Starting phenix.real_space_refine on Fri Jul 3 02:38:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eoa_28332/07_2026/8eoa_28332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eoa_28332/07_2026/8eoa_28332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eoa_28332/07_2026/8eoa_28332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eoa_28332/07_2026/8eoa_28332.map" model { file = "/net/cci-nas-00/data/ceres_data/8eoa_28332/07_2026/8eoa_28332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eoa_28332/07_2026/8eoa_28332.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8eoa_28332/07_2026/8eoa_28332.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eoa_28332/07_2026/8eoa_28332.cif" } resolution = 3.9 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= -0.007 sd= 0.728 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 7298 2.51 5 N 1939 2.21 5 O 2234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11535 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5092 Classifications: {'peptide': 629} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 611} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5072 Classifications: {'peptide': 627} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1307 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASP C 7 " occ=0.93 ... (6 atoms not shown) pdb=" OD2 ASP C 7 " occ=0.93 residue: pdb=" N LEU C 10 " occ=0.93 ... (6 atoms not shown) pdb=" CD2 LEU C 10 " occ=0.93 residue: pdb=" N LEU C 11 " occ=0.93 ... (6 atoms not shown) pdb=" CD2 LEU C 11 " occ=0.93 residue: pdb=" N LEU C 12 " occ=0.93 ... (6 atoms not shown) pdb=" CD2 LEU C 12 " occ=0.93 Time building chain proxies: 2.46, per 1000 atoms: 0.21 Number of scatterers: 11535 At special positions: 0 Unit cell: (94.848, 114.816, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 6 15.00 Mg 2 11.99 O 2234 8.00 N 1939 7.00 C 7298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 562.2 milliseconds 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 13 sheets defined 43.7% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 38 through 60 removed outlier: 3.810A pdb=" N ILE A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.868A pdb=" N THR A 290 " --> pdb=" O PRO A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 397 through 420 removed outlier: 4.105A pdb=" N LEU A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 444 removed outlier: 6.466A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.786A pdb=" N LEU A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 516 through 525 removed outlier: 4.249A pdb=" N TYR A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.733A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 Processing helix chain 'A' and resid 648 through 666 Processing helix chain 'A' and resid 672 through 689 removed outlier: 3.924A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 38 through 60 removed outlier: 4.066A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.681A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 397 through 420 removed outlier: 3.905A pdb=" N LEU B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 444 removed outlier: 6.444A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 469 through 476 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.669A pdb=" N VAL B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 525 removed outlier: 4.343A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 571 removed outlier: 5.397A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.819A pdb=" N MET B 620 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 645 Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.514A pdb=" N GLY B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 689 removed outlier: 3.775A pdb=" N HIS B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 74 through 83 removed outlier: 3.689A pdb=" N THR C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.656A pdb=" N LEU C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 139 through 147 removed outlier: 3.604A pdb=" N LYS C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.652A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE