Starting phenix.real_space_refine on Fri Aug 7 08:30:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t0y_40949/08_2026/8t0y_40949_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t0y_40949/08_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_40949/08_2026/8t0y_40949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t0y_40949/08_2026/8t0y_40949.map" model { file = "/net/cci-nas-00/data/ceres_data/8t0y_40949/08_2026/8t0y_40949_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t0y_40949/08_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-2.2rc3-6140/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, 46 Unusual residues: {' NA': 1, '8IJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 3.32, per 1000 atoms: 0.16 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: 1.84 Conformation dependent library (CDL) restraints added in 487.1 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: 0.36 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: 4.10 Time building geometry restraints manager: 2.37 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: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.060 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.880 ------------------------------------------------------------------------------- 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 : 0.542 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: 0.1895 time to fit residues: 87.5533 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 : 0.498 ------------------------------------------------------------------------------- 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 = 0.144845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.125683 restraints weight = 42365.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130248 restraints weight = 16940.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133103 restraints weight = 9630.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.134924 restraints weight = 6727.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.136097 restraints weight = 5268.589| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10418 Z= 0.153 Angle : 0.533 5.484 14066 Z= 0.290 Chirality : 0.034 0.154 1583 Planarity : 0.004 0.058 1693 Dihedral : 11.663 101.393 1570 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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: 2.19 (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 0.007 0.001 ARG B 500 TYR 0.011 0.001 TYR D 495 PHE 0.018 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 0.00321 / 0.15 (10418) covalent geometry : angle 0.53281 / 0.29 (14066) hydrogen bonds : bond 0.05147 / 3.45 ( 739) hydrogen bonds : angle 4.14288 / 3.01 ( 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 288 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 274 time to evaluate : 0.452 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: 0.8529 (mt) cc_final: 0.8174 (tt) REVERT: B 443 LEU cc_start: 0.8524 (tt) cc_final: 0.8038 (mt) REVERT: B 504 LYS cc_start: 0.7838 (mttt) cc_final: 0.7297 (tttm) REVERT: B 598 LEU cc_start: 0.8252 (tp) cc_final: 0.7812 (tp) REVERT: A 519 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8271 (tt0) REVERT: A 526 SER cc_start: 0.8757 (t) cc_final: 0.8392 (m) REVERT: A 644 MET cc_start: 0.7641 (tpt) cc_final: 0.7144 (mmt) REVERT: D 423 GLN cc_start: 0.7612 (tp-100) cc_final: 0.7159 (tp40) REVERT: D 437 ASN cc_start: 0.7931 (m110) cc_final: 0.7581 (m110) REVERT: D 478 GLU cc_start: 0.6755 (tm-30) cc_final: 0.6403 (tm-30) REVERT: D 565 TYR cc_start: 0.8693 (t80) cc_final: 0.8309 (t80) REVERT: C 432 ARG cc_start: 0.7702 (ptm160) cc_final: 0.7426 (mtp-110) REVERT: C 478 GLU cc_start: 0.7345 (tt0) cc_final: 0.6854 (tt0) REVERT: C 500 ARG cc_start: 0.5888 (mmt180) cc_final: 0.5582 (mmm160) REVERT: C 636 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7818 (mm-30) REVERT: C 684 GLU cc_start: 0.7718 (pp20) cc_final: 0.7337 (tt0) outliers start: 14 outliers final: 11 residues processed: 279 average time/residue: 0.1751 time to fit residues: 71.5873 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 : 0.426 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 0.0670 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.146247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127556 restraints weight = 42170.