Starting phenix.real_space_refine on Sat Mar 16 04:32:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd8_37457/03_2024/8wd8_37457.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd8_37457/03_2024/8wd8_37457.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/8wd8_37457/03_2024/8wd8_37457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd8_37457/03_2024/8wd8_37457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd8_37457/03_2024/8wd8_37457.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wd8_37457/03_2024/8wd8_37457.pdb" } 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= 0.001 sd= 0.145 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 8624 2.51 5 N 2334 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B GLU 739": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13667 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6174 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 29, 'TRANS': 720} 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: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6174 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 29, 'TRANS': 720} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.25, per 1000 atoms: 0.53 Number of scatterers: 13667 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 2612 8.00 N 2334 7.00 C 8624 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 - 3.50 Amino acid : False - 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: 5.18 Conformation dependent library (CDL) restraints added in 2.1 seconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 37.5% alpha, 25.3% beta 27 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 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 154 removed outlier: 3.546A pdb=" N VAL A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 204 through 218 removed outlier: 3.853A pdb=" N TYR A 217 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 231 Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.669A pdb=" N LEU A 271 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 removed outlier: 3.503A pdb=" N LYS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 303 removed outlier: 3.888A pdb=" N THR A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 326 removed outlier: 3.549A 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 346 through 350 removed outlier: 3.867A pdb=" N ARG A 349 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 350 " --> pdb=" O LYS A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 350' Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.544A pdb=" N LYS A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 412 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 433 through 448 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.693A pdb=" N LEU A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 693 through 704 removed outlier: 3.632A pdb=" N ILE A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 733 removed outlier: 3.642A pdb=" N LYS A 733 " --> pdb=" O ARG A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 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 154 removed outlier: 3.546A pdb=" N VAL B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 204 through 218 removed outlier: 3.854A pdb=" N TYR B 217 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 231 Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.669A pdb=" N LEU B 271 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 removed outlier: 3.502A pdb=" N LYS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 303 removed outlier: 3.889A pdb=" N THR B 303 " --> pdb=" O ASN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 326 removed outlier: 3.549A 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 346 through 350 removed outlier: 3.867A pdb=" N ARG B 349 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 350 " --> pdb=" O LYS B 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 346 through 350' Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.544A pdb=" N LYS B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 412 Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 433 through 448 Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 503 through 518 removed outlier: 3.694A pdb=" N LEU B 518 " --> pdb=" O ILE B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 693 through 704 removed outlier: 3.632A pdb=" N ILE B 697 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 733 removed outlier: 3.641A pdb=" N LYS B 733 " --> pdb=" O ARG B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 7.183A pdb=" N GLU A 316 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG A 652 