B 75 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.748A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215 removed outlier: 6.416A pdb=" N ILE A 73 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 219 Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 323 removed outlier: 3.764A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 354 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 353 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 364 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.939A pdb=" N HIS A 458 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 577 through 580 Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 323 removed outlier: 7.457A pdb=" N ILE B 353 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP B 364 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.804A pdb=" N HIS B 458 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 577 through 580 Processing sheet with id=AB3, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.805A pdb=" N LEU C 152 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 153 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR C 39 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 161 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG C 37 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS C 46 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 53 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.805A pdb=" N LEU C 152 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 153 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR C 39 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 161 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG C 37 " --> pdb=" O VAL C 161 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3772 1.34 - 1.46: 2432 1.46 - 1.58: 5426 1.58 - 1.69: 8 1.69 - 1.81: 97 Bond restraints: 11735 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.573 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 11730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 15758 3.71 - 7.42: 36 7.42 - 11.13: 8 11.13 - 14.83: 0 14.83 - 18.54: 2 Bond angle restraints: 15804 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 108.41 18.54 3.00e+00 1.11e-01 3.82e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.11 16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C ASN B 46 " pdb=" CA ASN B 46 " pdb=" CB ASN B 46 " ideal model delta sigma weight residual 110.92 105.37 5.55 1.59e+00 3.96e-01 1.22e+01 angle pdb=" N ASN B 46 " pdb=" CA ASN B 46 " pdb=" C ASN B 46 " ideal model delta sigma weight residual 111.02 107.02 4.00 1.22e+00 6.72e-01 1.08e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 110.25 9.83 3.00e+00 1.11e-01 1.07e+01 ... (remaining 15799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 7114 34.84 - 69.68: 69 69.68 - 104.52: 4 104.52 - 139.35: 0 139.35 - 174.19: 1 Dihedral angle restraints: 7188 sinusoidal: 3025 harmonic: 4163 Sorted by residual: dihedral pdb=" O1B ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PB ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sinusoidal sigma weight residual 35.15 -150.66 -174.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C ASN B 46 " pdb=" N ASN B 46 " pdb=" CA ASN B 46 " pdb=" CB ASN B 46 " ideal model delta harmonic sigma weight residual -122.60 -114.21 -8.39 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" CA ALA C 133 " pdb=" C ALA C 133 " pdb=" N TYR C 134 " pdb=" CA TYR C 134 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 7185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1520 0.056 - 0.112: 223 0.112 - 0.168: 13 0.168 - 0.224: 0 0.224 - 0.280: 3 Chirality restraints: 1759 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ASN B 46 " pdb=" N ASN B 46 " pdb=" C ASN B 46 " pdb=" CB ASN B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1756 not shown) Planarity restraints: 2011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 370 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 371 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 517 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C ILE A 517 