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.131985 restraints weight = 17716.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134741 restraints weight = 10307.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.136476 restraints weight = 7262.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.137642 restraints weight = 5735.435| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10418 Z= 0.142 Angle : 0.479 5.693 14066 Z= 0.269 Chirality : 0.033 0.145 1583 Planarity : 0.004 0.051 1693 Dihedral : 9.889 82.098 1567 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.36 % Allowed : 10.98 % Favored : 87.66 % 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: 2.43 (0.25), residues: 1194 helix: 2.43 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -1.47 (0.43), residues: 270 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 0.015 0.001 PHE C 448 TRP 0.010 0.001 TRP B 426 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (10418) covalent geometry : angle 0.47867 / 0.27 (14066) hydrogen bonds : bond 0.04921 / 3.31 ( 739) hydrogen bonds : angle 3.99379 / 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 277 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 262 time to evaluate : 0.498 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: B 413 LEU cc_start: 0.8544 (mt) cc_final: 0.8286 (tt) REVERT: B 443 LEU cc_start: 0.8501 (tt) cc_final: 0.8117 (mt) REVERT: B 504 LYS cc_start: 0.7763 (mttt) cc_final: 0.7304 (tttm) REVERT: B 592 SER cc_start: 0.8680 (t) cc_final: 0.8298 (p) REVERT: B 598 LEU cc_start: 0.8256 (tp) cc_final: 0.7805 (tp) REVERT: A 519 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8291 (tt0) REVERT: A 526 SER cc_start: 0.8768 (t) cc_final: 0.8467 (m) REVERT: A 579 ARG cc_start: 0.8323 (mtp180) cc_final: 0.7590 (mtt-85) REVERT: A 644 MET cc_start: 0.7552 (tpt) cc_final: 0.7058 (mmt) REVERT: D 423 GLN cc_start: 0.7614 (tp-100) cc_final: 0.7198 (tp40) REVERT: D 437 ASN cc_start: 0.8318 (m110) cc_final: 0.8010 (m110) REVERT: D 478 GLU cc_start: 0.6687 (tm-30) cc_final: 0.6295 (tm-30) REVERT: D 565 TYR cc_start: 0.8681 (t80) cc_final: 0.8348 (t80) REVERT: C 432 ARG cc_start: 0.7675 (ptm160) cc_final: 0.7436 (mtp-110) REVERT: C 478 GLU cc_start: 0.7269 (tt0) cc_final: 0.6847 (tt0) REVERT: C 500 ARG cc_start: 0.5889 (mmt180) cc_final: 0.5608 (mmm160) REVERT: C 636 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7738 (mm-30) REVERT: C 684 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7358 (tt0) outliers start: 15 outliers final: 9 residues processed: 271 average time/residue: 0.1746 time to fit residues: 69.9668 Evaluate side-chains 268 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 258 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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: 0.4980 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 97 optimal weight: 0.0670 chunk 43 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.144823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125466 restraints weight = 42427.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.130064 restraints weight = 17311.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.132957 restraints weight = 9928.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134718 restraints weight = 6929.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135945 restraints weight = 5464.827| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10418 Z= 0.127 Angle : 0.457 5.257 14066 Z= 0.256 Chirality : 0.032 0.138 1583 Planarity : 0.003 0.037 1693 Dihedral : 9.170 81.673 1563 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.81 % Allowed : 12.43 % Favored : 85.75 % 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: 2.64 (0.25), residues: 1194 helix: 2.59 (0.16), residues: 924 sheet: None (None), residues: 0 loop : -1.38 (0.43), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 428 TYR 0.010 0.001 TYR B 453 PHE 0.015 0.001 PHE C 448 TRP 0.008 0.001 TRP D 697 HIS 0.001 0.000 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (10418) covalent geometry : angle 0.45652 / 0.26 (14066) hydrogen bonds : bond 0.04670 / 3.15 ( 739) hydrogen bonds : angle 3.85190 / 2.78 ( 