Starting phenix.real_space_refine on Sat Jul 4 11:38:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t0y_40949/07_2026/8t0y_40949_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t0y_40949/07_2026/8t0y_40949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t0y_40949/07_2026/8t0y_40949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t0y_40949/07_2026/8t0y_40949.map" model { file = "/net/cci-nas-00/data/ceres_data/8t0y_40949/07_2026/8t0y_40949_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t0y_40949/07_2026/8t0y_40949_trim.cif" } resolution = 3.5 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 70 5.16 5 Na 1 4.78 5 C 6784 2.51 5 N 1533 2.21 5 O 1779 1.98 5 H 10143 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 20314 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4941 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 289} Chain breaks: 2 Chain: "A" Number of atoms: 5059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 5059 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 296} Chain breaks: 1 Chain: "D" Number of atoms: 5097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 5097 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 299} Chain: "C" Number of atoms: 5056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 5056 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 296} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Time building chain proxies: 4.14, per 1000 atoms: 0.20 Number of scatterers: 20314 At special positions: 0 Unit cell: (114.395, 112.725, 80.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 70 16.00 P 4 15.00 Na 1 11.00 O 1779 8.00 N 1533 7.00 C 6784 6.00 H 10143 1.00 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: 2.20 Conformation dependent library (CDL) restraints added in 573.6 milliseconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 82.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 430 through 454 Processing helix chain 'B' and resid 469 through 500 Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.659A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.609A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 4.050A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.822A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 689 Processing helix chain 'B' and resid 689 through 711 Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.500A pdb=" N TYR A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.736A pdb=" N LEU A 413 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 510 through 532 removed outlier: 3.636A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 552 removed outlier: 4.244A pdb=" N ALA A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.655A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 4.117A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 628 removed outlier: 3.571A pdb=" N ASN A 628 " --> pdb=" O GLY A 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 602 through 628' Processing helix chain 'A' and resid 629 through 640 removed outlier: 3.782A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.501A pdb=" N PHE A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 689 Processing helix chain 'A' and resid 689 through 712 removed outlier: 3.674A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.904A pdb=" N LEU D 413 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.564A pdb=" N TYR D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS D 442 " --> pdb=" O PHE D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 535 through 551 removed outlier: 4.385A pdb=" N ALA D 539 " --> pdb=" O LYS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.697A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 4.081A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 628 Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.532A pdb=" N THR D 633 " --> pdb=" O SER D 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 689 through 712 removed outlier: 3.529A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 408 through 414 removed outlier: 3.661A pdb=" N MET C 412 " --> pdb=" O ARG C 409 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 413 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 450 removed outlier: 5.370A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE C 448 " --> pdb=" O TYR C 444 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA C 450 " --> pdb=" O ILE C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 532 removed outlier: 3.814A pdb=" N ILE C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 556 removed outlier: 4.492A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 4.238A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.641A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 689 Processing helix chain 'C' and resid 689 through 712 739 hydrogen bonds defined for protein. 