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 517 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 518 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 370 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 371 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " 0.024 5.00e-02 4.00e+02 ... (remaining 2008 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 17 2.35 - 2.99: 6299 2.99 - 3.63: 16858 3.63 - 4.26: 25190 4.26 - 4.90: 42571 Nonbonded interactions: 90935 Sorted by model distance: nonbonded pdb=" O2A ANP A 801 " pdb="MG MG A 802 " model vdw 1.718 2.170 nonbonded pdb=" N3B ANP A 801 " pdb="MG MG A 802 " model vdw 1.887 2.250 nonbonded pdb=" PG ANP A 801 " pdb="MG MG A 802 " model vdw 2.112 2.530 nonbonded pdb=" N3B ANP A 801 " pdb=" O2A ANP A 801 " model vdw 2.122 3.120 nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 2.125 2.170 ... (remaining 90930 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 11 through 220 or resid 275 through 802)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.220 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 11735 Z= 0.197 Angle : 0.584 18.543 15804 Z= 0.287 Chirality : 0.040 0.280 1759 Planarity : 0.003 0.044 2011 Dihedral : 11.352 174.192 4492 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.64 % Allowed : 7.04 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1411 helix: 1.31 (0.23), residues: 568 sheet: 0.07 (0.33), residues: 258 loop : -0.86 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 41 TYR 0.016 0.001 TYR B 211 PHE 0.009 0.001 PHE A 668 TRP 0.018 0.002 TRP A 312 HIS 0.004 0.001 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 (11735) covalent geometry : angle 0.58427 / 0.29 (15804) hydrogen bonds : bond 0.14279 / 9.39 ( 547) hydrogen bonds : angle 6.16189 / 4.24 ( 1560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 366 time to evaluate : 0.464 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: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8536 (tpp) cc_final: 0.7945 (tmm) REVERT: A 606 MET cc_start: 0.8543 (ttm) cc_final: 0.8243 (tpp) REVERT: A 611 LEU cc_start: 0.9302 (mm) cc_final: 0.8687 (tp) REVERT: A 621 MET cc_start: 0.8701 (mmm) cc_final: 0.8458 (mmt) REVERT: A 626 LEU cc_start: 0.9202 (tp) cc_final: 0.8960 (tp) REVERT: B 25 MET cc_start: 0.8724 (tpp) cc_final: 0.8415 (tpp) REVERT: B 49 ASP cc_start: 0.8465 (m-30) cc_final: 0.8134 (m-30) REVERT: B 114 MET cc_start: 0.8558 (tpp) cc_final: 0.7980 (tpt) REVERT: B 311 ASP cc_start: 0.8560 (t0) cc_final: 0.8198 (t0) REVERT: B 362 ILE cc_start: 0.9469 (mm) cc_final: 0.9219 (tp) REVERT: B 436 ASN cc_start: 0.9027 (m110) cc_final: 0.8596 (m-40) REVERT: B 564 CYS cc_start: 0.9126 (m) cc_final: 0.8449 (m) REVERT: B 606 MET cc_start: 0.8595 (mmt) cc_final: 0.8318 (mmt) REVERT: B 681 TYR cc_start: 0.8381 (m-10) cc_final: 0.8081 (m-80) REVERT: C 5 HIS cc_start: 0.6998 (m90) cc_final: 0.6355 (m170) REVERT: C 40 PHE cc_start: 0.8601 (p90) cc_final: 0.7880 (p90) REVERT: C 45 MET cc_start: 0.9074 (mpp) cc_final: 0.8499 (mpp) REVERT: C 95 ASP cc_start: 0.8931 (m-30) cc_final: 0.8669 (m-30) REVERT: C 139 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.5880 (t80) REVERT: C 150 GLN cc_start: 0.7908 (mp10) cc_final: 0.7279 (mp-120) outliers start: 21 outliers final: 6 residues processed: 381 average time/residue: 0.1141 time to fit residues: 60.7556 Evaluate side-chains 222 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 215 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN B 18 GLN B 80 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN B 407 ASN B 609 GLN C 146 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.066038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.051380 restraints weight = 49781.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.053383 restraints weight = 28066.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.054810 restraints weight = 18965.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.055747 restraints weight = 14218.