Starting phenix.real_space_refine on Sun Nov 17 06:44:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsi_36621/11_2024/8jsi_36621.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsi_36621/11_2024/8jsi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsi_36621/11_2024/8jsi_36621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsi_36621/11_2024/8jsi_36621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsi_36621/11_2024/8jsi_36621.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jsi_36621/11_2024/8jsi_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-5513/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: 7.97, per 1000 atoms: 0.60 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: 3.23 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: 4.75 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: 5.04 Time building geometry restraints manager: 3.75 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: 0.740 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.880 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.240 ------------------------------------------------------------------------------- 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= 0.225 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 *********************** 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 : 1.492 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: 1.2945 time to fit residues: 232.2554 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 : 1.552 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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= 0.348 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 *********************** 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 : 1.527 Fit side-chains REVERT: A 169 ARG cc_start: 0.7846 (ttm110) cc_final: 0.7470 (ttm-80) REVERT: A 247 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7395 (mpt90) REVERT: A 574 MET cc_start: 0.8044 (ttm) cc_final: 0.7559 (ttt) REVERT: A 599 GLU cc_start: 0.8206 (tt0) cc_final: 0.8004 (tt0) REVERT: B 247 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7370 (mpt90) REVERT: B 413 TRP cc_start: 0.7005 (m100) cc_final: 0.6478 (m100) REVERT: B 574 MET cc_start: 0.8019 (ttm) cc_final: 0.7553 (ttt) REVERT: B 594 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6810 (t80) outliers start: 50 outliers final: 14 residues processed: 184 average time/residue: 1.1659 time to fit residues: 237.8888 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 : 1.559 ------------------------------------------------------------------------------- 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 75 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 135 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 248 GLN B 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13772 Z= 0.465 Angle : 0.757 17.110 18876 Z= 0.383 Chirality : 0.052 0.202 2142 Planarity : 0.006 0.067 2156 Dihedral : 17.325 165.602 2312 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.35 % Allowed : 29.57 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.22), residues: 1458 helix: 1.15 (0.23), residues: 528 sheet: 0.50 (0.27), residues: 352 loop : -1.87 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 735 HIS 0.008 0.001 HIS B 722 PHE 0.023 0.002 PHE A 591 TYR 0.013 0.002 TYR B 650 ARG 0.003 0.001 ARG A 638 *********************** 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 198 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 1.671 Fit side-chains REVERT: A 376 LYS cc_start: 0.7568 (mttp) cc_final: 0.7322 (mtmt) REVERT: A 563 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7197 (ptm160) REVERT: A 574 MET cc_start: 0.8015 (ttm) cc_final: 0.7488 (ttt) REVERT: A 665 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8333 (mttp) REVERT: B 376 LYS cc_start: 0.7546 (mttp) cc_final: 0.7304 (mtmt) REVERT: B 413 TRP cc_start: 0.7030 (m100) cc_final: 0.6579 (m100) REVERT: B 563 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7157 (ptm160) REVERT: B 574 MET cc_start: 0.8056 (ttm) cc_final: 0.7546 (ttt) REVERT: B 665 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8338 (mttp) outliers start: 59 outliers final: 19 residues processed: 187 average time/residue: 1.1688 time to fit residues: 241.6696 Evaluate side-chains 153 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 665 LYS 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 153 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 665 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 B 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1847 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= 0.247 Angle : 0.648 17.183 18876 Z= 0.329 Chirality : 0.047 0.214 2142 Planarity : 0.005 0.063 2156 Dihedral : 17.175 167.612 2304 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.98 % Allowed : 30.46 % 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: 0.12 (0.23), residues: 1458 helix: 1.47 (0.23), residues: 530 sheet: 0.64 (0.28), residues: 352 loop : -1.67 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 735 HIS 0.006 0.001 HIS A 722 PHE 0.025 0.001 PHE B 591 TYR 0.011 0.001 TYR B 650 ARG 0.002 0.000 ARG A 729 *********************** 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 191 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 1.697 Fit side-chains REVERT: A 376 LYS cc_start: 0.7522 (mttp) cc_final: 0.7299 (mtmt) REVERT: A 563 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7200 (ptp-170) REVERT: A 574 MET cc_start: 0.7978 (ttm) cc_final: 0.7453 (ttt) REVERT: B 376 LYS cc_start: 0.7559 (mttp) cc_final: 0.7331 (mtmt) REVERT: B 563 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7180 (ptp-170) REVERT: B 574 MET cc_start: 0.7974 (ttm) cc_final: 0.7454 (ttt) outliers start: 54 outliers final: 20 residues processed: 182 average time/residue: 1.2461 time to fit residues: 250.0050 Evaluate side-chains 146 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 628 ILE 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 123 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 710 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2030 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= 0.374 Angle : 0.715 16.889 18876 Z= 0.361 Chirality : 0.050 0.213 2142 Planarity : 0.005 0.064 2156 Dihedral : 17.091 166.548 2304 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.50 % Allowed : 30.75 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.23), residues: 