Starting phenix.real_space_refine on Tue Mar 3 23:26:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5b_24185/03_2026/7n5b_24185.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5b_24185/03_2026/7n5b_24185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n5b_24185/03_2026/7n5b_24185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5b_24185/03_2026/7n5b_24185.map" model { file = "/net/cci-nas-00/data/ceres_data/7n5b_24185/03_2026/7n5b_24185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5b_24185/03_2026/7n5b_24185.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5802 2.51 5 N 1566 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9122 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4528 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 12, 'TRANS': 567} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 3.61, per 1000 atoms: 0.40 Number of scatterers: 9122 At special positions: 0 Unit cell: (84.645, 76.095, 137.655, 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) V 2 22.97 S 34 16.00 P 4 15.00 Mg 2 11.99 O 1712 8.00 N 1566 7.00 C 5802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 341.7 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 71.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 117 through 132 removed outlier: 3.515A pdb=" N TYR A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 174 removed outlier: 4.127A pdb=" N ARG A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 196 through 245 removed outlier: 3.575A pdb=" N THR A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 279 removed outlier: 4.190A pdb=" N ASN A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 296 removed outlier: 3.523A pdb=" N THR A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 348 removed outlier: 4.113A pdb=" N LYS A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 358 through 408 removed outlier: 3.746A pdb=" N ALA A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 458 removed outlier: 3.857A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.583A pdb=" N VAL A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 4.015A pdb=" N GLY A 517 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 526 removed outlier: 4.170A pdb=" N LEU A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 554 removed outlier: 3.683A pdb=" N SER A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 575 Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.521A pdb=" N ARG A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 removed outlier: 3.596A pdb=" N ASN A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 617 through 633 Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.505A pdb=" N ALA A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 679 removed outlier: 4.062A pdb=" N ALA A 677 " --> pdb=" O ARG A 673 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 removed outlier: 3.661A pdb=" N SER A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 716 Processing helix chain 'B' and resid 118 through 132 removed outlier: 3.515A pdb=" N TYR B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 174 removed outlier: 4.127A pdb=" N ARG B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 196 through 245 removed outlier: 3.574A pdb=" N THR B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 279 removed outlier: 4.189A pdb=" N ASN B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 296 removed outlier: 3.523A pdb=" N THR B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 348 removed outlier: 4.113A pdb=" N LYS B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE B 327 " --> pdb=" O TRP B 323 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 358 through 408 removed outlier: 3.746A pdb=" N ALA B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 394 " --> pdb=" O GLN B 390 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 458 removed outlier: 3.857A pdb=" N LEU B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.583A pdb=" N VAL B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N MET B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 454 " --> pdb=" O MET B 450 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 4.015A pdb=" N GLY B 517 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 526 removed outlier: 4.170A pdb=" N LEU B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 554 removed outlier: 3.682A pdb=" N SER B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 575 Processing helix chain 'B' and resid 581 through 592 removed outlier: 3.522A pdb=" N ARG B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 600 removed outlier: 3.596A pdb=" N ASN B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 617 through 633 Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.504A pdb=" N ALA B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU B 653 " --> pdb=" O THR B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 679 removed outlier: 4.061A pdb=" N ALA B 677 " --> pdb=" O ARG B 673 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN B 679 " --> pdb=" O THR B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 704 removed outlier: 3.661A pdb=" N SER B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 716 Processing sheet with id=AA1, first strand: chain 'A' and resid 501 through 502 