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056508 restraints weight = 11595.793| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (15 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11735 Z= 0.149 Angle : 0.627 11.435 15804 Z= 0.323 Chirality : 0.042 0.198 1759 Planarity : 0.004 0.053 2011 Dihedral : 7.045 174.000 1552 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.49 % Allowed : 16.11 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1411 helix: 1.58 (0.22), residues: 560 sheet: 0.47 (0.34), residues: 262 loop : -0.62 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 583 TYR 0.013 0.002 TYR A 457 PHE 0.017 0.001 PHE B 133 TRP 0.013 0.002 TRP B 312 HIS 0.006 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (11735) covalent geometry : angle 0.62698 / 0.32 (15804) hydrogen bonds : bond 0.03869 / 2.58 ( 547) hydrogen bonds : angle 4.64463 / 3.24 ( 1560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.471 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9352 (mm-40) cc_final: 0.8843 (mm-40) REVERT: A 42 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8391 (mm-30) REVERT: A 111 LYS cc_start: 0.9560 (ttmm) cc_final: 0.9351 (ttpt) REVERT: A 114 MET cc_start: 0.9336 (tpp) cc_final: 0.8890 (tmm) REVERT: A 200 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8892 (tm-30) REVERT: A 441 ILE cc_start: 0.9636 (tp) cc_final: 0.9305 (pt) REVERT: A 499 PHE cc_start: 0.9196 (m-80) cc_final: 0.8967 (m-10) REVERT: A 602 MET cc_start: 0.9518 (tpp) cc_final: 0.9140 (tpp) REVERT: A 603 GLU cc_start: 0.9547 (OUTLIER) cc_final: 0.9308 (tp30) REVERT: A 606 MET cc_start: 0.9217 (ttm) cc_final: 0.8185 (tpp) REVERT: A 621 MET cc_start: 0.8321 (mmm) cc_final: 0.7482 (mpp) REVERT: A 672 ASP cc_start: 0.8973 (t70) cc_final: 0.8721 (p0) REVERT: B 49 ASP cc_start: 0.9022 (m-30) cc_final: 0.8801 (m-30) REVERT: B 203 LYS cc_start: 0.9600 (mmmt) cc_final: 0.8916 (tppt) REVERT: B 311 ASP cc_start: 0.8792 (t0) cc_final: 0.8576 (t0) REVERT: B 337 ARG cc_start: 0.8613 (mtp180) cc_final: 0.8143 (ttm110) REVERT: B 362 ILE cc_start: 0.9610 (mm) cc_final: 0.9326 (tp) REVERT: B 436 ASN cc_start: 0.9355 (m110) cc_final: 0.8656 (m-40) REVERT: B 553 MET cc_start: 0.9362 (tmm) cc_final: 0.8854 (ppp) REVERT: B 564 CYS cc_start: 0.9228 (m) cc_final: 0.8967 (m) REVERT: B 566 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9016 (mt) REVERT: B 567 MET cc_start: 0.9277 (mtm) cc_final: 0.8886 (mtm) REVERT: B 627 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8315 (pm20) REVERT: B 681 TYR cc_start: 0.9075 (m-10) cc_final: 0.8598 (m-80) REVERT: B 685 LYS cc_start: 0.9309 (mttt) cc_final: 0.8999 (mmtt) REVERT: C 45 MET cc_start: 0.9133 (mpp) cc_final: 0.8522 (mpp) REVERT: C 84 MET cc_start: 0.8844 (tpp) cc_final: 0.8426 (tpp) REVERT: C 95 ASP cc_start: 0.9047 (m-30) cc_final: 0.8726 (m-30) REVERT: C 102 TYR cc_start: 0.9113 (t80) cc_final: 0.8697 (t80) REVERT: C 143 ASP cc_start: 0.9686 (m-30) cc_final: 0.9481 (p0) outliers start: 19 outliers final: 11 residues processed: 236 average time/residue: 0.0998 time to fit residues: 34.7703 Evaluate side-chains 195 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 5.9990 chunk 87 optimal weight: 0.2980 chunk 105 optimal weight: 0.7980 chunk 47 optimal weight: 0.0030 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.052246 restraints weight = 49224.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054342 restraints weight = 27210.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055814 restraints weight = 18193.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056834 restraints weight = 13525.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.057615 restraints weight = 10849.330| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11735 Z= 0.109 Angle : 0.595 9.667 15804 Z= 0.299 Chirality : 0.041 0.149 1759 Planarity : 0.003 0.045 2011 Dihedral : 6.770 164.723 1551 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.03 % Allowed : 16.11 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1411 helix: 1.39 (0.22), residues: 570 sheet: 0.68 (0.34), residues: 261 loop : -0.75 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 679 TYR 0.016 0.001 TYR A 457 PHE 0.016 0.001 PHE C 42 TRP 0.011 0.001 TRP A 157 HIS 0.007 0.001 HIS C 