Starting phenix.real_space_refine on Sat Aug 23 15:50:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsi_36621/08_2025/8jsi_36621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsi_36621/08_2025/8jsi_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_36621/08_2025/8jsi_36621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsi_36621/08_2025/8jsi_36621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jsi_36621/08_2025/8jsi_36621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsi_36621/08_2025/8jsi_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-2.0-5787/lib/python3.9/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: 2.94, per 1000 atoms: 0.22 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: 0.82 Conformation dependent library (CDL) restraints added in 560.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.37 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: 2.24 Time building geometry restraints manager: 1.14 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=" CA ASN B 267 " pdb=" C ASN B 267 " ideal model delta sigma weight residual 1.520 1.483 0.037 1.20e-02 6.94e+03 9.33e+00 bond pdb=" CA ASN A 267 " pdb=" C ASN A 267 " ideal model delta sigma weight residual 1.520 1.483 0.037 1.20e-02 6.94e+03 9.30e+00 bond pdb=" C PHE A 416 " pdb=" N PRO A 417 " ideal model delta sigma weight residual 1.326 1.364 -0.038 1.44e-02 4.82e+03 6.84e+00 bond pdb=" CA ARG B 247 " pdb=" C ARG B 247 " ideal model delta sigma weight residual 1.527 1.493 0.034 1.34e-02 5.57e+03 6.35e+00 bond pdb=" C ARG B 247 " pdb=" N GLN B 248 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.42e-02 4.96e+03 6.15e+00 ... (remaining 13767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 18264 1.57 - 3.14: 530 3.14 - 4.71: 62 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=" CA ALA A 654 " pdb=" C ALA A 654 " pdb=" N ASN A 655 " ideal model delta sigma weight residual 119.98 116.87 3.11 8.50e-01 1.38e+00 1.33e+01 angle pdb=" N ASN A 267 " pdb=" CA ASN A 267 " pdb=" C ASN A 267 " ideal model delta sigma weight residual 108.69 102.34 6.35 1.77e+00 3.19e-01 1.29e+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 - 0.028: 1217 0.028 - 0.057: 555 0.057 - 0.085: 199 0.085 - 0.113: 122 0.113 - 0.141: 49 Chirality restraints: 2142 Sorted by residual: 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 chirality pdb=" CA ILE A 17 " pdb=" N ILE A 17 " pdb=" C ILE A 17 " pdb=" CB ILE A 17 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE B 17 " pdb=" N ILE B 17 " pdb=" C ILE B 17 " pdb=" CB ILE B 17 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 2139 not shown) Planarity restraints: 2156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 566 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 567 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 567 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 567 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 566 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO A 567 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 567 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 567 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 638 " 0.191 9.50e-02 1.11e+02 8.59e-02 4.79e+00 pdb=" NE ARG B 638 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 638 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 638 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 638 " 0.004 2.00e-02 2.50e+03 ... (remaining 2153 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 63 2.46 - 3.07: 8085 3.07 - 3.68: 18959 3.68 - 4.29: 29630 4.29 - 4.90: 50150 Nonbonded interactions: 106887 Sorted by model distance: nonbonded pdb=" OP1 DT U 6 " pdb="MG MG B 801 " model vdw 1.846 2.170 nonbonded pdb=" OD2 ASP A 538 " pdb="MG MG A 802 " model vdw 1.858 2.170 nonbonded pdb=" OP1 DT T 6 " pdb="MG MG A 802 " model vdw 1.924 2.170 nonbonded pdb=" ND1 HIS B 546 " pdb="ZN ZN A 801 " model vdw 1.935 2.310 nonbonded pdb=" ND1 HIS A 546 " pdb="ZN ZN A 801 " model vdw 1.936 2.310 ... (remaining 106882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 736) selection = (chain 'B' and resid 1 through 736) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.080 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.860 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 0.046 13772 Z= 0.188 Angle : 0.616 7.842 18876 Z= 0.364 Chirality : 0.044 0.141 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 aren 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 covalent geometry : bond 0.00352 (13772) covalent geometry : angle 0.61616 (18876) hydrogen bonds : bond 0.14405 ( 580) hydrogen bonds : angle 5.82042 ( 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 : 0.376 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: 0.5624 time to fit residues: 100.5365 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 : 0.439 ------------------------------------------------------------------------------- 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: 0.3980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 267 ASN A 639 HIS A 662 HIS B 639 HIS B 662 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126674 restraints weight = 15879.143| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.02 r_work: 0.3361 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13772 Z= 0.198 Angle : 0.629 16.706 18876 Z= 0.332 Chirality : 0.047 0.155 2142 Planarity : 0.005 0.058 2156 Dihedral : 17.292 166.936 2318 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.17 % Allowed : 29.35 % Favored : 67.48 % 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 aren not related in a simple way. whole: -0.09 (0.22), residues: 1458 helix: 1.25 (0.23), residues: 526 sheet: 0.59 (0.28), residues: 348 loop : -1.74 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 729 TYR 0.013 0.001 TYR B 650 PHE 0.019 0.002 PHE A 556 TRP 0.014 0.001 TRP A 735 HIS 0.006 0.001 HIS B 722 Details of bonding type rmsd covalent geometry : bond 0.00467 (13772) covalent geometry : angle 0.62919 (18876) hydrogen bonds : bond 0.04922 ( 580) hydrogen bonds : angle 4.43300 ( 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 196 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.414 Fit side-chains REVERT: A 169 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7616 (ttm-80) REVERT: A 247 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7235 (mpt90) REVERT: A 563 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7288 (ptp-170) REVERT: A 574 MET cc_start: 0.8098 (ttm) cc_final: 0.7575 (ttt) REVERT: B 169 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7839 (ttm110) REVERT: B 247 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7256 (mpt90) REVERT: B 413 TRP cc_start: 0.6694 (m100) cc_final: 0.6232 (m100) REVERT: B 563 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7323 (ptm160) REVERT: B 574 MET cc_start: 0.8099 (ttm) cc_final: 0.7578 (ttt) REVERT: B 594 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6836 (t80) outliers start: 43 outliers final: 11 residues processed: 185 average time/residue: 0.4803 time to fit residues: 98.0396 Evaluate side-chains 147 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 549 ILE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN B 51 GLN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127550 restraints weight = 16151.731| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.19 r_work: 0.3335 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13772 Z= 0.208 Angle : 0.673 17.253 18876 Z= 0.340 Chirality : 0.048 0.241 2142 Planarity : 0.005 0.061 2156 Dihedral : 17.371 167.052 2312 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.69 % Allowed : 29.42 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.22), residues: 1458 helix: 1.33 (0.23), residues: 528 sheet: 0.66 (0.28), residues: 348 loop : -1.66 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 729 TYR 0.013 0.001 TYR B 650 PHE 0.023 0.002 PHE A 591 TRP 0.017 0.002 TRP B 735 HIS 0.007 0.001 HIS B 722 Details of bonding type rmsd covalent geometry : bond 0.00498 (13772) covalent geometry : angle 0.67315 (18876) hydrogen bonds : bond 0.05000 ( 580) hydrogen bonds : angle 4.34281 ( 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 197 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.541 Fit side-chains REVERT: A 376 LYS cc_start: 0.7225 (mttp) cc_final: 0.6853 (mtmt) REVERT: A 543 LYS cc_start: 0.7098 (ttpt) cc_final: 0.6605 (tptt) REVERT: A 563 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7366 (ptp-170) REVERT: A 574 MET cc_start: 0.8051 (ttm) cc_final: 0.7470 (ttt) REVERT: A 599 GLU cc_start: 0.8439 (tt0) cc_final: 0.8177 (tt0) REVERT: B 376 LYS cc_start: 0.7225 (mttp) cc_final: 0.6843 (mtmt) REVERT: B 413 TRP cc_start: 0.6553 (m100) cc_final: 0.6189 (m100) REVERT: B 543 LYS cc_start: 0.7103 (ttpt) cc_final: 0.6637 (tptt) REVERT: B 563 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7305 (ptm160) REVERT: B 574 MET cc_start: 0.8047 (ttm) cc_final: 0.7464 (ttt) outliers start: 50 outliers final: 17 residues processed: 186 average time/residue: 0.5998 time to fit residues: 122.5590 Evaluate side-chains 