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU A 676 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 636 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU A 678 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN A 634 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 607 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 635 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR A 533 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU A 606 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 535 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP A 608 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE A 537 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6 removed outlier: 7.183A pdb=" N GLU A 316 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 5.170A 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: 5.411A pdb=" N VAL A 47 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA A 56 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 21 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU A 72 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 23 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA6, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA7, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA8, first strand: chain 'A' and resid 418 through 420 removed outlier: 8.313A pdb=" N PHE A 427 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 381 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE A 429 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL A 383 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 418 through 420 removed outlier: 6.570A pdb=" N GLY A 454 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLN A 484 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 456 " --> pdb=" O GLN A 484 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 486 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 6 removed outlier: 7.184A pdb=" N GLU B 316 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG B 652 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU B 676 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 636 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU B 678 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN B 634 " --> pdb=" O GLU B 678 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 607 " --> pdb=" O PHE B 633 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 635 " --> pdb=" O ARG B 607 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B 533 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU B 606 " --> pdb=" O TYR B 533 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 535 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASP B 608 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE B 537 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 6 removed outlier: 7.184A pdb=" N GLU B 316 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG B 652 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AB4, first strand: chain 'B' and resid 46 through 49 removed outlier: 5.411A pdb=" N VAL B 47 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA B 56 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 21 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU B 72 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 23 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB6, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB7, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AB8, first strand: chain 'B' and resid 418 through 420 removed outlier: 8.313A pdb=" N PHE B 427 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 381 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE B 429 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL B 383 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 418 through 420 removed outlier: 6.570A pdb=" N GLY B 454 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLN B 484 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 456 " --> pdb=" O GLN B 484 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL B 486 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 458 " --> pdb=" O VAL B 486 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 5.27 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2292 1.32 - 1.44: 3816 1.44 - 1.57: 7788 1.57 - 1.69: 124 1.69 - 1.81: 52 Bond restraints: 14072 Sorted by residual: bond pdb=" CA HIS B 546 " pdb=" C HIS B 546 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.11e-02 8.12e+03 1.43e+01 bond pdb=" CA HIS A 546 " pdb=" C HIS A 546 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.11e-02 8.12e+03 1.43e+01 bond