Processing sheet with id=AA2, first strand: chain 'A' and resid 484 through 486 removed outlier: 6.057A pdb=" N VAL A 484 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 497 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 486 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 558 removed outlier: 6.534A pdb=" N LEU A 637 " --> pdb=" O ILE A 668 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE A 670 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS A 639 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 510 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER A 507 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL A 684 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA A 509 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU A 686 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL A 511 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 683 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN A 694 " --> pdb=" O ILE A 683 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 685 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AA5, first strand: chain 'B' and resid 484 through 486 removed outlier: 6.057A pdb=" N VAL B 484 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 497 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 486 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 555 through 558 removed outlier: 6.534A pdb=" N LEU B 637 " --> pdb=" O ILE B 668 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE B 670 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS B 639 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 510 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER B 507 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL B 684 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 509 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU B 686 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL B 511 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 683 " --> pdb=" O GLN B 694 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN B 694 " --> pdb=" O ILE B 683 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 685 " --> pdb=" O VAL B 692 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 3010 1.36 - 1.50: 2337 1.50 - 1.64: 3863 1.64 - 1.77: 0 1.77 - 1.91: 70 Bond restraints: 9280 Sorted by residual: bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" CA LYS B 470 " pdb=" CB LYS B 470 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.51e-02 4.39e+03 7.00e-01 bond pdb=" CA LYS A 470 " pdb=" CB LYS A 470 " ideal model delta sigma weight residual 1.526 1.539 -0.012 1.51e-02 4.39e+03 6.79e-01 bond pdb=" CG GLU B 458 " pdb=" CD GLU B 458 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.52e-01 ... (remaining 9275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 12339 1.42 - 2.84: 153 2.84 - 4.25: 36 4.25 - 5.67: 26 5.67 - 7.09: 2 Bond angle restraints: 12556 Sorted by residual: angle pdb=" CB MET B 453 " pdb=" CG MET B 453 " pdb=" SD MET B 453 " ideal model delta sigma weight residual 112.70 105.61 7.09 3.00e+00 1.11e-01 5.59e+00 angle pdb=" CB MET A 453 " pdb=" CG MET A 453 " pdb=" SD MET A 453 " ideal model delta sigma weight residual 112.70 105.62 7.08 3.00e+00 1.11e-01 5.57e+00 angle pdb=" CB GLU B 458 " pdb=" CG GLU B 458 " pdb=" CD GLU B 458 " ideal model delta sigma weight residual 112.60 116.34 -3.74 1.70e+00 3.46e-01 4.85e+00 angle pdb=" CB GLU A 458 " pdb=" CG GLU A 458 " pdb=" CD GLU A 458 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.70e+00 3.46e-01 4.77e+00 angle pdb=" CA LYS B 297 " pdb=" CB LYS B 297 " pdb=" CG LYS B 297 " ideal model delta sigma weight residual 114.10 118.38 -4.28 2.00e+00 2.50e-01 4.58e+00 ... (remaining 12551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 5122 21.16 - 42.32: 364 42.32 - 63.48: 38 63.48 - 84.64: 8 84.64 - 105.80: 8 Dihedral angle restraints: 5540 sinusoidal: 2184 harmonic: 3356 Sorted by residual: dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 45.80 -105.80 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 45.73 -105.73 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 -150.08 90.08 1 2.00e+01 2.50e-03 2.40e+01 ... (remaining 5537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1069 0.031 - 0.063: 268 0.063 - 0.094: 87 0.094 - 0.126: 31 0.126 - 0.157: 3 Chirality restraints: 1458 Sorted by residual: chirality pdb=" CB ILE B 538 " pdb=" CA ILE B 538 " pdb=" CG1 ILE B 538 " pdb=" CG2 ILE B 538 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CB ILE A 538 " pdb=" CA ILE A 538 " pdb=" CG1 ILE A 538 " pdb=" CG2 ILE A 538 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA ILE B 683 " pdb=" N ILE B 683 " pdb=" C ILE B 683 " pdb=" CB ILE B 683 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1455 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 239 " 0.010 2.00e-02 2.50e+03 7.39e-03 9.57e-01 pdb=" CG PHE A 239 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 239 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 239 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 239 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 239 " -0.010 2.00e-02 2.50e+03 7.32e-03 9.37e-01 pdb=" CG PHE B 239 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE B 239 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 