Starting phenix.real_space_refine on Thu Jul 2 11:08:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mdi_48171/07_2026/9mdi_48171.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mdi_48171/07_2026/9mdi_48171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mdi_48171/07_2026/9mdi_48171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mdi_48171/07_2026/9mdi_48171.map" model { file = "/net/cci-nas-00/data/ceres_data/9mdi_48171/07_2026/9mdi_48171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mdi_48171/07_2026/9mdi_48171.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.085 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: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 11 5.16 5 C 5077 2.51 5 N 1323 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8139 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4076 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 20, 'TRANS': 502} Chain breaks: 2 Chain: "B" Number of atoms: 4057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4057 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 20, 'TRANS': 499} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CA': 3} Chain breaks: 3 Time building chain proxies: 1.42, per 1000 atoms: 0.17 Number of scatterers: 8139 At special positions: 0 Unit cell: (92.88, 89.44, 101.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 11 16.00 O 1722 8.00 N 1323 7.00 C 5077 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: 0.38 Conformation dependent library (CDL) restraints added in 290.4 milliseconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 18 sheets defined 12.2% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.100A pdb=" N ASP A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 removed outlier: 3.992A pdb=" N GLY A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 removed outlier: 4.015A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 659 through 663 Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.784A pdb=" N ASN B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.918A pdb=" N GLN B 428 " --> pdb=" O GLN B 425 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 429' Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.845A pdb=" N SER B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'B' and resid 581 through 595 removed outlier: 4.286A pdb=" N ASN B 586 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS B 587 " --> pdb=" O ASN B 583 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 663 Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 423 removed outlier: 6.968A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU A 305 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN A 329 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N GLY A 303 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 423 removed outlier: 6.968A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU A 305 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN A 329 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N GLY A 303 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 460 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.372A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA6, first strand: chain 'A' and resid 558 through 560 Processing sheet with id=AA7, first strand: chain 'A' and resid 618 through 620 removed outlier: 3.590A pdb=" N LEU A 733 " --> pdb=" O ASN A 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 618 through 620 removed outlier: 5.244A pdb=" N LEU A 733 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS A 676 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASN A 735 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 674 " --> pdb=" O ASN A 735 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG A 668 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 653 through 658 Processing sheet with id=AB1, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB2, first strand: chain 'B' and resid 447 through 448 removed outlier: 3.828A pdb=" N ILE B 460 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 447 through 448 removed outlier: 3.944A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N GLY B 303 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASN B 329 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU B 305 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 352 through 353 removed outlier: 6.557A pdb=" N ASN B 352 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 413 through 414 Processing sheet with id=AB6, first strand: chain 'B' and resid 558 through 560 removed outlier: 3.910A pdb=" N LEU B 564 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 618 through 620 removed outlier: 3.607A pdb=" N TYR B 618 " --> pdb=" O ILE B 738 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 618 through 620 removed outlier: 3.607A pdb=" N TYR B 618 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG B 668 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 675 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR B 705 " --> pdb=" O SER B 675 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 653 through 658 removed