2181 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: 4.71 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10125 1.03 - 1.23: 39 1.23 - 1.42: 4492 1.42 - 1.62: 5776 1.62 - 1.81: 129 Bond restraints: 20561 Sorted by residual: bond pdb=" OAB NKN D 901 " pdb=" PAC NKN D 901 " ideal model delta sigma weight residual 1.668 1.455 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" OAA NKN D 901 " pdb=" PAC NKN D 901 " ideal model delta sigma weight residual 1.667 1.459 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C SER D 510 " pdb=" O SER D 510 " ideal model delta sigma weight residual 1.234 1.178 0.055 1.44e-02 4.82e+03 1.48e+01 bond pdb=" C ARG B 701 " pdb=" O ARG B 701 " ideal model delta sigma weight residual 1.236 1.191 0.046 1.26e-02 6.30e+03 1.31e+01 bond pdb=" CAG NKN D 901 " pdb=" OAF NKN D 901 " ideal model delta sigma weight residual 1.467 1.396 0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 20556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.92: 36927 9.92 - 19.84: 8 19.84 - 29.77: 5 29.77 - 39.69: 0 39.69 - 49.61: 1 Bond angle restraints: 36941 Sorted by residual: angle pdb=" OAA NKN D 901 " pdb=" PAC NKN D 901 " pdb=" OAB NKN D 901 " ideal model delta sigma weight residual 54.49 104.10 -49.61 3.00e+00 1.11e-01 2.73e+02 angle pdb=" OAB NKN D 901 " pdb=" PAC NKN D 901 " pdb=" OAD NKN D 901 " ideal model delta sigma weight residual 128.49 104.15 24.34 3.00e+00 1.11e-01 6.58e+01 angle pdb=" O1 8IJ B 901 " pdb=" P2 8IJ B 901 " pdb=" O3 8IJ B 901 " ideal model delta sigma weight residual 121.24 97.23 24.01 3.00e+00 1.11e-01 6.40e+01 angle pdb=" O1 8IJ A 901 " pdb=" P2 8IJ A 901 " pdb=" O3 8IJ A 901 " ideal model delta sigma weight residual 121.24 97.27 23.97 3.00e+00 1.11e-01 6.38e+01 angle pdb=" OAA NKN D 901 " pdb=" PAC NKN D 901 " pdb=" OAD NKN D 901 " ideal model delta sigma weight residual 128.00 104.85 23.15 3.00e+00 1.11e-01 5.95e+01 ... (remaining 36936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.09: 9396 34.09 - 68.17: 358 68.17 - 102.26: 54 102.26 - 136.34: 24 136.34 - 170.43: 6 Dihedral angle restraints: 9838 sinusoidal: 5225 harmonic: 4613 Sorted by residual: dihedral pdb=" CD ARG B 500 " pdb=" NE ARG B 500 " pdb=" CZ ARG B 500 " pdb=" NH1 ARG B 500 " ideal model delta sinusoidal sigma weight residual 0.00 -77.07 77.07 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CD ARG D 409 " pdb=" NE ARG D 409 " pdb=" CZ ARG D 409 " pdb=" NH1 ARG D 409 " ideal model delta sinusoidal sigma weight residual 0.00 -76.55 76.55 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CD ARG B 432 " pdb=" NE ARG B 432 " pdb=" CZ ARG B 432 " pdb=" NH1 ARG B 432 " ideal model delta sinusoidal sigma weight residual 0.00 65.90 -65.90 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 9835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.025: 1574 1.025 - 2.049: 0 2.049 - 3.074: 0 3.074 - 4.099: 0 4.099 - 5.123: 9 Chirality restraints: 1583 Sorted by residual: chirality pdb=" C18 8IJ A 901 " pdb=" C17 8IJ A 901 " pdb=" C19 8IJ A 901 " pdb=" O40 8IJ A 901 " both_signs ideal model delta sigma weight residual False -2.58 2.55 -5.12 2.00e-01 2.50e+01 6.56e+02 chirality pdb=" C18 8IJ B 901 " pdb=" C17 8IJ B 901 " pdb=" C19 8IJ B 901 " pdb=" O40 8IJ B 901 " both_signs ideal model delta sigma weight residual False -2.58 2.55 -5.12 2.00e-01 2.50e+01 6.56e+02 chirality pdb=" C18 8IJ C 901 " pdb=" C17 8IJ C 901 " pdb=" C19 8IJ C 901 " pdb=" O40 8IJ C 901 " both_signs ideal model delta sigma weight residual False -2.58 2.48 -5.06 2.00e-01 2.50e+01 6.40e+02 ... (remaining 1580 not shown) Planarity restraints: 2870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 428 " 0.301 9.50e-02 1.11e+02 4.79e-01 4.96e+03 pdb=" NE ARG B 428 " -0.214 2.00e-02 2.50e+03 pdb=" CZ ARG B 428 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG B 428 " 0.062 2.00e-02 2.50e+03 pdb=" NH2 ARG B 428 " -0.014 2.00e-02 2.50e+03 pdb="HH11 ARG B 428 " -0.661 2.00e-02 2.50e+03 pdb="HH12 ARG B 428 " 0.857 2.00e-02 2.50e+03 pdb="HH21 ARG B 428 " -0.611 2.00e-02 2.50e+03 pdb="HH22 ARG B 428 " 0.617 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 701 " 0.601 9.50e-02 1.11e+02 4.84e-01 4.40e+03 pdb=" NE ARG B 701 " 0.116 2.00e-02 2.50e+03 pdb=" CZ ARG B 701 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG B 701 " -0.067 2.00e-02 2.50e+03 pdb=" NH2 ARG B 701 " 0.030 2.00e-02 2.50e+03 pdb="HH11 ARG B 701 " -0.842 2.00e-02 2.50e+03 pdb="HH12 ARG B 701 " 0.646 2.00e-02 2.50e+03 pdb="HH21 ARG B 701 " 0.578 2.00e-02 2.50e+03 pdb="HH22 ARG B 701 " -0.515 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 420 " 0.587 9.50e-02 1.11e+02 4.17e-01 3.10e+03 pdb=" NE ARG A 420 " 0.088 2.00e-02 2.50e+03 pdb=" CZ ARG A 420 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 420 " -0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 420 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG A 420 " -0.809 2.00e-02 2.50e+03 pdb="HH12 ARG A 420 " 0.713 2.00e-02 2.50e+03 pdb="HH21 ARG A 420 " 0.148 2.00e-02 2.50e+03 pdb="HH22 ARG A 420 " -0.168 2.00e-02 2.50e+03 ... (remaining 2867 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 2498 2.26 - 2.84: 45163 2.84 - 3.43: 53839 3.43 - 4.01: 69746 4.01 - 4.60: 107953 Nonbonded interactions: 279199 Sorted by model distance: nonbonded pdb="HD21 ASN B 687 " pdb=" OE1 GLU A 684 " model vdw 1.670 2.450 nonbonded pdb=" O ILE B 399 " pdb=" HG SER B 402 " model vdw 1.687 2.450 nonbonded pdb=" O SER A 505 " pdb=" H ASP A 509 " model vdw 1.692 2.450 nonbonded pdb=" O ASN C 551 " pdb=" H TYR C 554 " model vdw 1.708 2.450 nonbonded pdb=" OE1 GLN C 691 " pdb=" H GLN C 691 " model vdw 1.722 2.450 ... (remaining 279194 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 387 through 463 or resid 468 through 712)) selection = (chain 'B' and resid 387 through 712) selection = (chain 'C' and (resid 387 through 456 or resid 460 through 463 or resid 468 thro \ ugh 712)) selection = (chain 'D' and (resid 387 through 456 or resid 460 through 463 or resid 468 thro \ ugh 712)) } 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: 6.420 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: 0.140 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.710 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 : 0.006 0.213 10418 Z= 0.368 Angle : 1.107 49.612 14066 Z= 0.585 Chirality : 0.380 5.123 1583 Planarity : 0.030 0.480 1693 Dihedral : 21.374 170.430 3905 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.36 % Allowed : 1.72 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.74 (0.25), residues: 1194 helix: 1.91 (0.17), residues: 923 sheet: None (None), residues: 0 loop : -1.56 (0.43), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 432 TYR 0.018 0.001 TYR B 537 PHE 0.025 0.001 PHE C 448 TRP 0.012 0.002 TRP B 426 HIS 0.001 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.37 (10418) covalent geometry : angle 1.10728 / 0.58 (14066) hydrogen bonds : bond 0.11294 / 7.24 ( 739) hydrogen bonds : angle 5.32208 / 3.92 ( 2181) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 320 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 LEU cc_start: 0.8539 (mt) cc_final: 0.8271 (tt) REVERT: B 430 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8062 (t) REVERT: B 443 LEU cc_start: 0.8615 (tt) cc_final: 0.8150 (mt) REVERT: B 504 LYS cc_start: 0.7588 (mttt) cc_final: 0.7289 (tttm) REVERT: B 598 LEU cc_start: 0.8263 (tp) cc_final: 0.7857 (tp) REVERT: A 519 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8246 (tt0) REVERT: A 579 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7793 (mtt-85) REVERT: A 644 MET cc_start: 0.7644 (tpt) cc_final: 0.7059 (mmt) REVERT: D 423 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7005 (tp-100) REVERT: D 437 ASN cc_start: 0.7655 (m110) cc_final: 0.7101 (m110) REVERT: D 478 GLU cc_start: 0.6464 (tm-30) cc_final: 0.6206 (tm-30) REVERT: C 432 ARG cc_start: 0.7546 (ptm160) cc_final: 0.7301 (mtp-110) REVERT: C 478 GLU cc_start: 0.7235 (tt0) cc_final: 0.6791 (tt0) REVERT: C 500 ARG cc_start: 0.5780 (mmt180) cc_final: 0.5537 (mmm160) REVERT: C 636 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7496 (mm-30) outliers start: 15 outliers final: 4 residues processed: 328 average time/residue: 0.2222 time to fit residues: 102.2615 Evaluate side-chains 272 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 448 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 652 ASN B 687 ASN C 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.125699 restraints weight = 42400.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130262 restraints weight = 16947.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133115 restraints weight = 9639.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.134860 restraints weight = 6718.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136088 restraints weight = 5306.620| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10418 Z= 0.154 Angle : 0.533 5.524 14066 Z= 0.291 Chirality : 0.034 0.153 1583 Planarity : 0.004 0.062 1693 Dihedral : 11.754 104.170 1570 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.27 % Allowed : 9.98 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.20 (0.25), residues: 1194 helix: 2.27 (0.17), residues: 921 sheet: None (None), residues: 0 loop : -1.51 (0.43), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 409 TYR 0.010 0.001 TYR D 495 PHE 0.019 0.001 PHE C 448 TRP 0.009 0.001 TRP D 697 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (10418) covalent geometry : angle 0.53328 / 0.29 (14066) hydrogen bonds : bond 0.05146 / 3.45 ( 739) hydrogen bonds : angle 4.14388 / 3.02 ( 2181) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 275 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 LEU cc_start: 0.8525 (mt) cc_final: 0.8175 (tt) REVERT: B 443 LEU cc_start: 0.8526 (tt) cc_final: 0.8039 (mt) REVERT: B 504 LYS cc_start: 0.7826 (mttt) cc_final: 0.7296 (tttm) REVERT: B 598 LEU cc_start: 0.8251 (tp) cc_final: 0.7809 (tp) REVERT: A 519 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8271 (tt0) REVERT: A 526 SER cc_start: 0.8759 (t) cc_final: 0.8390 (m) REVERT: A 644 MET cc_start: 0.7533 (tpt) cc_final: 0.7045 (mmt) REVERT: D 423 GLN cc_start: 0.7608 (tp-100) cc_final: 0.7161 (tp40) REVERT: D 437 ASN cc_start: 0.7931 (m110) cc_final: 0.7580 (m110) REVERT: D 478 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6400 (tm-30) REVERT: D 565 TYR cc_start: 0.8699 (t80) cc_final: 0.8301 (t80) REVERT: C 432 ARG cc_start: 0.7698 (ptm160) cc_final: 0.7417 (mtp-110) REVERT: C 478 GLU cc_start: 0.7342 (tt0) cc_final: 0.6862 (tt0) REVERT: C 500 ARG cc_start: 0.5891 (mmt180) cc_final: 0.5583 (mmm160) REVERT: C 636 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7790 (mm-30) REVERT: C 684 GLU cc_start: 0.7722 (pp20) cc_final: 0.7344 (tt0) outliers start: 14 outliers final: 11 residues processed: 280 average time/residue: 0.1986 time to fit residues: 81.2193 Evaluate side-chains 271 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 260 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 556 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 ASN A 551 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.143657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.124151 restraints weight = 42494.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128761 restraints weight = 17307.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131643 restraints weight = 9917.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133428 restraints weight = 6933.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134614 restraints weight = 5466.560| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10418 Z= 0.144 Angle : 0.479 5.657 14066 Z= 0.269 Chirality : 0.033 0.142 1583 Planarity : 0.004 0.048 1693 Dihedral : 9.874 82.704 1567 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.27 % Allowed : 11.25 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.37 (0.25), residues: 1194 helix: 2.37 (0.16), residues: 930 sheet: None (None), residues: 0 loop : -1.51 (0.44), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 557 TYR 0.010 0.001 TYR B 453 PHE 0.016 0.001 PHE C 448 TRP 0.009 0.001 TRP B 426 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (10418) covalent geometry : angle 0.47918 / 0.27 (14066) hydrogen bonds : bond 0.04928 / 3.31 ( 739) hydrogen bonds : angle 3.99901 / 2.89 ( 2181) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 259 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 LEU cc_start: 0.8559 (mt) cc_final: 0.8293 (tt) REVERT: B 443 LEU cc_start: 0.8479 (tt) cc_final: 0.8094 (mt) REVERT: B 504 LYS cc_start: 0.7816 (mttt) cc_final: 0.7303 (tttm) REVERT: B 598 LEU cc_start: 0.8241 (tp) cc_final: 0.7783 (tp) REVERT: A 519 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8262 (tt0) REVERT: A 526 SER cc_start: 0.8773 (t) cc_final: 0.8457 (m) REVERT: A 579 ARG cc_start: 0.8329 (mtp180) cc_final: 0.7565 (mtt-85) REVERT: A 644 MET cc_start: 0.7515 (tpt) cc_final: 0.7015 (mmt) REVERT: D 423 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7160 (tp40) REVERT: D 437 ASN cc_start: 0.8290 (m110) cc_final: 0.7966 (m110) REVERT: D 478 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6317 (tm-30) REVERT: D 565 TYR cc_start: 0.8710 (t80) cc_final: 0.8374 (t80) REVERT: C 432 ARG cc_start: 0.7714 (ptm160) cc_final: 0.7458 (mtp-110) REVERT: C 478 GLU cc_start: 0.7290 (tt0) cc_final: 0.6799 (tt0) REVERT: C 500 ARG cc_start: 0.5905 (mmt180) cc_final: 0.5596 (mmm160) REVERT: C 636 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7757 (mm-30) REVERT: C 684 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7381 (tt0) outliers start: 14 outliers final: 9 residues processed: 267 average time/residue: 0.1953 time to fit residues: 76.1355 Evaluate side-chains 267 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 257 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 444 TYR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 ASN A 551 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.122884 restraints weight = 42674.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127279 restraints weight = 17942.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.130063 restraints weight = 10492.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.131811 restraints weight = 7424.