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6390 (mt) REVERT: B 543 LYS cc_start: 0.7018 (ttpt) cc_final: 0.6663 (tptp) REVERT: B 563 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7194 (ptp-170) REVERT: B 574 MET cc_start: 0.8100 (ttm) cc_final: 0.7465 (ttt) REVERT: B 594 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6892 (t80) outliers start: 42 outliers final: 14 residues processed: 174 average time/residue: 0.4686 time to fit residues: 90.4008 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 : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 316 GLU Chi-restraints excluded: chain A residue 350 LEU 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 594 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 481 ILE 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: 0.2980 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.3830 r_free = 0.3830 target = 0.158846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130376 restraints weight = 15938.080| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.92 r_work: 0.3403 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13772 Z= 0.127 Angle : 0.612 16.685 18876 Z= 0.317 Chirality : 0.047 0.379 2142 Planarity : 0.004 0.055 2156 Dihedral : 16.884 172.374 2304 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.47 % Allowed : 31.78 % Favored : 64.75 % 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: 0.48 (0.23), residues: 1458 helix: 1.65 (0.23), residues: 532 sheet: 0.95 (0.29), residues: 346 loop : -1.40 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 501 TYR 0.011 0.001 TYR A 650 PHE 0.015 0.001 PHE B 556 TRP 0.017 0.001 TRP B 735 HIS 0.010 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (13772) covalent geometry : angle 0.61227 / 0.32 (18876) hydrogen bonds : bond 0.03973 / 2.63 ( 580) hydrogen bonds : angle 4.11444 / 2.87 ( 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 188 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 44 HIS cc_start: 0.8222 (m-70) cc_final: 0.7679 (m-70) REVERT: A 349 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7302 (ttm110) REVERT: A 350 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7162 (pp) REVERT: A 376 LYS cc_start: 0.7214 (mttp) cc_final: 0.6870 (mtmt) REVERT: A 455 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7439 (tp) REVERT: A 528 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7209 (mmtt) REVERT: A 543 LYS cc_start: 0.6969 (ttpt) cc_final: 0.6582 (tptt) REVERT: A 563 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7104 (ptp-170) REVERT: A 574 MET cc_start: 0.8076 (ttm) cc_final: 0.7432 (ttt) REVERT: B 44 HIS cc_start: 0.8219 (m-70) cc_final: 0.7672 (m-70) REVERT: B 349 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7286 (ttm110) REVERT: B 350 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7129 (pp) REVERT: B 376 LYS cc_start: 0.7273 (mttp) cc_final: 0.6913 (mtmt) REVERT: B 455 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7450 (tp) REVERT: B 543 LYS cc_start: 0.6930 (ttpt) cc_final: 0.6546 (tptt) REVERT: B 563 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7269 (ptp-170) REVERT: B 574 MET cc_start: 0.8102 (ttm) cc_final: 0.7467 (ttt) outliers start: 47 outliers final: 20 residues processed: 181 average time/residue: 0.4049 time to fit residues: 81.7451 Evaluate side-chains 158 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 455 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 563 ARG 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 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 455 LEU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 563 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 146 optimal weight: 0.0670 chunk 72 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.155795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127198 restraints weight = 15878.606| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.92 r_work: 0.3378 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1768 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= 0.179 Angle : 0.667 16.053 18876 Z= 0.341 Chirality : 0.048 0.424 2142 Planarity : 0.005 0.057 2156 Dihedral : 16.787 172.250 2304 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.32 % Allowed : 31.78 % Favored : 64.90 % 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: 0.41 (0.23), residues: 1458 helix: 1.57 (0.23), residues: 532 sheet: 0.88 (0.28), residues: 346 loop : -1.39 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 501 TYR 0.012 0.001 TYR A 650 PHE 0.014 0.001 PHE B 556 TRP 0.022 0.002 TRP A 735 HIS 0.010 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (13772) covalent geometry : angle 0.66742 / 0.34 (18876) hydrogen bonds : bond 0.04686 / 3.05 ( 580) hydrogen bonds : angle 4.19850 / 2.93 ( 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 178 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.513 Fit side-chains REVERT: A 349 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7276 (ttm110) REVERT: A 350 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7244 (pp) REVERT: A 376 LYS cc_start: 0.7263 (mttp) cc_final: 0.6934 (mtmt) REVERT: A 455 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7444 (tp) REVERT: A 543 LYS cc_start: 0.6989 (ttpt) cc_final: 0.6594 (tptt) REVERT: A 563 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7254 (ptp-170) REVERT: A 574 MET cc_start: 0.8134 (ttm) cc_final: 0.7473 (ttt) REVERT: A 593 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7194 (ptpt) REVERT: B 42 ARG cc_start: 0.6971 (mtp-110) cc_final: 0.6574 (mtp180) REVERT: B 44 HIS cc_start: 0.8262 (m-70) cc_final: 0.7684 (m-70) REVERT: B 349 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7276 (ttm110) REVERT: B 350 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7179 (pp) REVERT: B 376 LYS cc_start: 0.7330 (mttp) cc_final: 0.7024 (mtmt) REVERT: B 455 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7450 (tp) REVERT: B 543 LYS cc_start: 0.6938 (ttpt) cc_final: 0.6548 (tptt) REVERT: B 563 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7232 (ptp-170) REVERT: B 574 MET cc_start: 0.8122 (ttm) cc_final: 0.7473 (ttt) REVERT: B 593 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7218 (ptpt) outliers start: 45 outliers final: 28 residues processed: 169 average time/residue: 0.4655 time to fit residues: 87.0122 Evaluate side-chains 162 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 455 LEU 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 563 ARG Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 641 LEU 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 1 MET 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 455 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 593 LYS Chi-restraints excluded: chain B residue 641 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 