outlier: 3.648A pdb=" N GLU B 722 " --> pdb=" O LYS B 689 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 618 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: 1.08 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2642 1.34 - 1.46: 1367 1.46 - 1.57: 4240 1.57 - 1.69: 2 1.69 - 1.81: 20 Bond restraints: 8271 Sorted by residual: bond pdb=" CB PRO B 435 " pdb=" CG PRO B 435 " ideal model delta sigma weight residual 1.492 1.607 -0.115 5.00e-02 4.00e+02 5.32e+00 bond pdb=" CB PRO A 570 " pdb=" CG PRO A 570 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.88e+00 bond pdb=" CB ASP B 218 " pdb=" CG ASP B 218 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.55e+00 bond pdb=" CA ASP B 218 " pdb=" CB ASP B 218 " ideal model delta sigma weight residual 1.530 1.564 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" CB LYS B 490 " pdb=" CG LYS B 490 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.94e+00 ... (remaining 8266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 10959 2.41 - 4.81: 223 4.81 - 7.22: 35 7.22 - 9.62: 5 9.62 - 12.03: 2 Bond angle restraints: 11224 Sorted by residual: angle pdb=" CA PRO B 435 " pdb=" N PRO B 435 " pdb=" CD PRO B 435 " ideal model delta sigma weight residual 112.00 101.59 10.41 1.40e+00 5.10e-01 5.52e+01 angle pdb=" CB LYS B 490 " pdb=" CG LYS B 490 " pdb=" CD LYS B 490 " ideal model delta sigma weight residual 111.30 123.33 -12.03 2.30e+00 1.89e-01 2.73e+01 angle pdb=" C ARG A 232 " pdb=" N ASN A 233 " pdb=" CA ASN A 233 " ideal model delta sigma weight residual 122.61 129.77 -7.16 1.56e+00 4.11e-01 2.11e+01 angle pdb=" C LEU A 414 " pdb=" N ASP A 415 " pdb=" CA ASP A 415 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.09e+01 angle pdb=" CA PRO A 570 " pdb=" N PRO A 570 " pdb=" CD PRO A 570 " ideal model delta sigma weight residual 112.00 105.69 6.31 1.40e+00 5.10e-01 2.03e+01 ... (remaining 11219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 4211 18.02 - 36.04: 597 36.04 - 54.07: 166 54.07 - 72.09: 33 72.09 - 90.11: 10 Dihedral angle restraints: 5017 sinusoidal: 1970 harmonic: 3047 Sorted by residual: dihedral pdb=" CA GLU A 710 " pdb=" C GLU A 710 " pdb=" N PHE A 711 " pdb=" CA PHE A 711 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA SER B 434 " pdb=" C SER B 434 " pdb=" N PRO B 435 " pdb=" CA PRO B 435 " ideal model delta harmonic sigma weight residual -180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA TYR A 464 " pdb=" C TYR A 464 " pdb=" N ASP A 465 " pdb=" CA ASP A 465 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1112 0.076 - 0.152: 154 0.152 - 0.229: 10 0.229 - 0.305: 2 0.305 - 0.381: 1 Chirality restraints: 1279 Sorted by residual: chirality pdb=" CB VAL A 302 " pdb=" CA VAL A 302 " pdb=" CG1 VAL A 302 " pdb=" CG2 VAL A 302 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB ILE B 658 " pdb=" CA ILE B 658 " pdb=" CG1 ILE B 658 " pdb=" CG2 ILE B 658 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ASP A 415 " pdb=" N ASP A 415 " pdb=" C ASP A 415 " pdb=" CB ASP A 415 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1276 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 434 " -0.076 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO B 435 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO B 435 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 435 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 537 " -0.055 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO B 538 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 538 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 538 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 628 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO A 629 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 629 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 629 " 0.045 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1676 2.78 - 3.31: 6629 3.31 - 3.84: 12729 3.84 - 4.37: 13641 4.37 - 4.90: 25523 Nonbonded interactions: 60198 Sorted by model distance: nonbonded pdb="CA CA B 901 " pdb="CA CA B 902 " model vdw 2.248 3.460 nonbonded pdb=" O SER A 280 " pdb=" OG SER A 280 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR B 409 " pdb=" O GLN B 482 " model vdw 2.316 3.040 nonbonded pdb=" OG SER B 434 " pdb=" OD2 ASP B 437 " model vdw 2.327 3.040 nonbonded pdb=" O VAL A 302 " pdb=" ND2 ASN A 363 " model vdw 2.332 3.120 ... (remaining 60193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 218 through 313 or resid 320 through 678 or resid 682 thro \ ugh 746 or resid 901 through 903)) selection = (chain 'B' and (resid 218 through 451 or resid 457 through 903)) } 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: 2.410 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: 0.010 Process input model: 6.