239 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 239 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 510 " -0.004 2.00e-02 2.50e+03 8.48e-03 7.19e-01 pdb=" C ILE B 510 " 0.015 2.00e-02 2.50e+03 pdb=" O ILE B 510 " -0.006 2.00e-02 2.50e+03 pdb=" N VAL B 511 " -0.005 2.00e-02 2.50e+03 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 38 2.50 - 3.10: 6719 3.10 - 3.70: 13441 3.70 - 4.30: 18400 4.30 - 4.90: 29859 Nonbonded interactions: 68457 Sorted by model distance: nonbonded pdb=" V VO4 A 802 " pdb="MG MG A 803 " model vdw 1.903 2.180 nonbonded pdb=" V VO4 B 802 " pdb="MG MG B 803 " model vdw 1.903 2.180 nonbonded pdb=" O1 VO4 A 802 " pdb="MG MG A 803 " model vdw 2.115 2.170 nonbonded pdb=" O1 VO4 B 802 " pdb="MG MG B 803 " model vdw 2.116 2.170 nonbonded pdb=" O2 VO4 A 802 " pdb="MG MG A 803 " model vdw 2.127 2.170 ... (remaining 68452 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.002 0.024 9280 Z= 0.093 Angle : 0.482 7.092 12556 Z= 0.240 Chirality : 0.035 0.157 1458 Planarity : 0.002 0.024 1584 Dihedral : 14.243 105.795 3372 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.20 % Allowed : 0.41 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.24), residues: 1152 helix: 2.03 (0.18), residues: 754 sheet: 2.83 (0.61), residues: 74 loop : -0.60 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 665 TYR 0.014 0.001 TYR B 205 PHE 0.016 0.001 PHE A 239 TRP 0.003 0.000 TRP B 323 HIS 0.001 0.000 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00171 ( 9280) covalent geometry : angle 0.48219 (12556) hydrogen bonds : bond 0.22143 ( 605) hydrogen bonds : angle 5.18246 ( 1767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.305 Fit side-chains REVERT: A 276 MET cc_start: 0.7701 (ttp) cc_final: 0.7463 (tmm) REVERT: A 498 ILE cc_start: 0.7578 (mt) cc_final: 0.7334 (mm) REVERT: B 498 ILE cc_start: 0.7584 (mt) cc_final: 0.7323 (mm) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.0705 time to fit residues: 13.3420 Evaluate side-chains 94 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0670 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 overall best weight: 1.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 243 HIS B 159 GLN B 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.150210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113025 restraints weight = 14226.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.116432 restraints weight = 8482.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.118761 restraints weight = 5974.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.120114 restraints weight = 4750.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.121270 restraints weight = 4108.960| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9280 Z= 0.201 Angle : 0.641 9.199 12556 Z= 0.329 Chirality : 0.040 0.132 1458 Planarity : 0.004 0.032 1584 Dihedral : 7.139 131.016 1278 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.04 % Allowed : 8.18 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.24), residues: 1152 helix: 2.54 (0.19), residues: 768 sheet: 2.39 (0.60), residues: 74 loop : -0.79 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 665 TYR 0.014 0.002 TYR B 440 PHE 0.017 0.002 PHE A 486 TRP 0.006 0.001 TRP B 711 HIS 0.008 0.002 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9280) covalent geometry : angle 0.64082 (12556) hydrogen bonds : bond 0.07040 ( 605) hydrogen bonds : angle 3.89284 ( 1767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.333 Fit side-chains REVERT: A 276 MET cc_start: 0.7928 (ttp) cc_final: 0.7426 (tmm) REVERT: A 450 MET cc_start: 0.7101 (tpp) cc_final: 0.6866 (tpp) REVERT: A 646 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8251 (mp) REVERT: B 450 MET cc_start: 0.7148 (tpp) cc_final: 0.6908 (tpp) REVERT: B 646 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8263 (mp) outliers start: 20 outliers final: 10 residues processed: 123 average time/residue: 0.0668 time to fit residues: 12.5663 Evaluate side-chains 96 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 0.1980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS A 357 ASN B 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.148642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.111277 restraints weight = 14254.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.114609 restraints weight = 8508.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116708 restraints weight = 6032.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.118322 restraints weight = 4844.