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.132932 restraints weight = 5868.685| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10418 Z= 0.154 Angle : 0.480 5.473 14066 Z= 0.271 Chirality : 0.033 0.141 1583 Planarity : 0.003 0.043 1693 Dihedral : 9.397 81.350 1563 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.81 % Allowed : 12.52 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.25), residues: 1194 helix: 2.45 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -1.44 (0.43), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 557 TYR 0.012 0.001 TYR B 453 PHE 0.016 0.001 PHE C 448 TRP 0.010 0.001 TRP B 426 HIS 0.001 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10418) covalent geometry : angle 0.48013 / 0.27 (14066) hydrogen bonds : bond 0.05009 / 3.37 ( 739) hydrogen bonds : angle 3.95791 / 2.85 ( 2181) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 432 ARG cc_start: 0.6836 (mpt180) cc_final: 0.6495 (mmt90) REVERT: B 443 LEU cc_start: 0.8474 (tt) cc_final: 0.8133 (mt) REVERT: B 478 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5613 (tm-30) REVERT: B 504 LYS cc_start: 0.7756 (mttt) cc_final: 0.7267 (tttm) REVERT: B 506 LEU cc_start: 0.6894 (pt) cc_final: 0.6486 (pp) REVERT: B 598 LEU cc_start: 0.8214 (tp) cc_final: 0.7748 (tp) REVERT: A 519 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8293 (tt0) REVERT: A 526 SER cc_start: 0.8760 (t) cc_final: 0.8436 (m) REVERT: A 579 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7656 (mtt-85) REVERT: A 644 MET cc_start: 0.7532 (tpt) cc_final: 0.6982 (mmt) REVERT: A 648 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7189 (tp30) REVERT: D 423 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7247 (tp40) REVERT: D 437 ASN cc_start: 0.8397 (m110) cc_final: 0.8058 (m110) REVERT: D 478 GLU cc_start: 0.6632 (tm-30) cc_final: 0.6215 (tm-30) REVERT: D 565 TYR cc_start: 0.8665 (t80) cc_final: 0.8351 (t80) REVERT: C 387 ILE cc_start: 0.3854 (mp) cc_final: 0.3624 (mp) REVERT: C 432 ARG cc_start: 0.7643 (ptm160) cc_final: 0.7420 (mtp-110) REVERT: C 478 GLU cc_start: 0.7299 (tt0) cc_final: 0.7090 (tt0) REVERT: C 500 ARG cc_start: 0.5868 (mmt180) cc_final: 0.5595 (mmm160) REVERT: C 636 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7758 (mm-30) REVERT: C 648 GLU cc_start: 0.7766 (pt0) cc_final: 0.7441 (pt0) REVERT: C 684 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7373 (tt0) outliers start: 20 outliers final: 16 residues processed: 274 average time/residue: 0.2097 time to fit residues: 83.7600 Evaluate side-chains 276 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 258 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 112 optimal weight: 0.0980 chunk 8 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 ASN A 551 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.146893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128626 restraints weight = 42425.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133029 restraints weight = 17449.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.135774 restraints weight = 10001.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.137448 restraints weight = 6986.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138618 restraints weight = 5515.569| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10418 Z= 0.143 Angle : 0.477 5.806 14066 Z= 0.268 Chirality : 0.032 0.135 1583 Planarity : 0.003 0.047 1693 Dihedral : 9.196 79.151 1561 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.09 % Allowed : 13.07 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.62 (0.25), residues: 1194 helix: 2.57 (0.16), residues: 918 sheet: None (None), residues: 0 loop : -1.31 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 474 TYR 0.011 0.001 TYR B 453 PHE 0.015 0.001 PHE C 448 TRP 0.008 0.001 TRP D 697 HIS 0.002 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (10418) covalent geometry : angle 0.47741 / 0.27 (14066) hydrogen bonds : bond 0.04874 / 3.28 ( 739) hydrogen bonds : angle 3.91611 / 2.82 ( 2181) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 443 LEU cc_start: 0.8465 (tt) cc_final: 0.8150 (mt) REVERT: B 478 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5652 (tm-30) REVERT: B 504 LYS cc_start: 0.7707 (mttt) cc_final: 0.7226 (tttm) REVERT: B 506 LEU cc_start: 0.6900 (pt) cc_final: 0.6474 (pp) REVERT: B 598 LEU cc_start: 0.8215 (tp) cc_final: 0.7725 (tp) REVERT: A 519 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8289 (tt0) REVERT: A 526 SER cc_start: 0.8732 (t) cc_final: 0.8387 (m) REVERT: A 644 MET cc_start: 0.7529 (tpt) cc_final: 0.6949 (mmt) REVERT: A 648 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7206 (tp30) REVERT: D 423 GLN cc_start: 0.7595 (tp-100) cc_final: 0.7270 (tp40) REVERT: D 437 ASN cc_start: 0.8433 (m110) cc_final: 0.8146 (m110) REVERT: D 478 GLU cc_start: 0.6517 (tm-30) cc_final: 0.6117 (tm-30) REVERT: D 565 TYR cc_start: 0.8670 (t80) cc_final: 0.8378 (t80) REVERT: C 387 ILE cc_start: 0.3855 (mp) cc_final: 0.3379 (mp) REVERT: C 478 GLU cc_start: 0.7282 (tt0) cc_final: 0.7058 (tt0) REVERT: C 500 ARG cc_start: 0.5873 (mmt180) cc_final: 0.5602 (mmm160) REVERT: C 636 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7757 (mm-30) outliers start: 23 outliers final: 17 residues processed: 267 average time/residue: 0.1959 time to fit residues: 76.7233 Evaluate side-chains 269 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 251 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 556 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 96 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 102 optimal weight: 0.0370 chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.139875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121405 restraints weight = 42847.