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 0.115 8271 Z= 0.182 Angle : 0.813 12.027 11224 Z= 0.447 Chirality : 0.053 0.381 1279 Planarity : 0.006 0.109 1460 Dihedral : 18.387 90.109 3067 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.76 % Allowed : 33.62 % Favored : 65.62 % 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: -2.59 (0.24), residues: 1031 helix: -2.92 (0.34), residues: 112 sheet: 0.07 (0.32), residues: 275 loop : -2.46 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 607 TYR 0.041 0.001 TYR B 261 PHE 0.018 0.002 PHE A 281 TRP 0.016 0.002 TRP A 503 HIS 0.000 0.000 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 8271) covalent geometry : angle 0.81342 / 0.45 (11224) hydrogen bonds : bond 0.16973 / 10.61 ( 214) hydrogen bonds : angle 7.04091 / 4.68 ( 618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 GLU cc_start: 0.7321 (pm20) cc_final: 0.6883 (pm20) REVERT: B 654 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8068 (p) outliers start: 7 outliers final: 2 residues processed: 106 average time/residue: 0.0762 time to fit residues: 11.8041 Evaluate side-chains 97 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain B residue 627 ASN Chi-restraints excluded: chain B residue 654 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117132 restraints weight = 11858.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120663 restraints weight = 7127.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123177 restraints weight = 5090.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124836 restraints weight = 4010.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125906 restraints weight = 3397.141| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8271 Z= 0.234 Angle : 0.662 6.703 11224 Z= 0.356 Chirality : 0.047 0.177 1279 Planarity : 0.005 0.061 1460 Dihedral : 5.470 38.204 1120 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 5.42 % Allowed : 30.15 % Favored : 64.43 % 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: -2.40 (0.25), residues: 1031 helix: -1.87 (0.40), residues: 124 sheet: -0.22 (0.32), residues: 276 loop : -2.30 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 529 TYR 0.019 0.002 TYR B 396 PHE 0.024 0.002 PHE A 281 TRP 0.022 0.002 TRP A 503 HIS 0.001 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 ( 8271) covalent geometry : angle 0.66158 / 0.36 (11224) hydrogen bonds : bond 0.04224 / 2.83 ( 214) hydrogen bonds : angle 5.37612 / 3.66 ( 618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 89 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7811 (t70) REVERT: B 251 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: B 297 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.5638 (p90) REVERT: B 537 ASP cc_start: 0.8288 (m-30) cc_final: 0.7415 (t0) REVERT: B 595 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5510 (mm) REVERT: B 627 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8160 (t0) outliers start: 50 outliers final: 28 residues processed: 130 average time/residue: 0.0760 time to fit residues: 14.3933 Evaluate side-chains 116 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 627 ASN Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 739 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 225 ASN B 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121490 restraints weight = 11408.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124658 restraints weight = 7319.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126883 restraints weight = 5395.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128338 restraints weight = 4346.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129324 restraints weight = 3741.042| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8271 Z= 0.127 Angle : 0.545 6.393 11224 Z= 0.292 Chirality : 0.044 0.166 1279 Planarity : 0.004 0.048 1460 Dihedral : 5.000 39.260 1119 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.34 % Allowed : 30.69 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.22 (0.25), residues: 1031 helix: -1.34 (0.44), residues: 124 sheet: -0.16 (0.31), residues: 283 loop : -2.26 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 528 TYR 0.013 0.001 TYR A 464 PHE 0.014 0.002 PHE A 281 TRP 0.012 0.001 TRP A 503 HIS 0.001 0.000 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8271) covalent geometry : angle 0.54468 / 0.29 (11224) hydrogen bonds : bond 0.03265 / 2.20 ( 214) hydrogen bonds : angle 4.96082 / 3.38 ( 618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7290 (t70) cc_final: 0.6941 (t0) REVERT: B 251 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: B 537 ASP cc_start: 0.8148 (m-30) cc_final: 0.7446 (t0) REVERT: B 627 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8012 (t0) outliers start: 40 outliers final: 19 residues processed: 122 average time/residue: 0.0667 time to fit residues: 12.1610 Evaluate side-chains 106 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 627 ASN Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 744 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 47 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 15 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 682 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125294 restraints weight = 11585.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128551 restraints weight = 7278.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130813 restraints weight = 5302.