pdb=" C PRO B 541 " pdb=" O PRO B 541 " ideal model delta sigma weight residual 1.233 1.203 0.030 1.18e-02 7.18e+03 6.31e+00 bond pdb=" C PRO A 541 " pdb=" O PRO A 541 " ideal model delta sigma weight residual 1.233 1.204 0.029 1.18e-02 7.18e+03 6.17e+00 bond pdb=" C ARG A 736 " pdb=" O ARG A 736 " ideal model delta sigma weight residual 1.234 1.206 0.028 1.22e-02 6.72e+03 5.17e+00 ... (remaining 14067 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.87: 692 106.87 - 113.71: 7766 113.71 - 120.56: 5685 120.56 - 127.40: 4952 127.40 - 134.24: 189 Bond angle restraints: 19284 Sorted by residual: angle pdb=" N ARG A 736 " pdb=" CA ARG A 736 " pdb=" C ARG A 736 " ideal model delta sigma weight residual 109.23 116.66 -7.43 1.55e+00 4.16e-01 2.30e+01 angle pdb=" N GLU B 739 " pdb=" CA GLU B 739 " pdb=" C GLU B 739 " ideal model delta sigma weight residual 111.14 116.28 -5.14 1.08e+00 8.57e-01 2.26e+01 angle pdb=" N GLU A 739 " pdb=" CA GLU A 739 " pdb=" C GLU A 739 " ideal model delta sigma weight residual 111.14 115.78 -4.64 1.08e+00 8.57e-01 1.85e+01 angle pdb=" N LYS A 543 " pdb=" CA LYS A 543 " pdb=" C LYS A 543 " ideal model delta sigma weight residual 111.14 115.66 -4.52 1.08e+00 8.57e-01 1.75e+01 angle pdb=" CB ILE A 17 " pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sigma weight residual 113.80 122.54 -8.74 2.10e+00 2.27e-01 1.73e+01 ... (remaining 19279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 7618 28.46 - 56.92: 703 56.92 - 85.38: 58 85.38 - 113.84: 5 113.84 - 142.30: 4 Dihedral angle restraints: 8388 sinusoidal: 3946 harmonic: 4442 Sorted by residual: dihedral pdb=" CA TYR B 561 " pdb=" C TYR B 561 " pdb=" N ILE B 562 " pdb=" CA ILE B 562 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR A 561 " pdb=" C TYR A 561 " pdb=" N ILE A 562 " pdb=" CA ILE A 562 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+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 77.70 142.30 1 3.50e+01 8.16e-04 1.40e+01 ... (remaining 8385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1652 0.049 - 0.097: 358 0.097 - 0.146: 153 0.146 - 0.194: 17 0.194 - 0.243: 2 Chirality restraints: 2182 Sorted by residual: chirality pdb=" CB VAL B 728 " pdb=" CA VAL B 728 " pdb=" CG1 VAL B 728 " pdb=" CG2 VAL B 728 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL A 728 " pdb=" CA VAL A 728 " pdb=" CG1 VAL A 728 " pdb=" CG2 VAL A 728 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 2179 not shown) Planarity restraints: 2210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 29 " 0.064 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO B 30 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 29 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO A 30 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 734 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C GLY A 734 " 0.054 2.00e-02 2.50e+03 pdb=" O GLY A 734 " -0.020 2.00e-02 2.50e+03 pdb=" N TRP A 735 " -0.019 2.00e-02 2.50e+03 ... (remaining 2207 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 37 2.46 - 3.07: 7396 3.07 - 3.68: 19820 3.68 - 4.29: 31258 4.29 - 4.90: 51892 Nonbonded interactions: 110403 Sorted by model distance: nonbonded pdb=" ND1 HIS A 546 " pdb="ZN ZN A 801 " model vdw 1.852 2.310 nonbonded pdb=" ND1 HIS B 546 " pdb="ZN ZN A 801 " model vdw 1.870 2.310 nonbonded pdb=" O VAL B 750 " pdb="MG MG B 801 " model vdw 2.095 2.170 nonbonded pdb=" O VAL A 750 " pdb="MG MG A 802 " model vdw 2.095 2.170 nonbonded pdb=" OP1 DT U 6 " pdb="MG MG B 802 " model vdw 2.108 2.170 ... (remaining 110398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 750 or resid 802 through 803)) selection = (chain 'B' and (resid 1 through 750 or resid 802 through 803)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'T' and resid 0 through 15) 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.270 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 39.610 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 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 0.054 14072 Z= 0.254 Angle : 0.703 9.649 19284 Z= 0.409 Chirality : 0.048 0.243 2182 Planarity : 0.007 0.097 2210 Dihedral : 19.785 142.302 5516 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.65 % Allowed : 24.64 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.91 (0.18), residues: 1496 helix: -1.83 (0.17), residues: 528 sheet: 0.31 (0.26), residues: 360 loop : -1.59 (0.21), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 151 HIS 0.005 0.001 HIS A 639 PHE 0.011 0.001 PHE A 164 TYR 0.015 0.001 TYR A 650 ARG 0.010 0.001 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 1.561 Fit side-chains REVERT: A 229 