1458 helix: 1.33 (0.23), residues: 532 sheet: 0.70 (0.28), residues: 344 loop : -1.60 (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 0.029 0.002 PHE A 591 TYR 0.012 0.002 TYR A 650 ARG 0.007 0.000 ARG B 501 *********************** 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 187 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 1.684 Fit side-chains REVERT: A 376 LYS cc_start: 0.7561 (mttp) cc_final: 0.7334 (mtmt) REVERT: A 563 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7309 (ptm160) REVERT: A 574 MET cc_start: 0.8045 (ttm) cc_final: 0.7500 (ttt) REVERT: B 376 LYS cc_start: 0.7559 (mttp) cc_final: 0.7327 (mtmt) REVERT: B 563 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7300 (ptm160) REVERT: B 574 MET cc_start: 0.8042 (ttm) cc_final: 0.7504 (ttt) outliers start: 61 outliers final: 30 residues processed: 176 average time/residue: 1.2105 time to fit residues: 234.9926 Evaluate side-chains 151 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 123 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 421 ILE 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 556 PHE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 123 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 421 ILE Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 556 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13772 Z= 0.297 Angle : 0.671 16.707 18876 Z= 0.340 Chirality : 0.048 0.201 2142 Planarity : 0.005 0.061 2156 Dihedral : 17.098 167.258 2304 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.87 % Allowed : 31.27 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.23), residues: 1458 helix: 1.42 (0.23), residues: 530 sheet: 0.72 (0.29), residues: 346 loop : -1.46 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 735 HIS 0.006 0.001 HIS B 546 PHE 0.013 0.001 PHE B 584 TYR 0.011 0.001 TYR B 650 ARG 0.006 0.000 ARG B 501 *********************** 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 190 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 124 time to evaluate : 1.614 Fit side-chains REVERT: A 316 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 350 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7678 (pp) REVERT: A 481 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6788 (mt) REVERT: A 563 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7253 (ptm160) REVERT: A 574 MET cc_start: 0.8027 (ttm) cc_final: 0.7476 (ttt) REVERT: A 593 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7407 (ptpt) REVERT: A 599 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: A 695 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7120 (t0) REVERT: B 350 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7681 (pp) REVERT: B 563 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7232 (ptm160) REVERT: B 574 MET cc_start: 0.8015 (ttm) cc_final: 0.7472 (ttt) REVERT: B 593 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7384 (ptpt) REVERT: B 599 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7724 (tt0) outliers start: 66 outliers final: 28 residues processed: 179 average time/residue: 1.1082 time to fit residues: 220.7800 Evaluate side-chains 159 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 123 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 316 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 599 GLU 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 695 ASN 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 123 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 599 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 7.9990 chunk 82 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 573 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2042 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= 0.243 Angle : 0.641 16.524 18876 Z= 0.325 Chirality : 0.047 0.182 2142 Planarity : 0.005 0.058 2156 Dihedral : 17.050 168.042 2304 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.20 % Allowed : 32.23 % Favored : 63.57 % 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: 1.50 (0.24), residues: 530 sheet: 0.82 (0.29), residues: 344 loop : -1.36 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 735 HIS 0.008 0.001 HIS A 546 PHE 0.034 0.001 PHE A 591 TYR 0.011 0.001 TYR A 650 ARG 0.005 0.000 ARG B 501 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 1.568 Fit side-chains REVERT: A 316 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: A 563 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7213 (ptm160) REVERT: A 574 MET cc_start: 0.7971 (ttm) cc_final: 0.7422 (ttt) REVERT: A 695 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7102 (t0) REVERT: B 350 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7658 (pp) REVERT: B 574 MET cc_start: 0.7965 (ttm) cc_final: 0.7425 (ttt) REVERT: B 593 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7310 (ptpt) outliers start: 57 outliers final: 33 residues processed: 178 average time/residue: 1.1862 time to fit residues: 233.4824 Evaluate side-chains 161 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 123 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 316 GLU 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 556 PHE Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 594 PHE 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 695 ASN 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 123 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 593 LYS 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 86 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 0.0060 chunk 13 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2090 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= 0.251 Angle : 0.657 16.023 18876 Z= 0.331 Chirality : 0.047 0.179 2142 Planarity : 0.005 0.058 2156 Dihedral : 17.012 167.813 2304 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.83 % Allowed : 32.52 % Favored : 63.64 % 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: 0.36 (0.23), residues: 1458 helix: 1.52 (0.24), residues: 526 sheet: 0.83 (0.29), residues: 344 loop : -1.35 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 735 HIS 0.010 0.001 HIS B 546 PHE 0.013 0.001 PHE A 556 TYR 0.011 0.001 TYR B 650 ARG 0.005 0.000 ARG B 169 *********************** 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: 52 poor density : 129 time to evaluate : 1.630 Fit side-chains REVERT: A 316 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: A 563 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7270 (ptm160) REVERT: A 574 MET cc_start: 0.7965 (ttm) cc_final: 0.7417 (ttt) REVERT: A 599 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: B 574 MET cc_start: 0.7946 (ttm) cc_final: 0.7383 (ttt) REVERT: B 593 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7229 (ptpt) REVERT: B 599 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7714 (tt0) outliers start: 52 outliers final: 33 residues processed: 171 average time/residue: 1.2259 time to fit residues: 231.0894 Evaluate side-chains 163 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 123 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 316 GLU 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 556 PHE 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 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 6 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 599 GLU 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 134 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 573 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13772 Z= 0.359 Angle : 0.726 16.229 18876 Z= 0.366 Chirality : 0.050 0.192 2142 Planarity : 0.005 0.078 2156 Dihedral : 17.068 166.486 2304 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.76 % Allowed : 32.82 % Favored : 63.42 % 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: 0.21 (0.23), residues: 1458 helix: 1.32 (0.23), residues: 530 sheet: 0.78 (0.29), residues: 344 loop : -1.39 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 735 HIS 0.011 0.001 HIS A 546 PHE 0.015 0.002 PHE A 584 TYR 0.013 0.001 TYR A 650 ARG 0.018 0.001 ARG A 349 *********************** 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 174 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 1.589 Fit side-chains REVERT: A 316 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 349 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7479 (mtp85) REVERT: A 471 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: A 563 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7299 (ptm160) REVERT: A 574 MET cc_start: 0.8031 (ttm) cc_final: 0.7489 (ttt) REVERT: A 599 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: A 695 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7184 (t0) REVERT: B 349 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7682 (ttm110) REVERT: B 555 MET cc_start: 0.7576 (mpp) cc_final: 0.7229 (mtp) REVERT: B 574 MET cc_start: 0.8013 (ttm) cc_final: 0.7487 (ttt) REVERT: B 593 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7279 (ptpt) REVERT: B 599 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7742 (tt0) outliers start: 51 outliers final: 32 residues processed: 164 average time/residue: 1.1502 time to fit residues: 209.5880 Evaluate side-chains 158 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 123 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 316 GLU 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 556 PHE 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 664 ILE Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 695 ASN 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 123 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 599 GLU 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 67 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN B 573 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13772 Z= 0.284 Angle : 0.680 16.075 18876 Z= 0.342 Chirality : 0.048 0.190 2142 Planarity : 0.005 0.067 2156 Dihedral : 17.048 167.343 2304 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.02 % Allowed : 33.48 % Favored : 63.50 % 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: 0.27 (0.23), residues: 1458 helix: 1.40 (0.23), residues: 528 sheet: 0.79 (0.29), residues: 344 loop : -1.36 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 735 HIS 0.012 0.001 HIS B 546 PHE 0.014 0.001 PHE B 584 TYR 0.011 0.001 TYR B 650 ARG 0.019 0.001 ARG A 349 ********************** 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: 41 poor density : 119 time to evaluate : 1.629 Fit side-chains REVERT: A 316 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: A 349 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7464 (mtp85) REVERT: A 501 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7676 (mmm-85) REVERT: A 563 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7278 (ptm160) REVERT: A 574 MET cc_start: 0.8035 (ttm) cc_final: 0.7474 (ttt) REVERT: A 599 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: B 349 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7664 (ttm110) REVERT: B 555 MET cc_start: 0.7494 (mpp) cc_final: 0.7109 (mtp) REVERT: B 574 MET cc_start: 0.8008 (ttm) cc_final: 0.7460 (ttt) REVERT: B 599 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7723 (tt0) outliers start: 41 outliers final: 33 residues processed: 152 average time/residue: 1.2365 time to fit residues: 208.9085 Evaluate side-chains 154 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 123 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 316 GLU 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 556 PHE 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 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 123 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 151 TRP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 556 PHE Chi-restraints excluded: chain B residue 599 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 503 ASN A 573 GLN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 503 ASN B 573 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.159665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130028 restraints weight = 15721.882| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.01 r_work: 0.3401 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2187 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= 0.189 Angle : 0.625 16.030 18876 Z= 0.314 Chirality : 0.045 0.176 2142 Planarity : 0.005 0.070 2156 Dihedral : 16.954 169.114 2304 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.65 % Allowed : 34.22 % Favored : 63.13 % 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: 0.51 (0.23), residues: 1458 helix: 1.62 (0.24), residues: 526 sheet: 0.90 (0.29), residues: 340 loop : -1.22 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 735 HIS 0.015 0.001 HIS B 546 PHE 0.012 0.001 PHE A 556 TYR 0.012 0.001 TYR B 650 ARG 0.018 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4326.39 seconds wall clock time: 78 minutes 39.25 seconds (4719.25 seconds total)