151 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 234 VAL 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 587 MET 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 234 VAL 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 587 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 728 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121726 restraints weight = 16107.499| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.02 r_work: 0.3296 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13772 Z= 0.265 Angle : 0.727 17.520 18876 Z= 0.368 Chirality : 0.051 0.318 2142 Planarity : 0.005 0.066 2156 Dihedral : 17.143 166.110 2304 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.50 % Allowed : 30.38 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.22), residues: 1458 helix: 1.37 (0.23), residues: 524 sheet: 0.62 (0.28), residues: 346 loop : -1.67 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 501 TYR 0.012 0.002 TYR A 650 PHE 0.017 0.002 PHE B 556 TRP 0.022 0.002 TRP B 735 HIS 0.007 0.001 HIS B 722 Details of bonding type rmsd covalent geometry : bond 0.00641 (13772) covalent geometry : angle 0.72653 (18876) hydrogen bonds : bond 0.05605 ( 580) hydrogen bonds : angle 4.46018 ( 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 188 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 127 time to evaluate : 0.499 Fit side-chains REVERT: A 376 LYS cc_start: 0.7327 (mttp) cc_final: 0.7033 (mtmt) REVERT: A 549 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6708 (mt) REVERT: A 563 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7349 (ptm160) REVERT: A 574 MET cc_start: 0.8171 (ttm) cc_final: 0.7599 (ttt) REVERT: A 599 GLU cc_start: 0.8435 (tt0) cc_final: 0.8226 (tt0) REVERT: B 376 LYS cc_start: 0.7387 (mttp) cc_final: 0.7088 (mtmt) REVERT: B 413 TRP cc_start: 0.6643 (m100) cc_final: 0.6270 (m100) REVERT: B 549 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6716 (mt) REVERT: B 563 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7338 (ptm160) REVERT: B 574 MET cc_start: 0.8147 (ttm) cc_final: 0.7573 (ttt) REVERT: B 599 GLU cc_start: 0.8428 (tt0) cc_final: 0.8218 (tt0) outliers start: 61 outliers final: 24 residues processed: 169 average time/residue: 0.5630 time to fit residues: 105.2070 Evaluate side-chains 152 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 710 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 3 optimal weight: 0.0040 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 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 = 0.3838 r_free = 0.3838 target = 0.159411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129890 restraints weight = 15939.931| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.02 r_work: 0.3403 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13772 Z= 0.122 Angle : 0.603 16.678 18876 Z= 0.305 Chirality : 0.045 0.286 2142 Planarity : 0.004 0.056 2156 Dihedral : 17.153 169.020 2304 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.91 % Allowed : 30.31 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.23), residues: 1458 helix: 1.73 (0.23), residues: 524 sheet: 0.80 (0.28), residues: 342 loop : -1.36 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 501 TYR 0.011 0.001 TYR B 650 PHE 0.012 0.001 PHE B 556 TRP 0.013 0.001 TRP B 735 HIS 0.007 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00271 (13772) covalent geometry : angle 0.60263 (18876) hydrogen bonds : bond 0.03712 ( 580) hydrogen bonds : angle 4.13688 ( 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 185 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 0.502 Fit side-chains REVERT: A 316 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: A 350 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7357 (pp) REVERT: A 481 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6334 (mt) REVERT: A 528 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7433 (mmtt) REVERT: A 543 LYS cc_start: 0.7127 (ttpt) cc_final: 0.6691 (tptt) REVERT: A 563 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7402 (ptm160) REVERT: A 574 MET cc_start: 0.8085 (ttm) cc_final: 0.7493 (ttt) REVERT: B 215 GLU cc_start: 0.8127 (tt0) cc_final: 0.7703 (mt-10) REVERT: B 316 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: B 350 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7368 (pp) REVERT: B 481 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6362 (mt) REVERT: B 543 LYS cc_start: 0.7125 (ttpt) cc_final: 0.6769 (tptt) REVERT: B 556 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8420 (t80) REVERT: B 563 