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8302 (ttmt) REVERT: A 543 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8763 (ttmm) REVERT: B 229 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8294 (ttmt) REVERT: B 543 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8809 (ttmm) REVERT: B 574 MET cc_start: 0.8439 (ttm) cc_final: 0.8221 (ttp) outliers start: 9 outliers final: 2 residues processed: 203 average time/residue: 1.3525 time to fit residues: 299.0542 Evaluate side-chains 160 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 543 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 64 optimal weight: 0.3980 chunk 39 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 181 HIS A 249 HIS A 325 ASN B 99 HIS B 181 HIS B 249 HIS B 325 ASN B 509 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14072 Z= 0.168 Angle : 0.472 6.952 19284 Z= 0.260 Chirality : 0.043 0.143 2182 Planarity : 0.005 0.063 2210 Dihedral : 16.009 149.882 2358 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.31 % Allowed : 24.35 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.21), residues: 1496 helix: 0.40 (0.22), residues: 540 sheet: 0.52 (0.25), residues: 394 loop : -1.20 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 413 HIS 0.004 0.001 HIS B 99 PHE 0.008 0.001 PHE A 584 TYR 0.009 0.001 TYR B 282 ARG 0.007 0.000 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7499 (mptt) cc_final: 0.7160 (mttm) REVERT: A 373 LYS cc_start: 0.7502 (mttt) cc_final: 0.6920 (mptp) REVERT: A 448 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7508 (ttt) REVERT: B 99 HIS cc_start: 0.7605 (t-90) cc_final: 0.7271 (t-90) REVERT: B 327 MET cc_start: 0.8936 (mtm) cc_final: 0.8714 (mtm) REVERT: B 373 LYS cc_start: 0.7526 (mttt) cc_final: 0.6944 (mptp) REVERT: B 448 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7568 (ttt) outliers start: 32 outliers final: 8 residues processed: 184 average time/residue: 1.2654 time to fit residues: 255.0526 Evaluate side-chains 159 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 509 ASN Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 686 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS A 335 ASN B 208 HIS B 335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 14072 Z= 0.456 Angle : 0.653 9.638 19284 Z= 0.343 Chirality : 0.050 0.164 2182 Planarity : 0.005 0.054 2210 Dihedral : 16.512 160.663 2350 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.89 % Allowed : 24.35 % Favored : 72.76 % 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: 0.02 (0.21), residues: 1496 helix: 0.91 (0.22), residues: 548 sheet: 0.68 (0.26), residues: 372 loop : -1.29 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 218 HIS 0.008 0.001 HIS A 99 PHE 0.015 0.002 PHE A 67 TYR 0.015 0.002 TYR B 548 ARG 0.005 0.001 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 1.577 Fit side-chains REVERT: A 29 LYS cc_start: 0.7471 (mptt) cc_final: 0.6902 (mttp) REVERT: A 202 ASN cc_start: 0.8121 (m-40) cc_final: 0.7862 (m-40) REVERT: A 373 LYS cc_start: 0.7644 (mttt) cc_final: 0.7176 (mptp) REVERT: A 448 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7605 (ttt) REVERT: A 474 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8992 (tttt) REVERT: A 624 LYS cc_start: 0.8281 (tttp) cc_final: 0.8008 (ttpp) REVERT: A 662 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7857 (p90) REVERT: A 702 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8681 (mt) REVERT: A 740 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: B 29 LYS cc_start: 0.7489 (mptt) cc_final: 0.6913 (mttp) REVERT: B 202 ASN cc_start: 0.8137 (m-40) cc_final: 0.7883 (m-40) REVERT: B 225 LYS cc_start: 0.8481 (mmmt) cc_final: 0.7699 (ttpp) REVERT: B 373 LYS cc_start: 0.7652 (mttt) cc_final: 0.7182 (mptp) REVERT: B 448 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7640 (ttt) REVERT: B 474 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8995 (tttt) REVERT: B 482 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8400 (mm) REVERT: B 624 LYS cc_start: 0.8281 (tttp) cc_final: 0.8006 (ttpp) REVERT: B 662 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7853 (p90) REVERT: B 702 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8693 (mt) outliers start: 40 outliers final: 15 residues processed: 184 average time/residue: 1.3829 time to fit residues: 276.7203 Evaluate side-chains 181 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14072 Z= 0.161 Angle : 0.477 8.629 19284 Z= 0.262 Chirality : 0.043 0.134 2182 Planarity : 0.004 0.051 2210 Dihedral : 16.217 160.385 2346 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.60 % Allowed : 24.64 % Favored : 72.76 % 