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.119146 restraints weight = 4169.144| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.004 0.039 9280 Z= 0.187 Angle : 0.605 7.344 12556 Z= 0.310 Chirality : 0.039 0.131 1458 Planarity : 0.003 0.030 1584 Dihedral : 7.520 145.305 1278 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.45 % Allowed : 12.68 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.25), residues: 1152 helix: 2.59 (0.19), residues: 764 sheet: 1.61 (0.57), residues: 86 loop : -1.03 (0.30), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 665 TYR 0.014 0.001 TYR B 205 PHE 0.015 0.002 PHE A 271 TRP 0.006 0.001 TRP A 132 HIS 0.012 0.002 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9280) covalent geometry : angle 0.60475 (12556) hydrogen bonds : bond 0.06801 ( 605) hydrogen bonds : angle 3.82167 ( 1767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.356 Fit side-chains REVERT: A 276 MET cc_start: 0.7837 (ttp) cc_final: 0.7408 (tmm) REVERT: A 450 MET cc_start: 0.7214 (tpp) cc_final: 0.6922 (tpp) REVERT: A 646 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B 450 MET cc_start: 0.7125 (tpp) cc_final: 0.6872 (tpp) REVERT: B 646 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8272 (mp) outliers start: 24 outliers final: 16 residues processed: 99 average time/residue: 0.0647 time to fit residues: 10.1304 Evaluate side-chains 96 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 60 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.153131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115328 restraints weight = 14206.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.118856 restraints weight = 8402.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.121294 restraints weight = 5889.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.122691 restraints weight = 4630.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.123797 restraints weight = 3995.235| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9280 Z= 0.127 Angle : 0.520 7.090 12556 Z= 0.265 Chirality : 0.037 0.129 1458 Planarity : 0.003 0.026 1584 Dihedral : 7.664 153.530 1278 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.33 % Allowed : 15.44 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.25), residues: 1152 helix: 2.85 (0.19), residues: 754 sheet: 1.56 (0.57), residues: 86 loop : -0.88 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 665 TYR 0.013 0.001 TYR B 205 PHE 0.011 0.001 PHE A 271 TRP 0.008 0.001 TRP A 132 HIS 0.006 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9280) covalent geometry : angle 0.52039 (12556) hydrogen bonds : bond 0.05581 ( 605) hydrogen bonds : angle 3.43734 ( 1767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.355 Fit side-chains REVERT: A 276 MET cc_start: 0.7729 (ttp) cc_final: 0.7070 (tmm) outliers start: 13 outliers final: 5 residues processed: 88 average time/residue: 0.0598 time to fit residues: 8.8422 Evaluate side-chains 79 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.152968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115491 restraints weight = 14228.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119898 restraints weight = 8720.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.122307 restraints weight = 5157.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122579 restraints weight = 4534.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122611 restraints weight = 4041.109| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9280 Z= 0.127 Angle : 0.525 8.202 12556 Z= 0.265 Chirality : 0.037 0.141 1458 Planarity : 0.003 0.023 1584 Dihedral : 7.610 152.502 1278 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.12 % Allowed : 16.77 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.25), residues: 1152 helix: 2.88 (0.19), residues: 754 sheet: 1.42 (0.56), residues: 86 loop : -0.83 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 665 TYR 0.028 0.001 TYR A 354 PHE 0.011 0.001 PHE A 271 TRP 0.009 0.001 TRP B 132 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9280) covalent geometry : angle 0.52519 (12556) hydrogen bonds : bond 0.05423 ( 605) hydrogen bonds : angle 3.38522 ( 1767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.276 Fit side-chains REVERT: A 276 MET cc_start: 0.7645 (ttp) cc_final: 0.7039 (tmm) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.0715 time to fit residues: 9.6697 Evaluate side-chains 81 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 683 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 58 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 85 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.151886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.114552 restraints weight = 14226.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.118671 restraints weight = 8679.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.121443 restraints weight = 5215.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.121498 restraints weight = 4537.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.121519 restraints weight = 4011.477| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9280 Z= 0.133 Angle : 0.537 8.891 12556 Z= 0.269 Chirality : 0.037 0.125 1458 Planarity : 0.003 0.027 1584 Dihedral : 7.697 155.227 1278 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.66 % Allowed : 16.87 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.25), residues: 1152 helix: 2.90 (0.19), residues: 754 sheet: 1.26 (0.55), residues: 86 loop : -0.80 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 324 TYR 0.028 0.001 TYR A 354 PHE 0.012 0.001 PHE A 271 TRP 0.009 0.001 TRP B 132 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9280) covalent geometry : angle 0.53670 (12556) hydrogen bonds : bond 0.05416 ( 605) hydrogen bonds : angle 3.39638 ( 1767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.366 Fit side-chains REVERT: A 228 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7239 (mp) REVERT: A 276 MET cc_start: 0.7486 (ttp) cc_final: 0.6952 (tmm) REVERT: A 450 MET cc_start: 0.7104 (tpp) cc_final: 0.6835 (tpp) REVERT: A 624 VAL cc_start: 0.6454 (OUTLIER) cc_final: 0.5363 (m) REVERT: A 646 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8156 (mp) REVERT: B 228 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7282 (mp) REVERT: B 450 MET cc_start: 0.7025 (tpp) cc_final: 0.6778 (tpp) REVERT: B 646 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8207 (mp) outliers start: 26 outliers final: 14 residues processed: 100 average time/residue: 0.0591 time to fit residues: 9.8486 Evaluate side-chains 95 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.153535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115639 restraints weight = 14153.