Starting phenix.real_space_refine on Thu Jul 31 04:37:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jsi_36621/07_2025/8jsi_36621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsi_36621/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jsi_36621/07_2025/8jsi_36621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsi_36621/07_2025/8jsi_36621.map" model { file = "/net/cci-nas-00/data/ceres_data/8jsi_36621/07_2025/8jsi_36621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsi_36621/07_2025/8jsi_36621.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.111 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.78, per 1000 atoms: 0.66 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: 3.51 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 5.27 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: 5.44 Time building geometry restraints manager: 4.20 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: 0.820 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.020 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.070 ------------------------------------------------------------------------------- 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 : 8.85 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (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 TRP 0.018 0.001 TRP B 735 HIS 0.009 0.001 HIS B 546 PHE 0.018 0.002 PHE A 529 TYR 0.010 0.001 TYR A 723 ARG 0.009 0.000 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.14405 ( 580) hydrogen bonds : angle 5.82042 ( 1626) covalent geometry : bond 0.00352 (13772) covalent geometry : angle 0.61616 (18876) *********************** 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 : 1.459 Fit side-chains REVERT: A 169 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7167 (ttm-80) REVERT: A 348 THR cc_start: 0.7942 (p) cc_final: 0.7632 (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: 0.6468 (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: 0.7652 (t) REVERT: B 574 MET cc_start: 0.7992 (ttm) cc_final: 0.7599 (ttt) outliers start: 11 outliers final: 5 residues processed: 164 average time/residue: 1.4226 time to fit residues: 256.4373 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 : 1.537 ------------------------------------------------------------------------------- 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 126 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 662 HIS B 639 HIS B 662 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.154115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126820 restraints weight = 15912.805| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.24 r_work: 0.3324 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13772 Z= 0.233 Angle : 0.660 16.027 18876 Z= 0.348 Chirality : 0.048 0.162 2142 Planarity : 0.005 0.061 2156 Dihedral : 17.423 166.181 2318 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.69 % Allowed : 28.91 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1458 helix: 1.21 (0.23), residues: 524 sheet: 0.58 (0.28), residues: 348 loop : -1.78 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 735 HIS 0.007 0.001 HIS B 722 PHE 0.014 0.002 PHE B 584 TYR 0.014 0.002 TYR A 505 ARG 0.004 0.001 ARG A 729 Details of bonding type rmsd hydrogen bonds : bond 0.05482 ( 580) hydrogen bonds : angle 4.49762 ( 1626) covalent geometry : bond 0.00559 (13772) covalent geometry : angle 0.66048 (18876) *********************** 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: 50 poor density : 146 time to evaluate : 1.537 Fit side-chains REVERT: A 169 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7709 (ttm-80) REVERT: A 247 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7181 (mpt90) REVERT: A 574 MET cc_start: 0.8118 (ttm) cc_final: 0.7557 (ttt) REVERT: A 599 GLU cc_start: 0.8455 (tt0) cc_final: 0.8177 (tt0) REVERT: B 247 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7211 (mpt90) REVERT: B 413 TRP cc_start: 0.6612 (m100) cc_final: 0.6163 (m100) REVERT: B 574 MET cc_start: 0.8091 (ttm) cc_final: 0.7531 (ttt) REVERT: B 594 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6866 (t80) outliers start: 50 outliers final: 14 residues processed: 184 average time/residue: 1.3261 time to fit residues: 272.1824 Evaluate side-chains 151 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 549 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 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 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: 10.0000 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.159395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129856 restraints weight = 15914.368| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.02 r_work: 0.3417 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1463 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= 0.131 Angle : 0.603 16.943 18876 Z= 0.304 Chirality : 0.045 0.223 2142 Planarity : 0.004 0.055 2156 Dihedral : 17.350 168.464 2312 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.17 % Allowed : 28.98 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1458 helix: 1.45 (0.23), residues: 530 sheet: 0.74 (0.28), residues: 348 loop : -1.56 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 735 HIS 0.005 0.001 HIS A 546 PHE 0.019 0.001 PHE A 591 TYR 0.012 0.001 TYR B 650 ARG 0.002 0.000 ARG B 563 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 580) hydrogen bonds : angle 4.18026 ( 1626) covalent geometry : bond 0.00296 (13772) covalent geometry : angle 0.60302 (18876) *********************** 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 190 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 1.487 Fit side-chains REVERT: A 44 HIS cc_start: 0.8282 (m-70) cc_final: 0.7738 (m-70) REVERT: A 169 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7627 (ttm-80) REVERT: A 349 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7404 (ttm110) REVERT: A 376 LYS cc_start: 0.7311 (mttp) cc_final: 0.6884 (mtmt) REVERT: A 543 LYS cc_start: 0.7052 (ttpt) cc_final: 0.6659 (tptt) REVERT: A 556 PHE cc_start: 0.7965 (t80) cc_final: 0.7749 (t80) REVERT: A 563 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7371 (ptm160) REVERT: A 574 MET cc_start: 0.8051 (ttm) cc_final: 0.7548 (ttt) REVERT: A 582 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7958 (mm-30) REVERT: A 594 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6905 (t80) REVERT: B 2 LEU cc_start: 0.8722 (tt) cc_final: 0.8419 (tm) REVERT: B 44 HIS cc_start: 0.8296 (m-70) cc_final: 0.7749 (m-70) REVERT: B 169 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7640 (ttm-80) REVERT: B 376 LYS cc_start: 0.7282 (mttp) cc_final: 0.6858 (mtmt) REVERT: B 413 TRP cc_start: 0.6589 (m100) cc_final: 0.6193 (m100) REVERT: B 528 LYS cc_start: 0.7881 (mppt) cc_final: 0.7324 (mmtt) REVERT: B 543 LYS cc_start: 0.7116 (ttpt) cc_final: 0.6749 (tptt) REVERT: B 556 PHE cc_start: 0.7985 (t80) cc_final: 0.7765 (t80) REVERT: B 563 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7299 (ptp-170) REVERT: B 574 MET cc_start: 0.8078 (ttm) cc_final: 0.7571 (ttt) REVERT: B 582 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7986 (mm-30) outliers start: 43 outliers final: 10 residues processed: 184 average time/residue: 1.1692 time to fit residues: 237.4794 Evaluate side-chains 148 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 151 TRP 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 6 LEU Chi-restraints excluded: chain B residue 151 TRP 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 710 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 106 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122209 restraints weight = 15985.848| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.01 r_work: 0.3302 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 13772 Z= 0.274 Angle : 0.729 17.291 18876 Z= 0.368 Chirality : 0.051 0.225 2142 Planarity : 0.005 0.062 2156 Dihedral : 17.224 166.074 2304 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.06 % Allowed : 30.38 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1458 helix: 1.34 (0.23), residues: 530 sheet: 0.70 (0.28), residues: 346 loop : -1.64 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 735 HIS 0.007 0.001 HIS B 722 PHE 0.019 0.002 PHE B 584 TYR 0.013 0.002 TYR B 650 ARG 0.006 0.001 ARG B 501 Details of bonding type rmsd hydrogen bonds : bond 0.05669 ( 580) hydrogen bonds : angle 4.42946 ( 1626) covalent geometry : bond 0.00665 (13772) covalent geometry : angle 0.72875 (18876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 1.517 Fit side-chains REVERT: A 376 LYS cc_start: 0.7361 (mttp) cc_final: 0.7055 (mtmt) REVERT: A 549 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6272 (mt) REVERT: A 563 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7368 (ptm160) REVERT: A 574 MET cc_start: 0.8131 (ttm) cc_final: 0.7560 (ttt) REVERT: A 599 GLU cc_start: 0.8432 (tt0) cc_final: 0.8177 (tt0) REVERT: B 376 LYS cc_start: 0.7375 (mttp) cc_final: 0.7065 (mtmt) REVERT: B 413 TRP cc_start: 0.6627 (m100) cc_final: 0.6261 (m100) REVERT: B 549 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6242 (mt) REVERT: B 563 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7369 (ptm160) REVERT: B 574 MET cc_start: 0.8113 (ttm) cc_final: 0.7542 (ttt) REVERT: B 599 GLU cc_start: 0.8447 (tt0) cc_final: 0.8190 (tt0) outliers start: 55 outliers final: 20 residues processed: 171 average time/residue: 1.0720 time to fit residues: 204.2300 Evaluate side-chains 154 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 234 VAL 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 628 ILE 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 477 PHE 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 628 ILE 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 109 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.156223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127452 restraints weight = 15982.678| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.94 r_work: 0.3352 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1852 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= 0.159 Angle : 0.634 16.850 18876 Z= 0.321 Chirality : 0.046 0.186 2142 Planarity : 0.005 0.059 2156 Dihedral : 17.133 167.788 2304 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.76 % Allowed : 31.