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 (0.22), residues: 1496 helix: 1.51 (0.23), residues: 548 sheet: 0.74 (0.26), residues: 372 loop : -1.02 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 413 HIS 0.003 0.001 HIS A 722 PHE 0.010 0.001 PHE B 227 TYR 0.009 0.001 TYR A 650 ARG 0.005 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 170 time to evaluate : 1.438 Fit side-chains REVERT: A 29 LYS cc_start: 0.7516 (mptt) cc_final: 0.6966 (mttp) REVERT: A 202 ASN cc_start: 0.8145 (m-40) cc_final: 0.7892 (m-40) REVERT: A 225 LYS cc_start: 0.8489 (mmmt) cc_final: 0.7782 (ttpp) REVERT: A 373 LYS cc_start: 0.7574 (mttt) cc_final: 0.7100 (mptp) REVERT: A 448 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7529 (ttt) REVERT: A 482 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8319 (mm) REVERT: B 202 ASN cc_start: 0.8150 (m-40) cc_final: 0.7894 (m-40) REVERT: B 225 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7662 (ttpp) REVERT: B 373 LYS cc_start: 0.7579 (mttt) cc_final: 0.7114 (mptp) REVERT: B 448 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7545 (ttt) REVERT: B 624 LYS cc_start: 0.8213 (tttp) cc_final: 0.7893 (ttpp) outliers start: 36 outliers final: 14 residues processed: 195 average time/residue: 1.4431 time to fit residues: 307.9024 Evaluate side-chains 183 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 480 ASN B 325 ASN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14072 Z= 0.333 Angle : 0.566 9.633 19284 Z= 0.301 Chirality : 0.046 0.146 2182 Planarity : 0.004 0.046 2210 Dihedral : 16.354 162.119 2346 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.25 % Allowed : 23.84 % Favored : 72.90 % 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: 0.51 (0.22), residues: 1496 helix: 1.53 (0.23), residues: 548 sheet: 0.70 (0.26), residues: 372 loop : -1.09 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 413 HIS 0.006 0.001 HIS B 99 PHE 0.010 0.001 PHE B 67 TYR 0.012 0.001 TYR B 548 ARG 0.006 0.000 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 1.577 Fit side-chains REVERT: A 29 LYS cc_start: 0.7445 (mptt) cc_final: 0.6859 (mttp) REVERT: A 202 ASN cc_start: 0.8112 (m-40) cc_final: 0.7874 (m-40) REVERT: A 225 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7698 (ttpp) REVERT: A 373 LYS cc_start: 0.7589 (mttt) cc_final: 0.7104 (mptp) REVERT: A 448 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7621 (ttt) REVERT: A 482 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8385 (mm) REVERT: A 624 LYS cc_start: 0.8264 (tttp) cc_final: 0.7977 (ttpp) REVERT: B 29 LYS cc_start: 0.7417 (mptt) cc_final: 0.6829 (mttp) REVERT: B 202 ASN cc_start: 0.8114 (m-40) cc_final: 0.7878 (m-40) REVERT: B 373 LYS cc_start: 0.7592 (mttt) cc_final: 0.7117 (mptp) REVERT: B 448 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7593 (ttt) REVERT: B 624 LYS cc_start: 0.8263 (tttp) cc_final: 0.7976 (ttpp) outliers start: 45 outliers final: 22 residues processed: 201 average time/residue: 1.3109 time to fit residues: 287.3238 Evaluate side-chains 185 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14072 Z= 0.219 Angle : 0.503 9.293 19284 Z= 0.272 Chirality : 0.044 0.133 2182 Planarity : 0.004 0.046 2210 Dihedral : 16.250 161.664 2346 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.89 % Allowed : 24.13 % Favored : 72.98 % 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: 0.72 (0.22), residues: 1496 helix: 1.74 (0.23), residues: 548 sheet: 0.79 (0.27), residues: 366 loop : -0.96 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 413 HIS 0.004 0.001 HIS B 722 PHE 0.011 0.001 PHE A 227 TYR 0.009 0.001 TYR B 548 ARG 0.006 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 1.553 Fit side-chains REVERT: A 29 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6819 (mttp) REVERT: A 202 ASN cc_start: 0.8095 (m-40) cc_final: 0.7863 (m-40) REVERT: A 373 LYS cc_start: 0.7474 (mttt) cc_final: 0.7025 (mptp) REVERT: A 448 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7596 (ttt) REVERT: A 482 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8336 (mm) REVERT: A 487 ASN cc_start: 0.8313 (p0) cc_final: 0.8111 (p0) REVERT: A 562 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.5692 (mp) REVERT: A 624 LYS cc_start: 0.8209 (tttp) cc_final: 0.7915 (ttpp) REVERT: B 29 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6823 (mttp) REVERT: B 202 ASN cc_start: 0.8099 (m-40) cc_final: 0.7865 (m-40) REVERT: B 225 LYS cc_start: 0.8394 (mmmt) cc_final: 0.7629 (ttpp) REVERT: B 373 LYS cc_start: 0.7477 (mttt) cc_final: 0.7036 (mptp) REVERT: B 448 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7577 (ttt) REVERT: B 487 ASN cc_start: 0.8313 (p0) cc_final: 0.8109 (p0) REVERT: B 562 ILE cc_start: 0.6309 (OUTLIER) cc_final: 0.5687 (mp) REVERT: B 624 LYS cc_start: 0.8220 (tttp) cc_final: 0.7921 (ttpp) REVERT: B 740 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7945 (pm20) outliers start: 40 outliers final: 27 residues processed: 198 average time/residue: 1.3346 time to fit residues: 287.8985 Evaluate side-chains 198 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.0370 chunk 16 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14072 Z= 0.184 Angle : 0.485 9.054 19284 Z= 0.264 Chirality : 0.043 0.133 2182 Planarity : 0.004 0.045 2210 Dihedral : 16.190 161.720 2346 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.18 % Allowed : 24.64 % Favored : 72.18 % 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: 0.87 (0.22), residues: 1496 helix: 1.89 (0.23), residues: 548 sheet: 0.88 (0.26), residues: 368 loop : -0.92 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 413 HIS 0.004 0.001 HIS B 722 PHE 0.011 0.001 PHE B 227 TYR 0.009 0.001 TYR B 650 ARG 0.008 0.000 ARG A 738 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 1.475 Fit side-chains REVERT: A 29 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6932 (mttm) REVERT: A 202 ASN cc_start: 0.8093 (m-40) cc_final: 0.7855 (m-40) REVERT: A 225 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7629 (ttpp) REVERT: A 373 LYS cc_start: 0.7412 (mttt) cc_final: 0.6991 (mptp) REVERT: A 448 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7593 (ttt) REVERT: A 482 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8293 (mm) REVERT: A 487 ASN cc_start: 0.8235 (p0) cc_final: 0.7911 (p0) REVERT: A 562 ILE cc_start: 0.6323 (OUTLIER) cc_final: 0.5686 (mp) REVERT: A 624 LYS cc_start: 0.8196 (tttp) cc_final: 0.7896 (ttpp) REVERT: B 29 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6968 (mttm) REVERT: B 202 ASN cc_start: 0.8098 (m-40) cc_final: 0.7858 (m-40) REVERT: B 225 LYS cc_start: 0.8400 (mmmt) cc_final: 0.7658 (ttpp) REVERT: B 373 LYS cc_start: 0.7413 (mttt) cc_final: 0.7007 (mptp) REVERT: B 448 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7586 (ttt) REVERT: B 487 ASN cc_start: 0.8233 (p0) cc_final: 0.7905 (p0) REVERT: B 562 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5683 (mp) REVERT: B 624 LYS cc_start: 0.8194 (tttp) cc_final: 0.7890 (ttpp) outliers start: 44 outliers final: 29 residues processed: 201 average time/residue: 1.2146 time to fit residues: 268.5507 Evaluate side-chains 204 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14072 Z= 0.326 Angle : 0.563 9.943 19284 Z= 0.298 Chirality : 0.046 0.147 2182 Planarity : 0.004 0.044 2210 Dihedral : 16.312 161.942 2346 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.47 % Allowed : 24.28 % Favored : 72.25 % 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: 0.65 (0.22), residues: 1496 helix: 1.76 (0.23), residues: 548 sheet: 0.73 (0.26), residues: 372 loop : -1.09 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 218 HIS 0.005 0.001 HIS B 722 PHE 0.010 0.001 PHE B 227 TYR 0.012 0.001 TYR B 548 ARG 0.009 0.000 ARG A 738 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 1.596 Fit side-chains REVERT: A 29 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6819 (mttp) REVERT: A 202 ASN cc_start: 0.8103 (m-40) cc_final: 0.7864 (m-40) REVERT: A 225 LYS cc_start: 0.8432 (mmmt) cc_final: 0.7641 (ttpp) REVERT: A 373 LYS cc_start: 0.7479 (mttt) cc_final: 0.7018 (mptp) REVERT: A 448 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7628 (ttt) REVERT: A 482 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8364 (mm) REVERT: A 562 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.5799 (mp) REVERT: A 624 LYS cc_start: 0.8243 (tttp) cc_final: 0.7958 (ttpp) REVERT: B 29 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6895 (mttm) REVERT: B 202 ASN cc_start: 0.8102 (m-40) cc_final: 0.7867 (m-40) REVERT: B 225 LYS cc_start: 0.8439 (mmmt) cc_final: 0.7676 (ttpp) REVERT: B 373 LYS cc_start: 0.7483 (mttt) cc_final: 0.7023 (mptp) REVERT: B 448 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7595 (ttt) REVERT: B 482 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8394 (mm) REVERT: B 562 ILE cc_start: 0.6406 (OUTLIER) cc_final: 0.5791 (mp) REVERT: B 624 LYS cc_start: 0.8231 (tttp) cc_final: 0.7941 (ttpp) outliers start: 48 outliers final: 28 residues processed: 195 average time/residue: 1.2755 time to fit residues: 271.9810 Evaluate side-chains 194 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14072 Z= 0.177 Angle : 0.483 9.147 19284 Z= 0.263 Chirality : 0.043 0.132 2182 Planarity : 0.004 0.045 2210 Dihedral : 16.202 161.783 2346 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.53 % Allowed : 25.43 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.22), residues: 1496 helix: 1.95 (0.23), residues: 548 sheet: 0.88 (0.27), residues: 368 loop : -0.91 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 413 HIS 0.004 0.001 HIS A 722 PHE 0.011 0.001 PHE B 227 TYR 0.010 0.001 TYR B 650 ARG 0.009 0.000 ARG A 738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.564 Fit side-chains REVERT: A 29 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6830 (mttp) REVERT: A 202 ASN cc_start: 0.8087 (m-40) cc_final: 0.7851 (m-40) REVERT: A 225 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7643 (ttpp) REVERT: A 373 LYS cc_start: 0.7382 (mttt) cc_final: 0.6971 (mptp) REVERT: A 448 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7564 (ttt) REVERT: A 482 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8303 (mm) REVERT: A 487 ASN cc_start: 0.8199 (p0) cc_final: 0.7947 (p0) REVERT: A 562 ILE cc_start: 0.6348 (OUTLIER) cc_final: 0.5710 (mp) REVERT: A 624 LYS cc_start: 0.8187 (tttp) cc_final: 0.7888 (ttpp) REVERT: B 29 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.6888 (mttp) REVERT: B 202 ASN cc_start: 0.8089 (m-40) cc_final: 0.7851 (m-40) REVERT: B 225 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7636 (ttpp) REVERT: B 373 LYS cc_start: 0.7383 (mttt) cc_final: 0.6982 (mptp) REVERT: B 448 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7564 (ttt) REVERT: B 487 ASN cc_start: 0.8196 (p0) cc_final: 0.7942 (p0) REVERT: B 562 ILE cc_start: 0.6340 (OUTLIER) cc_final: 0.5703 (mp) REVERT: B 624 LYS cc_start: 0.8191 (tttp) cc_final: 0.7884 (ttpp) outliers start: 35 outliers final: 30 residues processed: 190 average time/residue: 1.3514 time to fit residues: 280.6117 Evaluate side-chains 203 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 14072 Z= 0.446 Angle : 0.633 10.659 19284 Z= 0.331 Chirality : 0.049 0.162 2182 Planarity : 0.005 0.042 2210 Dihedral : 16.430 161.715 2346 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.03 % Allowed : 24.71 % Favored : 72.25 % 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: 0.48 (0.22), residues: 1496 helix: 1.62 (0.23), residues: 548 sheet: 0.67 (0.26), residues: 372 loop : -1.21 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 218 HIS 0.006 0.001 HIS B 722 PHE 0.013 0.002 PHE B 67 TYR 0.015 0.002 TYR A 548 ARG 0.007 0.001 ARG A 738 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 160 time to evaluate : 1.620 Fit side-chains REVERT: A 29 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6809 (mttp) REVERT: A 202 ASN cc_start: 0.8103 (m-40) cc_final: 0.7856 (m-40) REVERT: A 225 LYS cc_start: 0.8470 (mmmt) cc_final: 0.7673 (ttpp) REVERT: A 373 LYS cc_start: 0.7525 (mttt) cc_final: 0.7070 (mptp) REVERT: A 448 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7690 (ttt) REVERT: A 482 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8410 (mm) REVERT: A 562 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.5931 (mp) REVERT: A 624 LYS cc_start: 0.8280 (tttp) cc_final: 0.8008 (ttpp) REVERT: B 29 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6835 (mttp) REVERT: B 202 ASN cc_start: 0.8101 (m-40) cc_final: 0.7859 (m-40) REVERT: B 373 LYS cc_start: 0.7524 (mttt) cc_final: 0.7075 (mptp) REVERT: B 448 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7632 (ttt) REVERT: B 562 ILE cc_start: 0.6536 (OUTLIER) cc_final: 0.5924 (mp) REVERT: B 624 LYS cc_start: 0.8274 (tttp) cc_final: 0.8004 (ttpp) outliers start: 42 outliers final: 30 residues processed: 190 average time/residue: 1.2903 time to fit residues: 268.5139 Evaluate side-chains 196 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.121758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.098042 restraints weight = 15837.814| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.42 r_work: 0.2878 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14072 Z= 0.225 Angle : 0.518 10.007 19284 Z= 0.280 Chirality : 0.044 0.138 2182 Planarity : 0.004 0.043 2210 Dihedral : 16.302 162.219 2346 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.03 % Allowed : 25.00 % Favored : 71.97 % 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: 0.69 (0.22), residues: 1496 helix: 1.79 (0.23), residues: 548 sheet: 0.73 (0.27), residues: 366 loop : -1.03 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 413 HIS 0.004 0.001 HIS A 722 PHE 0.010 0.001 PHE B 227 TYR 0.010 0.001 TYR B 548 ARG 0.007 0.000 ARG A 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4850.54 seconds wall clock time: 86 minutes 23.11 seconds (5183.11 seconds total)