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125726 restraints weight = 17704.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128437 restraints weight = 10165.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.130176 restraints weight = 7115.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131294 restraints weight = 5576.519| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10418 Z= 0.162 Angle : 0.493 5.859 14066 Z= 0.277 Chirality : 0.033 0.135 1583 Planarity : 0.004 0.041 1693 Dihedral : 9.298 79.315 1561 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.09 % Allowed : 13.61 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.25), residues: 1194 helix: 2.52 (0.16), residues: 919 sheet: None (None), residues: 0 loop : -1.33 (0.42), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 474 TYR 0.013 0.001 TYR B 453 PHE 0.016 0.001 PHE A 516 TRP 0.007 0.001 TRP B 697 HIS 0.002 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (10418) covalent geometry : angle 0.49266 / 0.28 (14066) hydrogen bonds : bond 0.05010 / 3.37 ( 739) hydrogen bonds : angle 3.93922 / 2.84 ( 2181) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 443 LEU cc_start: 0.8484 (tt) cc_final: 0.8181 (mt) REVERT: B 478 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5454 (tm-30) REVERT: B 504 LYS cc_start: 0.7700 (mttt) cc_final: 0.7237 (tttm) REVERT: B 598 LEU cc_start: 0.8206 (tp) cc_final: 0.7726 (tp) REVERT: A 476 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8246 (t) REVERT: A 519 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8273 (tt0) REVERT: A 526 SER cc_start: 0.8738 (t) cc_final: 0.8467 (m) REVERT: A 644 MET cc_start: 0.7584 (tpt) cc_final: 0.6904 (mmt) REVERT: A 648 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7233 (tp30) REVERT: D 423 GLN cc_start: 0.7537 (tp-100) cc_final: 0.7248 (tp40) REVERT: D 437 ASN cc_start: 0.8472 (m110) cc_final: 0.8195 (m110) REVERT: D 478 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6095 (tm-30) REVERT: D 565 TYR cc_start: 0.8664 (t80) cc_final: 0.8383 (t80) REVERT: C 387 ILE cc_start: 0.3818 (mp) cc_final: 0.3331 (mp) REVERT: C 478 GLU cc_start: 0.7288 (tt0) cc_final: 0.7085 (tt0) REVERT: C 636 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7773 (mm-30) outliers start: 23 outliers final: 20 residues processed: 270 average time/residue: 0.1843 time to fit residues: 73.5275 Evaluate side-chains 279 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 257 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 556 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 ASN A 551 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.145061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.126915 restraints weight = 42725.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131217 restraints weight = 17706.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.133907 restraints weight = 10240.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.135600 restraints weight = 7183.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.136710 restraints weight = 5645.054| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10418 Z= 0.174 Angle : 0.507 6.064 14066 Z= 0.285 Chirality : 0.033 0.137 1583 Planarity : 0.004 0.034 1693 Dihedral : 9.365 79.321 1561 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.18 % Allowed : 14.61 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.25), residues: 1194 helix: 2.41 (0.17), residues: 921 sheet: None (None), residues: 0 loop : -1.28 (0.42), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 474 TYR 0.013 0.001 TYR B 453 PHE 0.016 0.001 PHE C 448 TRP 0.007 0.001 TRP B 697 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (10418) covalent geometry : angle 0.50744 / 0.29 (14066) hydrogen bonds : bond 0.05169 / 3.49 ( 739) hydrogen bonds : angle 3.97348 / 2.87 ( 2181) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 443 LEU cc_start: 0.8470 (tt) cc_final: 0.8166 (mt) REVERT: B 478 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.5460 (tm-30) REVERT: B 504 LYS cc_start: 0.7574 (mttt) cc_final: 0.7207 (tttm) REVERT: B 598 LEU cc_start: 0.8166 (tp) cc_final: 0.7696 (tp) REVERT: A 476 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8249 (t) REVERT: A 519 