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1458 helix: 1.58 (0.23), residues: 530 sheet: 0.81 (0.28), residues: 346 loop : -1.48 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 735 HIS 0.007 0.001 HIS A 546 PHE 0.016 0.001 PHE A 556 TYR 0.011 0.001 TYR B 650 ARG 0.005 0.000 ARG B 501 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 580) hydrogen bonds : angle 4.22751 ( 1626) covalent geometry : bond 0.00370 (13772) covalent geometry : angle 0.63420 (18876) *********************** 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 190 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 1.624 Fit side-chains REVERT: A 44 HIS cc_start: 0.8319 (m-70) cc_final: 0.7581 (m90) REVERT: A 316 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: A 481 ILE cc_start: 0.6666 (OUTLIER) cc_final: 0.6411 (mt) REVERT: A 549 ILE cc_start: 0.6642 (OUTLIER) cc_final: 0.6006 (mt) REVERT: A 563 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7315 (ptp-170) REVERT: A 574 MET cc_start: 0.8039 (ttm) cc_final: 0.7441 (ttt) REVERT: A 593 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7287 (ptpt) REVERT: B 376 LYS cc_start: 0.7312 (mttp) cc_final: 0.7107 (mtmt) REVERT: B 481 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6496 (mt) REVERT: B 543 LYS cc_start: 0.7048 (ttpt) cc_final: 0.6624 (tptt) REVERT: B 549 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6013 (mt) REVERT: B 563 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7284 (ptp-170) REVERT: B 574 MET cc_start: 0.8051 (ttm) cc_final: 0.7454 (ttt) REVERT: B 593 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7243 (ptpt) outliers start: 51 outliers final: 14 residues processed: 179 average time/residue: 1.1569 time to fit residues: 230.2407 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 : 1.543 ------------------------------------------------------------------------------- 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 316 GLU Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 481 ILE 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 628 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 481 ILE 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 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 107 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** 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 = 0.3781 r_free = 0.3781 target = 0.154202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127403 restraints weight = 16140.299| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.21 r_work: 0.3331 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13772 Z= 0.199 Angle : 0.666 16.798 18876 Z= 0.338 Chirality : 0.048 0.183 2142 Planarity : 0.005 0.059 2156 Dihedral : 17.036 167.254 2304 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.76 % Allowed : 31.78 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1458 helix: 1.53 (0.23), residues: 530 sheet: 0.90 (0.28), residues: 344 loop : -1.44 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 735 HIS 0.008 0.001 HIS A 546 PHE 0.027 0.002 PHE A 591 TYR 0.012 0.001 TYR B 650 ARG 0.004 0.000 ARG B 501 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 580) hydrogen bonds : angle 4.27089 ( 1626) covalent geometry : bond 0.00476 (13772) covalent geometry : angle 0.66641 (18876) *********************** 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 185 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 2.314 Fit side-chains REVERT: A 215 GLU cc_start: 0.8160 (tt0) cc_final: 0.7634 (mt-10) REVERT: A 349 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7314 (ttm110) REVERT: A 350 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7431 (pp) REVERT: A 549 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6534 (mt) REVERT: A 563 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7317 (ptp-170) REVERT: A 574 MET cc_start: 0.8163 (ttm) cc_final: 0.7568 (ttt) REVERT: B 215 GLU cc_start: 0.8176 (tt0) cc_final: 0.7698 (mt-10) REVERT: B 349 ARG cc_start: 0.7837 (mtp85) cc_final: 0.7318 (ttm110) REVERT: B 350 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7411 (pp) REVERT: B 543 LYS cc_start: 0.7096 (ttpt) cc_final: 0.6682 (tptt) REVERT: B 549 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6536 (mt) REVERT: B 563 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7322 (ptp-170) REVERT: B 574 MET cc_start: 0.8143 (ttm) cc_final: 0.7545 (ttt) outliers start: 51 outliers final: 20 residues processed: 174 average time/residue: 1.4061 time to fit residues: 270.4440 Evaluate side-chains 151 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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 234 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 628 ILE 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 16 ILE Chi-restraints excluded: chain B residue 140 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 639 HIS ** 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 = 0.3796 r_free = 0.3796 target = 0.155763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125960 restraints weight = 15923.893| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.02 r_work: 0.3337 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1997 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= 0.173 Angle : 0.639 16.631 18876 Z= 0.325 Chirality : 0.047 0.173 2142 Planarity : 0.005 0.057 2156 Dihedral : 17.048 167.745 2304 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.24 % Allowed : 32.30 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.23), residues: 1458 helix: 1.60 (0.23), residues: 526 sheet: 0.97 (0.29), residues: 344 loop : -1.43 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 735 HIS 0.009 0.001 HIS B 546 PHE 0.015 0.001 PHE A 556 TYR 0.011 0.001 TYR B 650 ARG 0.003 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 580) hydrogen bonds : angle 4.22574 ( 1626) covalent geometry : bond 0.00409 (13772) covalent geometry : angle 0.63923 (18876) *********************** 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 170 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 1.548 Fit side-chains REVERT: A 44 HIS cc_start: 0.8384 (m-70) cc_final: 0.8146 (m-70) REVERT: A 215 GLU cc_start: 0.8112 (tt0) cc_final: 0.7684 (mt-10) REVERT: A 350 