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (11735) covalent geometry : angle 0.59523 / 0.30 (15804) hydrogen bonds : bond 0.03227 / 2.11 ( 547) hydrogen bonds : angle 4.38154 / 3.08 ( 1560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.424 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: A 42 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8367 (mm-30) REVERT: A 64 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8734 (tptt) REVERT: A 93 MET cc_start: 0.8498 (mtm) cc_final: 0.8252 (mtm) REVERT: A 111 LYS cc_start: 0.9581 (ttmm) cc_final: 0.9247 (ttpt) REVERT: A 114 MET cc_start: 0.9308 (tpp) cc_final: 0.9045 (tmm) REVERT: A 183 LEU cc_start: 0.9481 (mt) cc_final: 0.9146 (pp) REVERT: A 200 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8851 (tm-30) REVERT: A 441 ILE cc_start: 0.9571 (tp) cc_final: 0.9274 (pt) REVERT: A 476 MET cc_start: 0.8453 (ttt) cc_final: 0.7837 (tpp) REVERT: A 499 PHE cc_start: 0.9285 (m-80) cc_final: 0.8998 (m-10) REVERT: A 513 MET cc_start: 0.8552 (mtt) cc_final: 0.8183 (mtt) REVERT: A 567 MET cc_start: 0.9152 (mmm) cc_final: 0.8798 (mmm) REVERT: A 602 MET cc_start: 0.9440 (tpp) cc_final: 0.9153 (tpp) REVERT: A 606 MET cc_start: 0.9154 (ttm) cc_final: 0.8265 (tpp) REVERT: A 613 ASP cc_start: 0.8677 (t0) cc_final: 0.8447 (t0) REVERT: A 660 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8828 (mt-10) REVERT: A 671 GLU cc_start: 0.9032 (mp0) cc_final: 0.8661 (pm20) REVERT: A 679 ARG cc_start: 0.8906 (ttm110) cc_final: 0.8299 (mtm-85) REVERT: A 683 MET cc_start: 0.8938 (tmm) cc_final: 0.8594 (ppp) REVERT: B 114 MET cc_start: 0.8906 (tpt) cc_final: 0.8570 (tpt) REVERT: B 280 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 311 ASP cc_start: 0.8757 (t0) cc_final: 0.8310 (t0) REVERT: B 328 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8064 (tm-30) REVERT: B 337 ARG cc_start: 0.8601 (mtp180) cc_final: 0.8101 (ttm110) REVERT: B 346 ASN cc_start: 0.9193 (OUTLIER) cc_final: 0.8971 (p0) REVERT: B 365 SER cc_start: 0.8612 (t) cc_final: 0.8099 (p) REVERT: B 385 ASP cc_start: 0.9120 (t0) cc_final: 0.8552 (p0) REVERT: B 436 ASN cc_start: 0.9367 (m110) cc_final: 0.8745 (m-40) REVERT: B 466 MET cc_start: 0.9198 (mtp) cc_final: 0.8936 (mtp) REVERT: B 484 TYR cc_start: 0.9198 (m-80) cc_final: 0.8813 (m-10) REVERT: B 513 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7422 (mtm) REVERT: B 553 MET cc_start: 0.9396 (tmm) cc_final: 0.8888 (ppp) REVERT: B 564 CYS cc_start: 0.9201 (m) cc_final: 0.8920 (m) REVERT: B 566 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9165 (mt) REVERT: B 567 MET cc_start: 0.9261 (mtm) cc_final: 0.8829 (mtm) REVERT: B 616 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.7881 (p) REVERT: B 627 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8330 (pm20) REVERT: B 685 LYS cc_start: 0.9298 (mttt) cc_final: 0.8992 (mmtt) REVERT: C 21 ILE cc_start: 0.8995 (mm) cc_final: 0.8761 (mm) REVERT: C 45 MET cc_start: 0.9096 (mpp) cc_final: 0.8664 (mpp) REVERT: C 72 PHE cc_start: 0.7167 (p90) cc_final: 0.6908 (p90) REVERT: C 75 GLU cc_start: 0.8965 (pp20) cc_final: 0.8342 (mp0) REVERT: C 95 ASP cc_start: 0.9032 (m-30) cc_final: 0.8590 (m-30) REVERT: C 102 TYR cc_start: 0.9061 (t80) cc_final: 0.8636 (t80) outliers start: 26 outliers final: 9 residues processed: 228 average time/residue: 0.0923 time to fit residues: 31.6972 Evaluate side-chains 193 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 124 optimal weight: 0.1980 chunk 89 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN C 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049446 restraints weight = 50662.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051413 restraints weight = 28094.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052806 restraints weight = 18869.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.053753 restraints weight = 14091.