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.119140 restraints weight = 8423.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.121554 restraints weight = 5890.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123190 restraints weight = 4644.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124233 restraints weight = 3972.350| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9280 Z= 0.122 Angle : 0.522 8.873 12556 Z= 0.261 Chirality : 0.036 0.130 1458 Planarity : 0.003 0.023 1584 Dihedral : 7.700 156.803 1278 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.94 % Allowed : 18.51 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.25), residues: 1152 helix: 2.95 (0.19), residues: 754 sheet: 1.20 (0.54), residues: 86 loop : -0.72 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 665 TYR 0.029 0.001 TYR B 354 PHE 0.011 0.001 PHE B 271 TRP 0.009 0.001 TRP B 132 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9280) covalent geometry : angle 0.52207 (12556) hydrogen bonds : bond 0.05123 ( 605) hydrogen bonds : angle 3.29728 ( 1767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.307 Fit side-chains REVERT: A 217 GLU cc_start: 0.7985 (mm-30) cc_final: 0.6999 (tm-30) REVERT: A 228 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7162 (mp) REVERT: A 276 MET cc_start: 0.7485 (ttp) cc_final: 0.6998 (tmm) REVERT: A 646 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8162 (mp) REVERT: B 217 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7010 (tm-30) REVERT: B 228 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7240 (mp) REVERT: B 450 MET cc_start: 0.7159 (tpp) cc_final: 0.6844 (tpp) outliers start: 19 outliers final: 13 residues processed: 96 average time/residue: 0.0613 time to fit residues: 9.5849 Evaluate side-chains 95 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 683 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.152015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.113831 restraints weight = 14163.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117333 restraints weight = 8459.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.119754 restraints weight = 5929.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.120906 restraints weight = 4675.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.122271 restraints weight = 4074.436| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9280 Z= 0.135 Angle : 0.541 9.304 12556 Z= 0.271 Chirality : 0.037 0.247 1458 Planarity : 0.003 0.022 1584 Dihedral : 7.752 158.020 1278 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.15 % Allowed : 19.02 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.25), residues: 1152 helix: 2.95 (0.19), residues: 752 sheet: 1.18 (0.54), residues: 86 loop : -0.75 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 665 TYR 0.025 0.001 TYR B 354 PHE 0.012 0.001 PHE B 271 TRP 0.008 0.001 TRP B 132 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9280) covalent geometry : angle 0.54140 (12556) hydrogen bonds : bond 0.05260 ( 605) hydrogen bonds : angle 3.34657 ( 1767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.334 Fit side-chains REVERT: A 217 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7102 (tm-30) REVERT: A 228 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7193 (mp) REVERT: A 276 MET cc_start: 0.7437 (ttp) cc_final: 0.6998 (tmm) REVERT: A 624 VAL cc_start: 0.6352 (OUTLIER) cc_final: 0.5284 (m) REVERT: A 646 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8166 (mp) REVERT: B 217 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7051 (tm-30) REVERT: B 228 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7309 (mp) REVERT: B 450 MET cc_start: 0.7184 (tpp) cc_final: 0.6827 (tpp) REVERT: B 646 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8197 (mp) outliers start: 21 outliers final: 16 residues processed: 96 average time/residue: 0.0612 time to fit residues: 9.5437 Evaluate side-chains 100 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.152872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.114398 restraints weight = 14118.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.117935 restraints weight = 8467.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.120386 restraints weight = 5925.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.121991 restraints weight = 4674.