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7405 (pp) REVERT: A 543 LYS cc_start: 0.7056 (ttpt) cc_final: 0.6619 (tptt) REVERT: A 549 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6529 (mt) REVERT: A 563 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7455 (ptm160) REVERT: A 574 MET cc_start: 0.8129 (ttm) cc_final: 0.7543 (ttt) REVERT: A 599 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: B 215 GLU cc_start: 0.8151 (tt0) cc_final: 0.7753 (mt-10) REVERT: B 350 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7365 (pp) REVERT: B 543 LYS cc_start: 0.7064 (ttpt) cc_final: 0.6699 (tptt) REVERT: B 549 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6558 (mt) REVERT: B 563 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7448 (ptm160) REVERT: B 574 MET cc_start: 0.8126 (ttm) cc_final: 0.7535 (ttt) outliers start: 44 outliers final: 23 residues processed: 158 average time/residue: 1.1740 time to fit residues: 207.9620 Evaluate side-chains 152 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.767 ------------------------------------------------------------------------------- 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 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 563 ARG Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 628 ILE 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 234 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 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 72 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 0.0050 chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 115 optimal weight: 0.0370 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126104 restraints weight = 16037.031| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.03 r_work: 0.3358 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2047 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= 0.171 Angle : 0.645 16.455 18876 Z= 0.328 Chirality : 0.047 0.176 2142 Planarity : 0.005 0.056 2156 Dihedral : 17.009 167.764 2304 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.54 % Allowed : 31.93 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1458 helix: 1.60 (0.24), residues: 524 sheet: 0.99 (0.29), residues: 344 loop : -1.36 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 735 HIS 0.010 0.001 HIS B 546 PHE 0.015 0.001 PHE A 556 TYR 0.011 0.001 TYR B 650 ARG 0.003 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 580) hydrogen bonds : angle 4.23981 ( 1626) covalent geometry : bond 0.00405 (13772) covalent geometry : angle 0.64490 (18876) *********************** 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 181 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 1.523 Fit side-chains REVERT: A 44 HIS cc_start: 0.8390 (m-70) cc_final: 0.7672 (m90) REVERT: A 215 GLU cc_start: 0.8096 (tt0) cc_final: 0.7728 (mt-10) REVERT: A 349 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7363 (ttm110) REVERT: A 350 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7436 (pp) REVERT: A 471 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: A 501 ARG cc_start: 0.7870 (mmm-85) cc_final: 0.7646 (mmm-85) REVERT: A 543 LYS cc_start: 0.6948 (ttpt) cc_final: 0.6589 (tptt) REVERT: A 549 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6493 (mt) REVERT: A 555 MET cc_start: 0.8195 (mpp) cc_final: 0.7940 (mpp) REVERT: A 563 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7398 (ptp-170) REVERT: A 574 MET cc_start: 0.8128 (ttm) cc_final: 0.7535 (ttt) REVERT: A 599 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: B 215 GLU cc_start: 0.8070 (tt0) cc_final: 0.7693 (mt-10) REVERT: B 350 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7400 (pp) REVERT: B 471 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: B 543 LYS cc_start: 0.7091 (ttpt) cc_final: 0.6706 (tptt) REVERT: B 549 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6517 (mt) REVERT: B 563 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7368 (ptp-170) REVERT: B 574 MET cc_start: 0.8137 (ttm) cc_final: 0.7536 (ttt) outliers start: 48 outliers final: 29 residues processed: 170 average time/residue: 1.3392 time to fit residues: 251.9956 Evaluate side-chains 160 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.850 ------------------------------------------------------------------------------- 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 563 ARG Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 628 ILE 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 183 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 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 594 PHE 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 38 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 123 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** 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 = 0.3817 r_free = 0.3817 target = 0.157645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127983 restraints weight = 15828.435| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.02 r_work: 0.3376 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2070 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= 0.151 Angle : 0.624 16.522 18876 Z= 0.316 Chirality : 0.046 0.164 2142 Planarity : 0.004 0.055 2156 Dihedral : 16.984 168.309 2304 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.47 % Allowed : 32.15 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1458 helix: 1.62 (0.24), residues: 528 sheet: 1.04 (0.29), residues: 340 loop : -1.26 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 