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132300 restraints weight = 4244.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.133292 restraints weight = 3633.665| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8271 Z= 0.100 Angle : 0.514 10.334 11224 Z= 0.272 Chirality : 0.043 0.163 1279 Planarity : 0.003 0.041 1460 Dihedral : 4.661 39.841 1119 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.77 % Allowed : 30.26 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.00 (0.25), residues: 1031 helix: -0.91 (0.47), residues: 121 sheet: -0.05 (0.31), residues: 282 loop : -2.14 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 528 TYR 0.019 0.001 TYR B 261 PHE 0.011 0.001 PHE A 281 TRP 0.008 0.001 TRP A 503 HIS 0.001 0.000 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 8271) covalent geometry : angle 0.51357 / 0.27 (11224) hydrogen bonds : bond 0.02799 / 1.88 ( 214) hydrogen bonds : angle 4.61331 / 3.14 ( 618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 90 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7247 (t70) cc_final: 0.6849 (t0) REVERT: A 261 TYR cc_start: 0.7893 (p90) cc_final: 0.7403 (p90) REVERT: B 251 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: B 537 ASP cc_start: 0.8027 (m-30) cc_final: 0.7389 (t0) REVERT: B 595 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5836 (mm) REVERT: B 627 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.7879 (t0) outliers start: 44 outliers final: 25 residues processed: 124 average time/residue: 0.0654 time to fit residues: 11.8093 Evaluate side-chains 116 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 260 ASN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 627 ASN Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain B residue 739 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 682 ASN B 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124263 restraints weight = 11534.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127458 restraints weight = 7265.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129723 restraints weight = 5303.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131251 restraints weight = 4251.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.132204 restraints weight = 3626.176| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8271 Z= 0.105 Angle : 0.524 10.259 11224 Z= 0.275 Chirality : 0.043 0.160 1279 Planarity : 0.003 0.037 1460 Dihedral : 4.629 39.768 1119 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 5.10 % Allowed : 29.93 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.91 (0.26), residues: 1031 helix: -0.83 (0.48), residues: 121 sheet: 0.10 (0.33), residues: 275 loop : -2.11 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 394 TYR 0.011 0.001 TYR A 697 PHE 0.012 0.001 PHE A 281 TRP 0.009 0.001 TRP A 503 HIS 0.001 0.000 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 8271) covalent geometry : angle 0.52365 / 0.28 (11224) hydrogen bonds : bond 0.02841 / 1.89 ( 214) hydrogen bonds : angle 4.53263 / 3.09 ( 618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 92 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7400 (t70) cc_final: 0.6923 (t0) REVERT: A 261 TYR cc_start: 0.7873 (p90) cc_final: 0.7428 (p90) REVERT: A 376 ASN cc_start: 0.8318 (t0) cc_final: 0.8087 (t0) REVERT: A 522 GLU cc_start: 0.7386 (pm20) cc_final: 0.7163 (pm20) REVERT: B 251 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: B 537 ASP cc_start: 0.8082 (m-30) cc_final: 0.7389 (t0) REVERT: B 595 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5834 (mm) REVERT: B 627 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.7855 (t0) outliers start: 47 outliers final: 28 residues processed: 131 average time/residue: 0.0627 time to fit residues: 12.0281 Evaluate side-chains 115 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 627 ASN Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 739 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 ASN B 329 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114546 restraints weight = 11751.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118070 restraints weight = 7058.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120357 restraints weight = 5003.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122147 restraints weight = 3964.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123210 restraints weight = 3343.182| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 8271 Z= 0.244 Angle : 0.675 11.696 11224 Z= 0.360 Chirality : 0.048 0.169 1279 Planarity : 0.004 0.038 1460 Dihedral : 5.402 31.395 1119 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 5.53 % Allowed : 30.26 % Favored : 64.21 % 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: -2.11 (0.25), residues: 1031 helix: -1.10 (0.46), residues: 120 sheet: -0.13 (0.32), residues: 283 loop : -2.18 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 528 TYR 0.022 0.002 TYR A 395 PHE 0.021 0.002 PHE B 281 TRP 0.019 0.002 TRP A 503 HIS 0.001 0.000 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.24 ( 8271) covalent geometry : angle 0.67542 / 0.36 (11224) hydrogen bonds : bond 0.04185 / 2.78 ( 