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054500 restraints weight = 11390.220| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11735 Z= 0.213 Angle : 0.621 7.024 15804 Z= 0.323 Chirality : 0.042 0.150 1759 Planarity : 0.003 0.039 2011 Dihedral : 7.106 175.007 1548 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.81 % Allowed : 16.42 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1411 helix: 1.37 (0.22), residues: 571 sheet: 0.70 (0.33), residues: 261 loop : -0.77 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 583 TYR 0.017 0.002 TYR A 457 PHE 0.017 0.002 PHE B 429 TRP 0.006 0.001 TRP A 598 HIS 0.005 0.001 HIS C 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (11735) covalent geometry : angle 0.62055 / 0.32 (15804) hydrogen bonds : bond 0.03411 / 2.23 ( 547) hydrogen bonds : angle 4.56735 / 3.22 ( 1560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.487 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: A 23 GLN cc_start: 0.9610 (mm-40) cc_final: 0.9312 (mt0) REVERT: A 38 ILE cc_start: 0.9357 (pp) cc_final: 0.8147 (pp) REVERT: A 42 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8342 (mm-30) REVERT: A 110 THR cc_start: 0.9523 (m) cc_final: 0.9266 (p) REVERT: A 111 LYS cc_start: 0.9607 (ttmm) cc_final: 0.9372 (ttpt) REVERT: A 114 MET cc_start: 0.9375 (OUTLIER) cc_final: 0.9126 (tmm) REVERT: A 200 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8852 (tm-30) REVERT: A 363 MET cc_start: 0.8553 (ppp) cc_final: 0.8159 (ppp) REVERT: A 394 MET cc_start: 0.8718 (ptp) cc_final: 0.8369 (ptm) REVERT: A 430 TYR cc_start: 0.8580 (t80) cc_final: 0.7964 (t80) REVERT: A 513 MET cc_start: 0.8781 (mtt) cc_final: 0.8484 (mtt) REVERT: A 567 MET cc_start: 0.9434 (mmm) cc_final: 0.9018 (mmm) REVERT: A 602 MET cc_start: 0.9446 (tpp) cc_final: 0.9153 (tpp) REVERT: A 606 MET cc_start: 0.9157 (ttm) cc_final: 0.8699 (tpt) REVERT: A 671 GLU cc_start: 0.8798 (mp0) cc_final: 0.8583 (pm20) REVERT: A 683 MET cc_start: 0.8902 (tmm) cc_final: 0.8634 (ppp) REVERT: B 93 MET cc_start: 0.7733 (ttp) cc_final: 0.7267 (tmm) REVERT: B 200 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8657 (tm-30) REVERT: B 311 ASP cc_start: 0.8849 (t0) cc_final: 0.8368 (t0) REVERT: B 328 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 346 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8975 (p0) REVERT: B 362 ILE cc_start: 0.9416 (mm) cc_final: 0.9197 (tp) REVERT: B 385 ASP cc_start: 0.9213 (t0) cc_final: 0.8500 (p0) REVERT: B 436 ASN cc_start: 0.9435 (m110) cc_final: 0.9032 (m110) REVERT: B 476 MET cc_start: 0.8441 (ttt) cc_final: 0.7985 (tpt) REVERT: B 515 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8777 (mm-30) REVERT: B 553 MET cc_start: 0.9401 (tmm) cc_final: 0.8906 (ppp) REVERT: B 564 CYS cc_start: 0.9266 (m) cc_final: 0.8899 (m) REVERT: B 567 MET cc_start: 0.9344 (mtm) cc_final: 0.8951 (mtm) REVERT: B 584 LEU cc_start: 0.8803 (mp) cc_final: 0.8280 (mp) REVERT: B 590 CYS cc_start: 0.8315 (m) cc_final: 0.7510 (m) REVERT: B 591 ILE cc_start: 0.9530 (mm) cc_final: 0.9218 (tp) REVERT: B 627 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8523 (pm20) REVERT: B 668 PHE cc_start: 0.9193 (m-80) cc_final: 0.8645 (m-10) REVERT: B 681 TYR cc_start: 0.9168 (m-10) cc_final: 0.8673 (m-80) REVERT: B 685 LYS cc_start: 0.9346 (mttt) cc_final: 0.9144 (mtmm) REVERT: C 5 HIS cc_start: 0.7146 (m90) cc_final: 0.6893 (m90) REVERT: C 40 PHE cc_start: 0.9160 (p90) cc_final: 0.8778 (p90) REVERT: C 45 MET cc_start: 0.9091 (mpp) cc_final: 0.8574 (mpp) REVERT: C 75 GLU cc_start: 0.8997 (pp20) cc_final: 0.8297 (mp0) REVERT: C 84 MET cc_start: 0.8776 (tpp) cc_final: 0.8375 (tpp) REVERT: C 102 TYR cc_start: 0.9070 (t80) cc_final: 0.8743 (t80) REVERT: C 139 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.5782 (t80) outliers start: 36 outliers final: 21 residues processed: 199 average time/residue: 0.0848 time to fit residues: 26.2254 Evaluate side-chains 188 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 2 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN B 609 GLN C 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.049437 restraints weight = 50152.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.051405 restraints weight = 27710.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.052799 restraints weight = 18470.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053770 restraints weight = 13693.