735 HIS 0.014 0.001 HIS A 546 PHE 0.012 0.001 PHE A 227 TYR 0.011 0.001 TYR B 650 ARG 0.003 0.000 ARG B 169 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 580) hydrogen bonds : angle 4.16759 ( 1626) covalent geometry : bond 0.00353 (13772) covalent geometry : angle 0.62441 (18876) *********************** 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 173 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 2.033 Fit side-chains REVERT: A 44 HIS cc_start: 0.8340 (m-70) cc_final: 0.7650 (m90) REVERT: A 215 GLU cc_start: 0.8057 (tt0) cc_final: 0.7727 (mt-10) REVERT: A 349 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7395 (ttm110) REVERT: A 501 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7630 (mmm-85) REVERT: A 543 LYS cc_start: 0.6879 (ttpt) cc_final: 0.6533 (tptt) REVERT: A 549 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6405 (mt) REVERT: A 574 MET cc_start: 0.8174 (ttm) cc_final: 0.7561 (ttt) REVERT: A 599 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: B 215 GLU cc_start: 0.8058 (tt0) cc_final: 0.7693 (mt-10) REVERT: B 543 LYS cc_start: 0.7050 (ttpt) cc_final: 0.6691 (tptt) REVERT: B 549 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6469 (mt) REVERT: B 574 MET cc_start: 0.8080 (ttm) cc_final: 0.7504 (ttt) outliers start: 47 outliers final: 26 residues processed: 162 average time/residue: 1.6370 time to fit residues: 294.7194 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 : 2.821 ------------------------------------------------------------------------------- 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 477 PHE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 599 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 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 303 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 549 ILE 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 85 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 111 optimal weight: 0.0370 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 146 optimal weight: 0.0570 chunk 127 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.160297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130516 restraints weight = 15777.676| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.01 r_work: 0.3426 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13772 Z= 0.128 Angle : 0.610 16.230 18876 Z= 0.307 Chirality : 0.045 0.161 2142 Planarity : 0.004 0.054 2156 Dihedral : 16.923 169.064 2304 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.14 % Allowed : 33.55 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1458 helix: 1.72 (0.24), residues: 526 sheet: 1.05 (0.29), residues: 344 loop : -1.28 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 735 HIS 0.018 0.001 HIS A 546 PHE 0.019 0.001 PHE B 583 TYR 0.011 0.001 TYR A 650 ARG 0.006 0.000 ARG B 729 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 580) hydrogen bonds : angle 4.09536 ( 1626) covalent geometry : bond 0.00292 (13772) covalent geometry : angle 0.61017 (18876) ********************** 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 160 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.423 Fit side-chains REVERT: A 44 HIS cc_start: 0.8277 (m-70) cc_final: 0.7590 (m90) REVERT: A 215 GLU cc_start: 0.7958 (tt0) cc_final: 0.7634 (mt-10) REVERT: A 349 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7432 (ttm110) REVERT: A 543 LYS cc_start: 0.6770 (ttpt) cc_final: 0.6481 (tptt) REVERT: A 549 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.5761 (mt) REVERT: A 574 MET cc_start: 0.8055 (ttm) cc_final: 0.7479 (ttt) REVERT: B 215 GLU cc_start: 0.7996 (tt0) cc_final: 0.7674 (mt-10) REVERT: B 229 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8306 (tptm) REVERT: B 349 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7447 (ttm110) REVERT: B 543 LYS cc_start: 0.6945 (ttpt) cc_final: 0.6642 (tptt) REVERT: B 574 MET cc_start: 0.8070 (ttm) cc_final: 0.7499 (ttt) outliers start: 29 outliers final: 21 residues processed: 155 average time/residue: 1.0503 time to fit residues: 182.3127 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 : 1.392 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 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 183 VAL Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 528 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 100 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 639 HIS B 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125580 restraints weight = 16002.332| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.03 r_work: 0.3334 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2169 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= 0.199 Angle : 0.680 16.225 18876 Z= 0.341 Chirality : 0.048 0.193 2142 Planarity : 0.005 0.056 2156 Dihedral : 16.983 167.228 2304 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.36 % Allowed : 33.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1458 helix: 1.56 (0.23), residues: 526 sheet: 0.95 (0.29), residues: 344 loop : -1.29 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 735 HIS 0.017 0.002 HIS A 546 PHE 0.025 0.001 PHE B 583 TYR 0.011 0.001 TYR B 650 ARG 0.005 0.000 ARG B 729 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 580) hydrogen bonds : angle 4.25971 ( 1626) covalent geometry : bond 0.00476 (13772) covalent geometry : angle 0.67987 (18876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9288.10 seconds wall clock time: 167 minutes 38.57 seconds (10058.57 seconds total)