214) hydrogen bonds : angle 5.17613 / 3.55 ( 618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 85 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 ASP cc_start: 0.8211 (t0) cc_final: 0.7798 (t0) REVERT: A 522 GLU cc_start: 0.7518 (pm20) cc_final: 0.7265 (pm20) REVERT: B 246 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: B 297 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.5768 (p90) REVERT: B 537 ASP cc_start: 0.8454 (m-30) cc_final: 0.7458 (t0) REVERT: B 573 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7806 (pp20) REVERT: B 595 LEU cc_start: 0.5749 (OUTLIER) cc_final: 0.5464 (mm) outliers start: 51 outliers final: 33 residues processed: 127 average time/residue: 0.0642 time to fit residues: 11.8193 Evaluate side-chains 117 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 739 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113703 restraints weight = 11835.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116749 restraints weight = 7564.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118941 restraints weight = 5556.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120363 restraints weight = 4478.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121432 restraints weight = 3856.239| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8271 Z= 0.124 Angle : 0.560 6.427 11224 Z= 0.298 Chirality : 0.045 0.163 1279 Planarity : 0.003 0.036 1460 Dihedral : 4.790 23.504 1117 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.80 % Allowed : 31.78 % Favored : 64.43 % 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: -2.00 (0.26), residues: 1031 helix: -0.88 (0.46), residues: 124 sheet: -0.08 (0.32), residues: 286 loop : -2.14 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 528 TYR 0.013 0.001 TYR A 464 PHE 0.014 0.002 PHE A 281 TRP 0.011 0.001 TRP A 503 HIS 0.001 0.000 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 ( 8271) covalent geometry : angle 0.56014 / 0.30 (11224) hydrogen bonds : bond 0.03095 / 2.06 ( 214) hydrogen bonds : angle 4.84138 / 3.31 ( 618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 369 ASP cc_start: 0.8057 (t0) cc_final: 0.7659 (t0) REVERT: A 522 GLU cc_start: 0.7499 (pm20) cc_final: 0.7265 (pm20) REVERT: A 725 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7515 (pp) REVERT: B 251 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7140 (pm20) REVERT: B 297 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.5779 (p90) REVERT: B 537 ASP cc_start: 0.8198 (m-30) cc_final: 0.7469 (t0) REVERT: B 595 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5695 (mm) outliers start: 35 outliers final: 24 residues processed: 117 average time/residue: 0.0692 time to fit residues: 11.9282 Evaluate side-chains 112 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain B residue 739 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.0370 chunk 86 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 0.0030 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115632 restraints weight = 11664.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118719 restraints weight = 7499.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120885 restraints weight = 5534.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122360 restraints weight = 4475.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123315 restraints weight = 3845.502| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8271 Z= 0.111 Angle : 0.550 7.137 11224 Z= 0.292 Chirality : 0.044 0.163 1279 Planarity : 0.003 0.034 1460 Dihedral : 4.585 23.738 1117 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.01 % Allowed : 31.45 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.87 (0.26), residues: 1031 helix: -0.57 (0.48), residues: 119 sheet: -0.01 (0.32), residues: 286 loop : -2.09 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 394 TYR 0.022 0.001 TYR B 261 PHE 0.012 0.001 PHE A 281 TRP 0.010 0.001 TRP A 503 HIS 0.007 0.002 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 8271) covalent geometry : angle 0.55005 / 0.29 (11224) hydrogen bonds : bond 0.02892 / 1.93 ( 214) hydrogen bonds : angle 4.67980 / 3.20 ( 618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 522 GLU cc_start: 0.7418 (pm20) cc_final: 0.7197 (pm20) REVERT: A 725 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7455 (pp) REVERT: B 251 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: B 537 ASP cc_start: 0.8185 (m-30) cc_final: 0.7464 (t0) REVERT: B 595 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5707 (mm) outliers start: 37 outliers final: 28 residues processed: 116 average time/residue: 0.0605 time to fit residues: 10.4098 Evaluate side-chains 115 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 437 ASP Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 744 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118782 restraints weight = 11708.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122170 restraints weight = 7219.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124529 restraints weight = 5184.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126035 restraints weight = 4120.