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.122924 restraints weight = 3998.531| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9280 Z= 0.126 Angle : 0.535 9.834 12556 Z= 0.268 Chirality : 0.037 0.210 1458 Planarity : 0.003 0.023 1584 Dihedral : 7.765 158.704 1278 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.45 % Allowed : 19.12 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.25), residues: 1152 helix: 2.97 (0.19), residues: 752 sheet: 1.16 (0.54), residues: 86 loop : -0.70 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 665 TYR 0.023 0.001 TYR A 354 PHE 0.011 0.001 PHE B 271 TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS A 672 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9280) covalent geometry : angle 0.53469 (12556) hydrogen bonds : bond 0.05116 ( 605) hydrogen bonds : angle 3.32628 ( 1767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.316 Fit side-chains REVERT: A 156 LEU cc_start: 0.7990 (tp) cc_final: 0.7683 (tt) REVERT: A 217 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7093 (tm-30) REVERT: A 228 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7163 (mp) REVERT: A 276 MET cc_start: 0.7313 (ttp) cc_final: 0.6941 (tmm) REVERT: A 624 VAL cc_start: 0.6296 (OUTLIER) cc_final: 0.5231 (m) REVERT: A 646 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 217 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7097 (tm-30) REVERT: B 228 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7266 (mp) REVERT: B 646 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8195 (mp) outliers start: 24 outliers final: 18 residues processed: 104 average time/residue: 0.0633 time to fit residues: 10.2068 Evaluate side-chains 105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 111 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.153509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115017 restraints weight = 14063.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118525 restraints weight = 8467.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.121035 restraints weight = 5942.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.122687 restraints weight = 4675.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123692 restraints weight = 3984.470| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9280 Z= 0.124 Angle : 0.541 10.129 12556 Z= 0.269 Chirality : 0.037 0.209 1458 Planarity : 0.002 0.022 1584 Dihedral : 7.731 158.090 1278 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.15 % Allowed : 20.14 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.25), residues: 1152 helix: 2.97 (0.19), residues: 752 sheet: 1.11 (0.54), residues: 86 loop : -0.70 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 591 TYR 0.024 0.001 TYR A 354 PHE 0.016 0.001 PHE B 271 TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS B 672 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9280) covalent geometry : angle 0.54138 (12556) hydrogen bonds : bond 0.04990 ( 605) hydrogen bonds : angle 3.32655 ( 1767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.356 Fit side-chains REVERT: A 156 LEU cc_start: 0.7993 (tp) cc_final: 0.7688 (tt) REVERT: A 217 GLU cc_start: 0.7841 (mm-30) cc_final: 0.6845 (mt-10) REVERT: A 228 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7151 (mp) REVERT: A 276 MET cc_start: 0.7303 (ttp) cc_final: 0.6978 (tmm) REVERT: A 450 MET cc_start: 0.7097 (tpp) cc_final: 0.6721 (tpp) REVERT: A 624 VAL cc_start: 0.6343 (OUTLIER) cc_final: 0.5272 (m) REVERT: A 646 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 217 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7145 (tm-30) REVERT: B 228 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7242 (mp) REVERT: B 450 MET cc_start: 0.7004 (tpp) cc_final: 0.6755 (tpp) REVERT: B 646 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8200 (mp) outliers start: 21 outliers final: 16 residues processed: 98 average time/residue: 0.0724 time to fit residues: 11.0349 Evaluate side-chains 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 ASN Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 80 optimal weight: 0.0970 chunk 15 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.147039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108800 restraints weight = 14235.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.112034 restraints weight = 8642.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.114332 restraints weight = 6186.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115862 restraints weight = 4936.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.116713 restraints weight = 4257.274| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9280 Z= 0.198 Angle : 0.633 9.730 12556 Z= 0.322 Chirality : 0.040 0.200 1458 Planarity : 0.003 0.023 1584 Dihedral : 8.067 164.091 1278 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.45 % Allowed : 20.04 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.25), residues: 1152 helix: 2.70 (0.19), residues: 752 sheet: 0.86 (0.55), residues: 88 loop : -0.93 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 591 TYR 0.039 0.002 TYR B 354 PHE 0.014 0.002 PHE B 215 TRP 0.007 0.001 TRP B 132 HIS 0.008 0.002 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9280) covalent geometry : angle 0.63335 (12556) hydrogen bonds : bond 0.06182 ( 605) hydrogen bonds : angle 3.73284 ( 1767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1378.65 seconds wall clock time: 24 minutes 31.51 seconds (1471.51 seconds total)