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 279 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 0.413 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 432 ARG cc_start: 0.6777 (mpt180) cc_final: 0.6487 (mmt90) REVERT: B 443 LEU cc_start: 0.8436 (tt) cc_final: 0.8108 (mt) REVERT: B 504 LYS cc_start: 0.7751 (mttt) cc_final: 0.7237 (tttm) REVERT: B 506 LEU cc_start: 0.6880 (pt) cc_final: 0.6506 (pp) REVERT: B 592 SER cc_start: 0.8657 (t) cc_final: 0.8258 (p) REVERT: B 598 LEU cc_start: 0.8212 (tp) cc_final: 0.7776 (tp) REVERT: A 519 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8262 (tt0) REVERT: A 526 SER cc_start: 0.8713 (t) cc_final: 0.8349 (m) REVERT: A 579 ARG cc_start: 0.8319 (mtp180) cc_final: 0.7566 (mtt-85) REVERT: A 644 MET cc_start: 0.7527 (tpt) cc_final: 0.7038 (mmt) REVERT: A 648 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7186 (tp30) REVERT: D 423 GLN cc_start: 0.7626 (tp-100) cc_final: 0.7231 (tp40) REVERT: D 437 ASN cc_start: 0.8381 (m110) cc_final: 0.8095 (m110) REVERT: D 478 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6328 (tm-30) REVERT: D 565 TYR cc_start: 0.8642 (t80) cc_final: 0.8223 (t80) REVERT: C 387 ILE cc_start: 0.3857 (mp) cc_final: 0.3635 (mp) REVERT: C 432 ARG cc_start: 0.7652 (ptm160) cc_final: 0.7412 (mtp-110) REVERT: C 478 GLU cc_start: 0.7251 (tt0) cc_final: 0.7040 (tt0) REVERT: C 500 ARG cc_start: 0.5931 (mmt180) cc_final: 0.5595 (mmm160) REVERT: C 636 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7756 (mm-30) REVERT: C 684 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7378 (tt0) outliers start: 20 outliers final: 14 residues processed: 271 average time/residue: 0.1807 time to fit residues: 72.2569 Evaluate side-chains 264 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 249 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR 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 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 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 684 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 0.9980 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: 0.9990 chunk 112 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.141309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.121977 restraints weight = 42624.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.126504 restraints weight = 17452.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129327 restraints weight = 10049.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131145 restraints weight = 7063.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.132269 restraints weight = 5544.865| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2777 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= 0.179 Angle : 0.508 6.093 14066 Z= 0.285 Chirality : 0.033 0.139 1583 Planarity : 0.004 0.039 1693 Dihedral : 9.452 79.065 1561 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.18 % Allowed : 12.98 % 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: 2.52 (0.25), residues: 1194 helix: 2.49 (0.16), residues: 919 sheet: None (None), residues: 0 loop : -1.31 (0.42), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 557 TYR 0.013 0.001 TYR B 453 PHE 0.017 0.001 PHE C 448 TRP 0.010 0.001 TRP B 426 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (10418) covalent geometry : angle 0.50773 / 0.29 (14066) hydrogen bonds : bond 0.05192 / 3.50 ( 739) hydrogen bonds : angle 3.99479 / 2.88 ( 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 284 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 0.619 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: 0.8468 (tt) cc_final: 0.8136 (mt) REVERT: B 504 LYS cc_start: 0.7753 (mttt) cc_final: 0.7238 (tttm) REVERT: B 598 LEU cc_start: 0.8188 (tp) cc_final: 0.7726 (tp) REVERT: A 519 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8242 (tt0) REVERT: A 526 SER cc_start: 0.8722 (t) cc_final: 0.8460 (m) REVERT: A 579 ARG cc_start: 0.8353 (mtp180) cc_final: 0.7635 (mtt-85) REVERT: A 644 MET cc_start: 0.7599 (tpt) cc_final: 0.7023 (mmt) REVERT: A 648 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7245 (tp30) REVERT: D 409 ARG cc_start: 0.7710 (ppt170) cc_final: 0.7509 (pmt-80) REVERT: D 423 GLN cc_start: 0.7581 (tp-100) cc_final: 0.7223 (tp40) REVERT: D 437 ASN cc_start: 0.8459 (m110) cc_final: 0.8150 (m110) REVERT: D 478 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6153 (tm-30) REVERT: D 565 TYR cc_start: 0.8721 (t80) cc_final: 0.8458 (t80) REVERT: C 387 ILE cc_start: 0.3806 (mp) cc_final: 0.3328 (mp) REVERT: C 432 ARG cc_start: 0.7683 (ptm160) cc_final: 0.7459 (mtp-110) REVERT: C 471 ASP cc_start: 0.6896 (m-30) cc_final: 0.6676 (m-30) REVERT: C 478 GLU cc_start: 0.7329 (tt0) cc_final: 0.7113 (tt0) REVERT: C 500 ARG cc_start: 0.5873 (mmt180) cc_final: 0.5586 (mmm160) REVERT: C 684 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7458 (tt0) outliers start: 24 outliers final: 19 residues processed: 272 average time/residue: 0.1884 time to fit residues: 75.3963 Evaluate side-chains 274 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 254 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 708 THR 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 630 LEU 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 497 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 634 CYS Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 96 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.140918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.122395 restraints weight = 42738.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.126691 restraints weight = 17743.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129400 restraints weight = 10262.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131128 restraints weight = 7200.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132173 restraints weight = 5684.589| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10418 Z= 0.165 Angle : 0.497 5.853 14066 Z= 0.279 Chirality : 0.033 0.136 1583 Planarity : 0.003 0.034 1693 Dihedral : 9.302 79.716 1561 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.18 % Allowed : 14.43 % Favored : 83.39 % 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: 2.50 (0.25), residues: 1194 helix: 2.47 (0.16), residues: 919 sheet: None (None), residues: 0 loop : -1.31 (0.43), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 474 TYR 0.013 0.001 TYR B 453 PHE 0.016 0.001 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 0.00355 / 0.17 (10418) covalent geometry : angle 0.49684 / 0.28 (14066) hydrogen bonds : bond 0.05106 / 3.44 ( 739) hydrogen bonds : angle 3.95964 / 2.86 ( 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 277 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 0.491 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: 0.8470 (tt) cc_final: 0.8159 (mt) REVERT: B 504 LYS cc_start: 0.7611 (mttt) cc_final: 0.7209 (tttm) REVERT: B 598 LEU cc_start: 0.8181 (tp) cc_final: 0.7719 (tp) REVERT: A 476 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8250 (t) REVERT: A 519 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8274 (tt0) REVERT: A 526 SER cc_start: 0.8738 (t) cc_final: 0.8412 (m) REVERT: A 644 MET cc_start: 0.7534 (tpt) cc_final: 0.6926 (mmt) REVERT: A 648 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7238 (tp30) REVERT: D 423 GLN cc_start: 0.7561 (tp-100) cc_final: 0.7270 (tp40) REVERT: D 437 ASN cc_start: 0.8467 (m110) cc_final: 0.8235 (m110) REVERT: D 478 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6131 (tm-30) REVERT: D 565 TYR cc_start: 0.8662 (t80) cc_final: 0.8378 (t80) REVERT: D 644 MET cc_start: 0.8196 (tpt) cc_final: 0.7942 (tpt) REVERT: C 387 ILE cc_start: 0.3621 (mp) cc_final: 0.3112 (mp) REVERT: C 471 ASP cc_start: 0.6840 (m-30) cc_final: 0.6568 (m-30) outliers start: 24 outliers final: 20 residues processed: 264 average time/residue: 0.1819 time to fit residues: 71.1614 Evaluate side-chains 274 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR 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 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 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 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: 0.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.144134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.125624 restraints weight = 42683.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129947 restraints weight = 17655.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.132667 restraints weight = 10229.