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8284 (tt0) REVERT: A 526 SER cc_start: 0.8733 (t) cc_final: 0.8423 (m) REVERT: A 644 MET cc_start: 0.7597 (tpt) cc_final: 0.6854 (mmt) REVERT: A 648 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7321 (tp30) REVERT: D 423 GLN cc_start: 0.7549 (tp-100) cc_final: 0.7285 (tp40) REVERT: D 437 ASN cc_start: 0.8486 (m110) cc_final: 0.8222 (m110) REVERT: D 478 GLU cc_start: 0.6593 (tm-30) cc_final: 0.6119 (tm-30) REVERT: D 565 TYR cc_start: 0.8666 (t80) cc_final: 0.8420 (t80) REVERT: C 387 ILE cc_start: 0.3553 (mp) cc_final: 0.3003 (mp) REVERT: C 478 GLU cc_start: 0.7303 (tt0) cc_final: 0.7090 (tt0) outliers start: 24 outliers final: 20 residues processed: 269 average time/residue: 0.1771 time to fit residues: 70.9661 Evaluate side-chains 277 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 556 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 ASN C 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.143032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.124803 restraints weight = 42949.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129072 restraints weight = 17980.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131714 restraints weight = 10456.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.133439 restraints weight = 7388.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.134540 restraints weight = 5822.534| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10418 Z= 0.237 Angle : 0.560 6.496 14066 Z= 0.316 Chirality : 0.035 0.157 1583 Planarity : 0.004 0.035 1693 Dihedral : 9.688 79.480 1561 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.18 % Allowed : 15.43 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.08 (0.25), residues: 1194 helix: 2.19 (0.17), residues: 920 sheet: None (None), residues: 0 loop : -1.56 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 557 TYR 0.016 0.002 TYR B 453 PHE 0.016 0.002 PHE C 448 TRP 0.008 0.001 TRP B 426 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 (10418) covalent geometry : angle 0.55959 / 0.32 (14066) hydrogen bonds : bond 0.05648 / 3.80 ( 739) hydrogen bonds : angle 4.12976 / 2.98 ( 2181) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 443 LEU cc_start: 0.8490 (tt) cc_final: 0.8171 (mt) REVERT: B 478 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5537 (tm-30) REVERT: B 482 VAL cc_start: 0.8773 (m) cc_final: 0.8458 (p) REVERT: B 504 LYS cc_start: 0.7686 (mttt) cc_final: 0.7295 (tttm) REVERT: B 598 LEU cc_start: 0.8186 (tp) cc_final: 0.7729 (tp) REVERT: A 476 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8245 (t) REVERT: A 519 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8259 (tt0) REVERT: A 526 SER cc_start: 0.8767 (t) cc_final: 0.8462 (m) REVERT: A 644 MET cc_start: 0.7649 (tpt) cc_final: 0.6881 (mmt) REVERT: A 648 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7317 (tp30) REVERT: D 423 GLN cc_start: 0.7555 (tp-100) cc_final: 0.7298 (tp40) REVERT: D 437 ASN cc_start: 0.8524 (m110) cc_final: 0.8266 (m110) REVERT: D 565 TYR cc_start: 0.8709 (t80) cc_final: 0.8496 (t80) REVERT: C 478 GLU cc_start: 0.7335 (tt0) cc_final: 0.7122 (tt0) outliers start: 24 outliers final: 20 residues processed: 265 average time/residue: 0.1765 time to fit residues: 69.4992 Evaluate side-chains 269 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 556 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 105 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 ASN A 551 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.144792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.126535 restraints weight = 42560.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130850 restraints weight = 17590.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.133561 restraints weight = 10155.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135318 restraints weight = 7125.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.136450 restraints weight = 5566.116| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10418 Z= 0.166 Angle : 0.512 6.081 14066 Z= 0.287 Chirality : 0.033 0.140 1583 Planarity : 0.003 0.032 1693 Dihedral : 9.291 77.679 1561 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.27 % Allowed : 15.79 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.26 (0.25), residues: 1194 helix: 2.33 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.51 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 474 TYR 0.013 0.001 TYR B 453 PHE 0.014 0.001 PHE C 448 TRP 0.008 0.001 TRP B 697 HIS 0.001 0.000 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (10418) covalent geometry : angle 0.51198 / 0.29 (14066) hydrogen bonds : bond 0.05217 / 3.52 ( 739) hydrogen bonds : angle 3.98638 / 2.87 ( 2181) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 443 LEU cc_start: 0.8469 (tt) cc_final: 0.8175 (mt) REVERT: B 478 