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127186 restraints weight = 3516.996| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8271 Z= 0.142 Angle : 0.578 7.472 11224 Z= 0.306 Chirality : 0.045 0.161 1279 Planarity : 0.003 0.034 1460 Dihedral : 4.735 24.861 1117 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.12 % Allowed : 30.91 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.92 (0.26), residues: 1031 helix: -0.77 (0.46), residues: 126 sheet: -0.01 (0.32), residues: 285 loop : -2.11 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 528 TYR 0.016 0.001 TYR A 388 PHE 0.015 0.002 PHE A 281 TRP 0.012 0.002 TRP A 503 HIS 0.001 0.000 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 8271) covalent geometry : angle 0.57786 / 0.31 (11224) hydrogen bonds : bond 0.03174 / 2.10 ( 214) hydrogen bonds : angle 4.73695 / 3.25 ( 618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 369 ASP cc_start: 0.8116 (t0) cc_final: 0.7698 (t0) REVERT: A 522 GLU cc_start: 0.7573 (pm20) cc_final: 0.7319 (pm20) REVERT: A 725 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7248 (pp) REVERT: B 251 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: B 297 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.5518 (p90) REVERT: B 537 ASP cc_start: 0.8390 (m-30) cc_final: 0.7501 (t0) REVERT: B 595 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5515 (mm) outliers start: 38 outliers final: 28 residues processed: 120 average time/residue: 0.0643 time to fit residues: 11.3113 Evaluate side-chains 117 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 744 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118665 restraints weight = 11719.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122259 restraints weight = 7011.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124783 restraints weight = 4963.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126405 restraints weight = 3899.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127612 restraints weight = 3305.114| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8271 Z= 0.132 Angle : 0.566 7.736 11224 Z= 0.300 Chirality : 0.044 0.158 1279 Planarity : 0.003 0.034 1460 Dihedral : 4.684 24.342 1117 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.58 % Allowed : 31.24 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.86 (0.26), residues: 1031 helix: -0.70 (0.47), residues: 125 sheet: 0.03 (0.33), residues: 285 loop : -2.08 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.022 0.001 TYR B 261 PHE 0.015 0.002 PHE A 281 TRP 0.012 0.001 TRP A 503 HIS 0.001 0.000 HIS A 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 8271) covalent geometry : angle 0.56562 / 0.30 (11224) hydrogen bonds : bond 0.03055 / 2.03 ( 214) hydrogen bonds : angle 4.66846 / 3.20 ( 618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 522 GLU cc_start: 0.7583 (pm20) cc_final: 0.7332 (pm20) REVERT: A 725 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7213 (pp) REVERT: B 251 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: B 297 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.5565 (p90) REVERT: B 537 ASP cc_start: 0.8371 (m-30) cc_final: 0.7517 (t0) REVERT: B 595 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5530 (mm) outliers start: 33 outliers final: 27 residues processed: 113 average time/residue: 0.0697 time to fit residues: 11.5652 Evaluate side-chains 117 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 297 TYR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 744 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 0.0030 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.0040 chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 69 optimal weight: 0.0050 chunk 63 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 682 ASN B 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126936 restraints weight = 11432.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130176 restraints weight = 7223.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132500 restraints weight = 5256.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133972 restraints weight = 4205.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.135102 restraints weight = 3609.443| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8271 Z= 0.097 Angle : 0.525 7.622 11224 Z= 0.278 Chirality : 0.043 0.149 1279 Planarity : 0.003 0.059 1460 Dihedral : 4.343 22.692 1117 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.25 % Allowed : 31.78 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.66 (0.26), residues: 1031 helix: -0.32 (0.51), residues: 115 sheet: 0.10 (0.32), residues: 282 loop : -1.93 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 394 TYR 0.015 0.001 TYR A 388 PHE 0.010 0.001 PHE A 711 TRP 0.008 0.001 TRP B 503 HIS 0.000 0.000 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 8271) covalent geometry : angle 0.52530 / 0.28 (11224) hydrogen bonds : bond 0.02544 / 1.67 ( 214) hydrogen bonds : angle 4.42472 / 3.04 ( 618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1156.48 seconds wall clock time: 20 minutes 44.64 seconds (1244.64 seconds total)