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.134279 restraints weight = 7190.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135488 restraints weight = 5746.869| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3026 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= 0.152 Angle : 0.488 6.119 14066 Z= 0.274 Chirality : 0.033 0.134 1583 Planarity : 0.003 0.032 1693 Dihedral : 9.237 78.664 1561 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % 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: 2.51 (0.25), residues: 1194 helix: 2.45 (0.17), residues: 921 sheet: None (None), residues: 0 loop : -1.22 (0.43), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 474 TYR 0.013 0.001 TYR B 453 PHE 0.015 0.001 PHE B 429 TRP 0.008 0.001 TRP B 697 HIS 0.001 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (10418) covalent geometry : angle 0.48850 / 0.27 (14066) hydrogen bonds : bond 0.05006 / 3.38 ( 739) hydrogen bonds : angle 3.91534 / 2.83 ( 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 280 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 0.524 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: 0.8468 (tt) cc_final: 0.8185 (mt) REVERT: B 445 MET cc_start: 0.8701 (tpt) cc_final: 0.8412 (mmm) REVERT: B 482 VAL cc_start: 0.8745 (m) cc_final: 0.8416 (p) REVERT: B 504 LYS cc_start: 0.7668 (mttt) cc_final: 0.7253 (tttm) REVERT: B 592 SER cc_start: 0.8677 (t) cc_final: 0.8253 (p) REVERT: B 598 LEU cc_start: 0.8157 (tp) cc_final: 0.7691 (tp) REVERT: A 476 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8241 (t) REVERT: A 519 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8270 (tt0) REVERT: A 526 SER cc_start: 0.8729 (t) cc_final: 0.8458 (m) REVERT: A 644 MET cc_start: 0.7529 (tpt) cc_final: 0.6970 (mmt) REVERT: D 423 GLN cc_start: 0.7536 (tp-100) cc_final: 0.7094 (tp-100) REVERT: D 437 ASN cc_start: 0.8459 (m110) cc_final: 0.8244 (m110) REVERT: D 478 GLU cc_start: 0.6567 (tm-30) cc_final: 0.6100 (tm-30) REVERT: D 565 TYR cc_start: 0.8637 (t80) cc_final: 0.8356 (t80) REVERT: D 644 MET cc_start: 0.8212 (tpt) cc_final: 0.7933 (tpt) REVERT: C 387 ILE cc_start: 0.3563 (mp) cc_final: 0.2877 (mp) REVERT: C 530 TYR cc_start: 0.8472 (t80) cc_final: 0.8270 (t80) outliers start: 24 outliers final: 21 residues processed: 269 average time/residue: 0.1813 time to fit residues: 72.9814 Evaluate side-chains 273 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR 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 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 544 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 634 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.144881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126509 restraints weight = 42551.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.130851 restraints weight = 17547.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133622 restraints weight = 10092.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135350 restraints weight = 7024.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.136466 restraints weight = 5507.060| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10418 Z= 0.149 Angle : 0.489 6.478 14066 Z= 0.274 Chirality : 0.033 0.200 1583 Planarity : 0.003 0.045 1693 Dihedral : 9.172 78.517 1561 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.54 % Allowed : 14.88 % Favored : 82.58 % 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: 2.54 (0.25), residues: 1194 helix: 2.48 (0.17), residues: 922 sheet: None (None), residues: 0 loop : -1.26 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 474 TYR 0.012 0.001 TYR B 453 PHE 0.020 0.001 PHE B 429 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 0.00316 / 0.15 (10418) covalent geometry : angle 0.48879 / 0.27 (14066) hydrogen bonds : bond 0.04934 / 3.33 ( 739) hydrogen bonds : angle 3.90438 / 2.82 ( 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 281 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.499 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: 0.8442 (tt) cc_final: 0.8170 (mt) REVERT: B 445 MET cc_start: 0.8692 (tpt) cc_final: 0.8404 (mmm) REVERT: B 504 LYS cc_start: 0.7625 (mttt) cc_final: 0.7264 (tttm) REVERT: B 592 SER cc_start: 0.8609 (t) cc_final: 0.8223 (p) REVERT: B 598 LEU cc_start: 0.8181 (tp) cc_final: 0.7696 (tp) REVERT: A 476 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8242 (t) REVERT: A 519 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8274 (tt0) REVERT: A 526 SER cc_start: 0.8701 (t) cc_final: 0.8403 (m) REVERT: A 644 MET cc_start: 0.7478 (tpt) cc_final: 0.6925 (mmt) REVERT: D 423 GLN cc_start: 0.7542 (tp-100) cc_final: 0.7129 (tp-100) REVERT: D 437 ASN cc_start: 0.8459 (m110) cc_final: 0.8251 (m110) REVERT: D 478 GLU cc_start: 0.6560 (tm-30) cc_final: 0.6112 (tm-30) REVERT: D 565 TYR cc_start: 0.8631 (t80) cc_final: 0.8328 (t80) REVERT: D 627 TYR cc_start: 0.7980 (m-80) cc_final: 0.7742 (m-80) REVERT: D 644 MET cc_start: 0.8217 (tpt) cc_final: 0.7953 (tpt) outliers start: 28 outliers final: 25 residues processed: 268 average time/residue: 0.1747 time to fit residues: 69.8507 Evaluate side-chains 278 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 506 LEU 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 521 LEU 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 544 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 634 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 ASN ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124156 restraints weight = 42632.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.128498 restraints weight = 17769.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131226 restraints weight = 10269.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.132961 restraints weight = 7217.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134097 restraints weight = 5692.547| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10418 Z= 0.155 Angle : 0.499 6.194 14066 Z= 0.279 Chirality : 0.033 0.188 1583 Planarity : 0.004 0.037 1693 Dihedral : 9.172 78.549 1561 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.27 % Allowed : 15.25 % Favored : 82.49 % 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: 2.50 (0.25), residues: 1194 helix: 2.48 (0.17), residues: 919 sheet: None (None), residues: 0 loop : -1.33 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 474 TYR 0.020 0.001 TYR C 530 PHE 0.019 0.001 PHE B 429 TRP 0.008 0.001 TRP B 697 HIS 0.004 0.001 HIS D 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (10418) covalent geometry : angle 0.49924 / 0.28 (14066) hydrogen bonds : bond 0.04961 / 3.35 ( 739) hydrogen bonds : angle 3.90263 / 2.82 ( 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 280 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.500 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: B 432 ARG cc_start: 0.6971 (mmt90) cc_final: 0.6536 (mmt180) REVERT: B 443 LEU cc_start: 0.8431 (tt) cc_final: 0.8162 (mt) REVERT: B 445 MET cc_start: 0.8690 (tpt) cc_final: 0.8399 (mmm) REVERT: B 482 VAL cc_start: 0.8742 (m) cc_final: 0.8416 (p) REVERT: B 504 LYS cc_start: 0.7677 (mttt) cc_final: 0.7267 (tttm) REVERT: B 592 SER cc_start: 0.8614 (t) cc_final: 0.8209 (p) REVERT: B 598 LEU cc_start: 0.8177 (tp) cc_final: 0.7702 (tp) REVERT: A 476 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8246 (t) REVERT: A 519 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8232 (tt0) REVERT: A 526 SER cc_start: 0.8716 (t) cc_final: 0.8420 (m) REVERT: A 644 MET cc_start: 0.7481 (tpt) cc_final: 0.6920 (mmt) REVERT: D 423 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7109 (tp-100) REVERT: D 437 ASN cc_start: 0.8475 (m110) cc_final: 0.8255 (m110) REVERT: D 478 GLU cc_start: 0.6588 (tm-30) cc_final: 0.6126 (tm-30) REVERT: D 565 TYR cc_start: 0.8641 (t80) cc_final: 0.8367 (t80) REVERT: D 644 MET cc_start: 0.8190 (tpt) cc_final: 0.7938 (tpt) outliers start: 25 outliers final: 23 residues processed: 269 average time/residue: 0.1740 time to fit residues: 69.6961 Evaluate side-chains 280 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 506 LEU 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 521 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 468 THR 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 544 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 634 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 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 = 0.3559 r_free = 0.3559 target = 0.143033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.124401 restraints weight = 42791.