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7346 (ptm160) REVERT: B 574 MET cc_start: 0.8110 (ttm) cc_final: 0.7517 (ttt) outliers start: 53 outliers final: 17 residues processed: 172 average time/residue: 0.5484 time to fit residues: 104.5017 Evaluate side-chains 149 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 316 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 563 ARG 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 151 TRP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 563 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 51 GLN A 143 GLN B 44 HIS B 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.155041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125763 restraints weight = 15859.745| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.96 r_work: 0.3342 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13772 Z= 0.188 Angle : 0.659 16.739 18876 Z= 0.332 Chirality : 0.048 0.303 2142 Planarity : 0.005 0.054 2156 Dihedral : 17.007 167.510 2304 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.35 % Allowed : 30.31 % 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 aren not related in a simple way. whole: 0.45 (0.23), residues: 1458 helix: 1.66 (0.24), residues: 524 sheet: 0.85 (0.28), residues: 340 loop : -1.33 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 680 TYR 0.012 0.001 TYR B 650 PHE 0.015 0.001 PHE B 556 TRP 0.020 0.002 TRP B 735 HIS 0.008 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00448 (13772) covalent geometry : angle 0.65909 (18876) hydrogen bonds : bond 0.04603 ( 580) hydrogen bonds : angle 4.22547 ( 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 186 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 127 time to evaluate : 0.467 Fit side-chains REVERT: A 215 GLU cc_start: 0.8141 (tt0) cc_final: 0.7635 (mt-10) REVERT: A 229 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8231 (tptm) REVERT: A 349 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7368 (ttm110) REVERT: A 350 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7351 (pp) REVERT: A 543 LYS cc_start: 0.7032 (ttpt) cc_final: 0.6608 (tptt) REVERT: A 549 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6157 (mt) REVERT: A 563 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7390 (ptm160) REVERT: A 574 MET cc_start: 0.8105 (ttm) cc_final: 0.7511 (ttt) REVERT: B 215 GLU cc_start: 0.8144 (tt0) cc_final: 0.7675 (mt-10) REVERT: B 349 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7300 (ttm110) REVERT: B 350 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7336 (pp) REVERT: B 481 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6529 (mt) REVERT: B 543 LYS cc_start: 0.7062 (ttpt) cc_final: 0.6656 (tptt) REVERT: B 549 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6108 (mt) REVERT: B 563 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7332 (ptm160) REVERT: B 574 MET cc_start: 0.8100 (ttm) cc_final: 0.7508 (ttt) outliers start: 59 outliers final: 25 residues processed: 170 average time/residue: 0.5960 time to fit residues: 112.0242 Evaluate side-chains 158 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 563 ARG 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 16 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 563 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 32 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123413 restraints weight = 15996.252| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.03 r_work: 0.3312 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13772 Z= 0.233 Angle : 0.699 16.819 18876 Z= 0.354 Chirality : 0.050 0.311 2142 Planarity : 0.005 0.059 2156 Dihedral : 17.084 166.549 2304 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.13 % Allowed : 30.60 % 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 aren not related in a simple way. whole: 0.33 (0.23), residues: 1458 helix: 1.56 (0.24), residues: 520 sheet: 0.86 (0.29), residues: 344 loop : -1.43 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 501 TYR 0.012 0.001 TYR B 650 PHE 0.017 0.002 PHE B 556 TRP 0.029 0.002 TRP A 735 HIS 0.008 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00561 (13772) covalent geometry : angle 0.69882 (18876) hydrogen bonds : bond 0.05161 ( 580) hydrogen bonds : angle 4.38275 ( 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 186 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 0.557 Fit side-chains REVERT: A 215 GLU cc_start: 0.8146 (tt0) cc_final: 0.7698 (mt-10) REVERT: A 350 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7419 (pp) REVERT: A 471 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: A 549 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6767 (mt) REVERT: A 563 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7378 (ptm160) REVERT: A 574 MET cc_start: 0.8228 (ttm) cc_final: 0.7634 (ttt) REVERT: B 215 GLU cc_start: 0.8163 (tt0) cc_final: 0.7760 (mt-10) REVERT: B 350 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7342 (pp) REVERT: B 471 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: B 543 LYS cc_start: 0.7021 (ttpt) cc_final: 0.6576 (tptt) REVERT: B 549 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6742 (mt) REVERT: B 563 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7246 (ptp-170) REVERT: B 574 MET cc_start: 0.8202 (ttm) cc_final: 0.7605 (ttt) outliers start: 56 outliers final: 25 residues processed: 172 average time/residue: 0.5551 time to fit residues: 106.0240 Evaluate side-chains 153 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 471 GLU 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 556 PHE 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 16 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 528 LYS 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: 4.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.156860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127984 restraints weight = 15764.665| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.95 r_work: 0.3368 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13772 Z= 0.161 Angle : 0.644 16.741 18876 Z= 0.326 Chirality : 0.047 0.288 2142 Planarity : 0.005 0.057 2156 Dihedral : 17.058 167.981 2304 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.32 % Allowed : 31.34 % 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 aren not related in a simple way. whole: 0.51 (0.23), residues: 1458 helix: 1.71 (0.24), residues: 518 sheet: 0.93 (0.29), residues: 340 loop : -1.30 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 501 TYR 0.011 0.001 TYR B 650 PHE 0.012 0.001 PHE A 591 TRP 0.024 0.002 TRP A 735 HIS 0.010 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00379 (13772) covalent geometry : angle 0.64415 (18876) hydrogen bonds : bond 0.04231 ( 580) hydrogen bonds : angle 4.24730 ( 1626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 0.518 Fit side-chains REVERT: A 215 GLU cc_start: 0.8065 (tt0) cc_final: 0.7607 (mt-10) REVERT: A 471 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: A 543 LYS cc_start: 0.6965 (ttpt) cc_final: 0.6578 (tptt) REVERT: A 549 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6507 (mt) REVERT: A 563 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7346 (ptm160) REVERT: A 574 MET cc_start: 0.8138 (ttm) cc_final: 0.7512 (ttt) REVERT: B 215 GLU cc_start: 0.8068 (tt0) cc_final: 0.7679 (mt-10) REVERT: B 471 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: B 543 LYS cc_start: 0.7065 (ttpt) cc_final: 0.6667 (tptt) REVERT: B 549 ILE cc_start: 0.6714 (OUTLIER) cc_final: 0.6481 (mt) REVERT: B 563 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7236 (ptp-170) REVERT: B 574 MET cc_start: 0.8116 (ttm) cc_final: 0.7486 (ttt) outliers start: 45 outliers final: 23 residues processed: 162 average time/residue: 0.5386 time to fit residues: 96.3330 Evaluate side-chains 148 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 563 ARG 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 16 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 563 ARG 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: 4.9990 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123398 restraints weight = 16023.242| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.04 r_work: 0.3315 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13772 Z= 0.234 Angle : 0.709 16.839 18876 Z= 0.360 Chirality : 0.050 0.296 2142 Planarity : 0.005 0.059 2156 Dihedral : 17.079 166.624 2304 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.02 % Allowed : 32.15 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.23), residues: 1458 helix: 1.50 (0.24), residues: 524 sheet: 0.85 (0.29), residues: 344 loop : -1.36 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 501 TYR 0.012 0.001 TYR B 650 PHE 0.018 0.002 PHE B 556 TRP 0.035 0.002 TRP B 735 HIS 0.011 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00564 (13772) covalent geometry : angle 0.70870 (18876) hydrogen bonds : bond 0.05188 ( 580) hydrogen bonds : angle 4.39211 ( 1626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.512 Fit side-chains REVERT: A 215 GLU cc_start: 0.8124 (tt0) cc_final: 0.7714 (mt-10) REVERT: A 350 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7387 (pp) REVERT: A 471 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 549 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6749 (mt) REVERT: A 563 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7337 (ptm160) REVERT: A 574 MET cc_start: 0.8235 (ttm) cc_final: 0.7650 (ttt) REVERT: B 215 GLU cc_start: 0.8100 (tt0) cc_final: 0.7725 (mt-10) REVERT: B 471 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: B 543 LYS cc_start: 0.7034 (ttpt) cc_final: 0.6591 (tptt) REVERT: B 549 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6726 (mt) REVERT: B 563 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7396 (ptm160) REVERT: B 574 MET cc_start: 0.8163 (ttm) cc_final: 0.7560 (ttt) outliers start: 41 outliers final: 25 residues processed: 151 average time/residue: 0.4915 time to fit residues: 82.6975 Evaluate side-chains 150 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 471 GLU 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 556 PHE 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 16 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 528 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 144 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 108 optimal weight: 0.0570 chunk 56 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 143 GLN B 503 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.161822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132402 restraints weight = 15799.813| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.03 r_work: 0.3432 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13772 Z= 0.117 Angle : 0.607 16.289 18876 Z= 0.306 Chirality : 0.045 0.243 2142 Planarity : 0.004 0.056 2156 Dihedral : 17.006 169.331 2304 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.84 % Allowed : 33.48 % Favored : 64.68 % 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 aren not related in a simple way. whole: 0.64 (0.23), residues: 1458 helix: 1.77 (0.24), residues: 524 sheet: 1.03 (0.29), residues: 340 loop : -1.22 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 501 TYR 0.012 0.001 TYR B 650 PHE 0.035 0.001 PHE A 591 TRP 0.016 0.002 TRP A 735 HIS 0.016 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00261 (13772) covalent geometry : angle 0.60698 (18876) hydrogen bonds : bond 0.03560 ( 580) hydrogen bonds : angle 4.11416 ( 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 163 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.532 Fit side-chains REVERT: A 215 GLU cc_start: 0.8030 (tt0) cc_final: 0.7654 (mt-10) REVERT: A 471 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: A 543 LYS cc_start: 0.6923 (ttpt) cc_final: 0.6649 (tptt) REVERT: A 574 MET cc_start: 0.8141 (ttm) cc_final: 0.7580 (ttt) REVERT: B 215 GLU cc_start: 0.8032 (tt0) cc_final: 0.7675 (mt-10) REVERT: B 349 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7511 (ttm110) REVERT: B 396 LYS cc_start: 0.6746 (mtmm) cc_final: 0.6436 (mttp) REVERT: B 543 LYS cc_start: 0.6990 (ttpt) cc_final: 0.6720 (tptt) REVERT: B 574 MET cc_start: 0.8122 (ttm) cc_final: 0.7574 (ttt) outliers start: 25 outliers final: 19 residues processed: 159 average time/residue: 0.5330 time to fit residues: 93.9956 Evaluate side-chains 145 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 556 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 16 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 234 VAL 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 1 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126991 restraints weight = 15940.820| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.03 r_work: 0.3379 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13772 Z= 0.170 Angle : 0.655 16.273 18876 Z= 0.329 Chirality : 0.047 0.252 2142 Planarity : 0.005 0.056 2156 Dihedral : 16.910 167.952 2304 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.92 % Allowed : 34.00 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.23), residues: 1458 helix: 1.66 (0.24), residues: 524 sheet: 0.96 (0.29), residues: 348 loop : -1.31 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 501 TYR 0.010 0.001 TYR B 650 PHE 0.013 0.001 PHE A 227 TRP 0.035 0.002 TRP A 735 HIS 0.018 0.001 HIS A 546 Details of bonding type rmsd covalent geometry : bond 0.00403 (13772) covalent geometry : angle 0.65473 (18876) hydrogen bonds : bond 0.04300 ( 580) hydrogen bonds : angle 4.18880 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4293.54 seconds wall clock time: 73 minutes 59.10 seconds (4439.10 seconds total)