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5383 (tm-30) REVERT: B 482 VAL cc_start: 0.8790 (m) cc_final: 0.8467 (p) REVERT: B 504 LYS cc_start: 0.7691 (mttt) cc_final: 0.7284 (tttm) REVERT: B 598 LEU cc_start: 0.8151 (tp) cc_final: 0.7688 (tp) REVERT: A 476 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8217 (t) REVERT: A 519 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8228 (tt0) REVERT: A 526 SER cc_start: 0.8762 (t) cc_final: 0.8431 (m) REVERT: A 644 MET cc_start: 0.7590 (tpt) cc_final: 0.6844 (mmt) REVERT: A 648 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7283 (tp30) REVERT: D 423 GLN cc_start: 0.7555 (tp-100) cc_final: 0.7136 (tp-100) REVERT: D 437 ASN cc_start: 0.8500 (m110) cc_final: 0.8241 (m110) REVERT: D 565 TYR cc_start: 0.8693 (t80) cc_final: 0.8465 (t80) outliers start: 25 outliers final: 20 residues processed: 265 average time/residue: 0.1958 time to fit residues: 77.0096 Evaluate side-chains 274 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 556 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.144712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.126245 restraints weight = 42857.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130568 restraints weight = 17707.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133288 restraints weight = 10281.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.134999 restraints weight = 7240.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.136100 restraints weight = 5711.804| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 10418 Z= 0.192 Angle : 0.802 59.197 14066 Z= 0.483 Chirality : 0.036 0.553 1583 Planarity : 0.004 0.069 1693 Dihedral : 9.297 77.678 1561 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.27 % Allowed : 15.88 % Favored : 81.85 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 16.67 % 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: 2.26 (0.25), residues: 1194 helix: 2.33 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.52 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 409 TYR 0.013 0.001 TYR B 453 PHE 0.014 0.001 PHE C 448 TRP 0.008 0.001 TRP B 697 HIS 0.002 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (10418) covalent geometry : angle 0.80212 / 0.48 (14066) hydrogen bonds : bond 0.05220 / 3.52 ( 739) hydrogen bonds : angle 4.00450 / 2.88 ( 2181) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 443 LEU cc_start: 0.8470 (tt) cc_final: 0.8177 (mt) REVERT: B 478 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5388 (tm-30) REVERT: B 482 VAL cc_start: 0.8795 (m) cc_final: 0.8471 (p) REVERT: B 504 LYS cc_start: 0.7690 (mttt) cc_final: 0.7284 (tttm) REVERT: B 598 LEU cc_start: 0.8152 (tp) cc_final: 0.7692 (tp) REVERT: A 476 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8211 (t) REVERT: A 519 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8226 (tt0) REVERT: A 526 SER cc_start: 0.8749 (t) cc_final: 0.8437 (m) REVERT: A 644 MET cc_start: 0.7587 (tpt) cc_final: 0.6840 (mmt) REVERT: A 648 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7269 (tp30) REVERT: D 423 GLN cc_start: 0.7546 (tp-100) cc_final: 0.7140 (tp-100) REVERT: D 437 ASN cc_start: 0.8500 (m110) cc_final: 0.8243 (m110) REVERT: D 565 TYR cc_start: 0.8683 (t80) cc_final: 0.8420 (t80) outliers start: 25 outliers final: 23 residues processed: 265 average time/residue: 0.1902 time to fit residues: 75.0231 Evaluate side-chains 277 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 556 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.125919 restraints weight = 42860.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.130238 restraints weight = 17690.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.132953 restraints weight = 10235.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134593 restraints weight = 7196.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.135747 restraints weight = 5712.969| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 10418 Z= 0.185 Angle : 0.719 47.215 14066 Z= 0.428 Chirality : 0.037 0.593 1583 Planarity : 0.004 0.069 1693 Dihedral : 9.297 77.678 1561 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.27 % Allowed : 15.97 % Favored : 81.76 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 16.67 % 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: 2.26 (0.25), residues: 1194 helix: 2.33 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.52 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 409 TYR 0.013 0.001 TYR B 453 PHE 0.014 0.001 PHE C 448 TRP 0.008 0.001 TRP B 697 HIS 0.002 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (10418) covalent geometry : angle 0.71908 / 0.43 (14066) hydrogen bonds : bond 0.05220 / 3.52 ( 739) hydrogen bonds : angle 4.00450 / 2.88 ( 2181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.40 seconds wall clock time: 58 minutes 19.27 seconds (3499.27 seconds total)