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128757 restraints weight = 17601.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131471 restraints weight = 10118.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133180 restraints weight = 7096.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.134361 restraints weight = 5599.232| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3261 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= 0.142 Angle : 0.488 6.082 14066 Z= 0.273 Chirality : 0.033 0.184 1583 Planarity : 0.004 0.060 1693 Dihedral : 9.040 77.851 1561 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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: 2.58 (0.25), residues: 1194 helix: 2.54 (0.17), residues: 919 sheet: None (None), residues: 0 loop : -1.33 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 474 TYR 0.015 0.001 TYR C 530 PHE 0.022 0.001 PHE B 429 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 0.00301 / 0.14 (10418) covalent geometry : angle 0.48797 / 0.27 (14066) hydrogen bonds : bond 0.04820 / 3.26 ( 739) hydrogen bonds : angle 3.86948 / 2.79 ( 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 281 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 432 ARG cc_start: 0.7007 (mmt90) cc_final: 0.6574 (mmt180) REVERT: B 443 LEU cc_start: 0.8405 (tt) cc_final: 0.8175 (mt) REVERT: B 445 MET cc_start: 0.8679 (tpt) cc_final: 0.8388 (mmm) REVERT: B 504 LYS cc_start: 0.7682 (mttt) cc_final: 0.7291 (tttm) REVERT: B 592 SER cc_start: 0.8620 (t) cc_final: 0.8209 (p) REVERT: B 598 LEU cc_start: 0.8162 (tp) cc_final: 0.7699 (tp) REVERT: A 476 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8242 (t) REVERT: A 519 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8236 (tt0) REVERT: A 526 SER cc_start: 0.8713 (t) cc_final: 0.8377 (m) REVERT: A 644 MET cc_start: 0.7471 (tpt) cc_final: 0.6877 (mmt) REVERT: A 677 MET cc_start: 0.8295 (ttp) cc_final: 0.8020 (ttm) REVERT: D 423 GLN cc_start: 0.7537 (tp-100) cc_final: 0.7123 (tp-100) REVERT: D 437 ASN cc_start: 0.8452 (m110) cc_final: 0.8238 (m110) REVERT: D 478 GLU cc_start: 0.6574 (tm-30) cc_final: 0.6117 (tm-30) REVERT: D 565 TYR cc_start: 0.8647 (t80) cc_final: 0.8373 (t80) outliers start: 24 outliers final: 22 residues processed: 271 average time/residue: 0.1791 time to fit residues: 72.2071 Evaluate side-chains 276 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 506 LEU 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 551 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain D residue 468 THR 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 497 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 634 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 91 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 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 = 0.3588 r_free = 0.3588 target = 0.145345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.126997 restraints weight = 42529.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131323 restraints weight = 17519.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134041 restraints weight = 10077.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.135726 restraints weight = 7062.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.136901 restraints weight = 5566.214| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 10418 Z= 0.178 Angle : 0.788 59.158 14066 Z= 0.491 Chirality : 0.034 0.372 1583 Planarity : 0.004 0.095 1693 Dihedral : 9.051 77.862 1561 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.27 % Allowed : 15.61 % Favored : 82.12 % 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: 2.59 (0.25), residues: 1194 helix: 2.55 (0.17), residues: 919 sheet: None (None), residues: 0 loop : -1.34 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.014 0.001 TYR C 530 PHE 0.022 0.001 PHE B 429 TRP 0.007 0.001 TRP B 697 HIS 0.001 0.000 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (10418) covalent geometry : angle 0.78777 / 0.49 (14066) hydrogen bonds : bond 0.04822 / 3.26 ( 739) hydrogen bonds : angle 3.88411 / 2.80 ( 2181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3243.23 seconds wall clock time: 55 minutes 55.82 seconds (3355.82 seconds total)