149 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.155691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127016 restraints weight = 16029.817| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.94 r_work: 0.3363 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13772 Z= 0.176 Angle : 0.662 16.062 18876 Z= 0.339 Chirality : 0.048 0.416 2142 Planarity : 0.005 0.056 2156 Dihedral : 16.862 172.113 2304 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.80 % Allowed : 31.93 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1458 helix: 1.54 (0.23), residues: 532 sheet: 0.93 (0.28), residues: 344 loop : -1.37 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 501 TYR 0.012 0.001 TYR A 650 PHE 0.017 0.001 PHE B 556 TRP 0.025 0.002 TRP A 735 HIS 0.013 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (13772) covalent geometry : angle 0.66209 / 0.34 (18876) hydrogen bonds : bond 0.04638 / 3.02 ( 580) hydrogen bonds : angle 4.22866 / 2.95 ( 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 163 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7285 (ttm110) REVERT: A 350 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7268 (pp) REVERT: A 376 LYS cc_start: 0.7220 (mttp) cc_final: 0.6941 (mtmt) REVERT: A 455 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7453 (tp) REVERT: A 543 LYS cc_start: 0.6963 (ttpt) cc_final: 0.6570 (tptp) REVERT: A 549 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6027 (mt) REVERT: A 574 MET cc_start: 0.8143 (ttm) cc_final: 0.7491 (ttt) REVERT: A 593 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7204 (ptpt) REVERT: B 350 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7252 (pp) REVERT: B 376 LYS cc_start: 0.7304 (mttp) cc_final: 0.7009 (mtmt) REVERT: B 455 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7457 (tp) REVERT: B 543 LYS cc_start: 0.6923 (ttpt) cc_final: 0.6490 (tptt) REVERT: B 549 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.5900 (mt) REVERT: B 563 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7309 (ptp-170) REVERT: B 574 MET cc_start: 0.8132 (ttm) cc_final: 0.7481 (ttt) REVERT: B 593 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7172 (ptpt) outliers start: 38 outliers final: 20 residues processed: 157 average time/residue: 0.4348 time to fit residues: 76.3259 Evaluate side-chains 149 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU 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 455 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 593 LYS Chi-restraints excluded: chain A residue 641 LEU 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 140 LEU 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 455 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 593 LYS Chi-restraints excluded: chain B residue 641 LEU 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=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: 2.9990 chunk 89 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 56 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.159809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130666 restraints weight = 15848.038| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.98 r_work: 0.3412 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13772 Z= 0.119 Angle : 0.613 15.876 18876 Z= 0.317 Chirality : 0.046 0.360 2142 Planarity : 0.004 0.054 2156 Dihedral : 16.939 172.194 2304 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.36 % Allowed : 32.30 % 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: 0.54 (0.23), residues: 1458 helix: 1.64 (0.23), residues: 532 sheet: 1.00 (0.29), residues: 344 loop : -1.30 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 501 TYR 0.012 0.001 TYR A 650 PHE 0.011 0.001 PHE B 227 TRP 0.022 0.001 TRP A 735 HIS 0.014 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (13772) covalent geometry : angle 0.61341 / 0.32 (18876) hydrogen bonds : bond 0.03869 / 2.58 ( 580) hydrogen bonds : angle 4.14068 / 2.89 ( 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 158 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 44 HIS cc_start: 0.8233 (m-70) cc_final: 0.7601 (m90) REVERT: A 350 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7253 (pp) REVERT: A 376 LYS cc_start: 0.7205 (mttp) cc_final: 0.7004 (mtmt) REVERT: A 528 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7205 (mmtt) REVERT: A 543 LYS cc_start: 0.6935 (ttpt) cc_final: 0.6433 (tptt) REVERT: A 574 MET cc_start: 0.8087 (ttm) cc_final: 0.7433 (ttt) REVERT: A 593 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7092 (ptpt) REVERT: B 44 HIS cc_start: 0.8224 (m-70) cc_final: 0.7583 (m90) REVERT: B 349 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7348 (ttm110) REVERT: B 350 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7226 (pp) REVERT: B 376 LYS cc_start: 0.7179 (mttp) cc_final: 0.6970 (mtmt) REVERT: B 543 LYS cc_start: 0.6878 (ttpt) cc_final: 0.6468 (tptt) REVERT: B 563 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7355 (ptp-170) REVERT: B 574 MET cc_start: 0.8108 (ttm) cc_final: 0.7462 (ttt) REVERT: B 593 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7054 (ptpt) outliers start: 32 outliers final: 16 residues processed: 152 average time/residue: 0.4224 time to fit residues: 71.7762 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 : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 350 LEU 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 593 LYS 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 140 LEU 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 593 LYS 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: 0.6980 chunk 105 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.156455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127731 restraints weight = 16008.485| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.94 r_work: 0.3371 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1868 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= 0.176 Angle : 0.651 15.960 18876 Z= 0.333 Chirality : 0.048 0.418 2142 Planarity : 0.005 0.055 2156 Dihedral : 16.788 172.256 2304 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.92 % Allowed : 32.67 % Favored : 65.41 % 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: 0.52 (0.23), residues: 1458 helix: 1.61 (0.23), residues: 532 sheet: 0.94 (0.28), residues: 342 loop : -1.24 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 501 TYR 0.011 0.001 TYR B 650 PHE 0.015 0.001 PHE B 556 TRP 0.028 0.002 TRP A 735 HIS 0.016 0.001 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (13772) covalent geometry : angle 0.65139 / 0.33 (18876) hydrogen bonds : bond 0.04492 / 2.91 ( 580) hydrogen bonds : angle 4.15884 / 2.90 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3617.19 seconds wall clock time: 62 minutes 27.79 seconds (3747.79 seconds total)