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.054473 restraints weight = 10928.363| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11735 Z= 0.184 Angle : 0.594 7.481 15804 Z= 0.308 Chirality : 0.042 0.274 1759 Planarity : 0.003 0.038 2011 Dihedral : 7.076 170.989 1548 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.74 % Allowed : 16.73 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1411 helix: 1.30 (0.22), residues: 571 sheet: 0.75 (0.33), residues: 263 loop : -0.78 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 583 TYR 0.022 0.002 TYR A 457 PHE 0.018 0.001 PHE B 429 TRP 0.010 0.001 TRP B 289 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (11735) covalent geometry : angle 0.59361 / 0.31 (15804) hydrogen bonds : bond 0.03317 / 2.17 ( 547) hydrogen bonds : angle 4.54906 / 3.20 ( 1560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9602 (mm-40) cc_final: 0.9341 (mt0) REVERT: A 38 ILE cc_start: 0.9343 (pp) cc_final: 0.8120 (pp) REVERT: A 42 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8301 (mm-30) REVERT: A 51 LEU cc_start: 0.9543 (mt) cc_final: 0.9330 (mt) REVERT: A 111 LYS cc_start: 0.9593 (ttmm) cc_final: 0.9377 (ttpt) REVERT: A 114 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.9038 (tmm) REVERT: A 183 LEU cc_start: 0.9546 (mt) cc_final: 0.8986 (pp) REVERT: A 200 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8845 (tm-30) REVERT: A 394 MET cc_start: 0.8781 (ptp) cc_final: 0.8475 (ptm) REVERT: A 430 TYR cc_start: 0.8504 (t80) cc_final: 0.8125 (t80) REVERT: A 499 PHE cc_start: 0.9380 (m-80) cc_final: 0.9090 (m-10) REVERT: A 513 MET cc_start: 0.8671 (mtt) cc_final: 0.8408 (mtt) REVERT: A 567 MET cc_start: 0.9556 (mmm) cc_final: 0.9005 (mmm) REVERT: A 602 MET cc_start: 0.9441 (tpp) cc_final: 0.9144 (tpp) REVERT: A 606 MET cc_start: 0.9157 (ttm) cc_final: 0.8775 (tpt) REVERT: A 660 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8824 (mt-10) REVERT: B 93 MET cc_start: 0.8078 (ttp) cc_final: 0.7592 (tmm) REVERT: B 200 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8619 (tm-30) REVERT: B 311 ASP cc_start: 0.8884 (t0) cc_final: 0.8377 (t0) REVERT: B 328 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8129 (tm-30) REVERT: B 346 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8822 (p0) REVERT: B 362 ILE cc_start: 0.9427 (mm) cc_final: 0.9119 (tp) REVERT: B 385 ASP cc_start: 0.9148 (t0) cc_final: 0.8458 (p0) REVERT: B 476 MET cc_start: 0.8417 (ttt) cc_final: 0.7943 (tpt) REVERT: B 513 MET cc_start: 0.7976 (mtm) cc_final: 0.7579 (mtm) REVERT: B 515 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8625 (mm-30) REVERT: B 533 LEU cc_start: 0.9448 (mt) cc_final: 0.9202 (mp) REVERT: B 553 MET cc_start: 0.9403 (tmm) cc_final: 0.8878 (ppp) REVERT: B 564 CYS cc_start: 0.9263 (m) cc_final: 0.8737 (m) REVERT: B 567 MET cc_start: 0.9330 (mtm) cc_final: 0.8831 (mtm) REVERT: B 584 LEU cc_start: 0.8822 (mp) cc_final: 0.8360 (mp) REVERT: B 590 CYS cc_start: 0.8203 (m) cc_final: 0.7418 (m) REVERT: B 602 MET cc_start: 0.9084 (tpp) cc_final: 0.8403 (tpp) REVERT: B 617 MET cc_start: 0.8921 (mtp) cc_final: 0.8441 (mmm) REVERT: B 627 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8392 (pm20) REVERT: B 681 TYR cc_start: 0.9166 (m-10) cc_final: 0.8674 (m-80) REVERT: B 685 LYS cc_start: 0.9340 (mttt) cc_final: 0.9138 (mtmm) REVERT: C 40 PHE cc_start: 0.9188 (p90) cc_final: 0.8730 (p90) REVERT: C 45 MET cc_start: 0.9094 (mpp) cc_final: 0.8618 (mpp) REVERT: C 75 GLU cc_start: 0.8981 (pp20) cc_final: 0.8280 (mp0) REVERT: C 84 MET cc_start: 0.8667 (tpp) cc_final: 0.8390 (tpp) REVERT: C 95 ASP cc_start: 0.9161 (m-30) cc_final: 0.8690 (m-30) REVERT: C 102 TYR cc_start: 0.9076 (t80) cc_final: 0.8754 (t80) REVERT: C 139 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.5916 (t80) outliers start: 35 outliers final: 19 residues processed: 202 average time/residue: 0.0903 time to fit residues: 27.9332 Evaluate side-chains 181 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 107 optimal weight: 0.0570 chunk 30 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.049065 restraints weight = 50938.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.051005 restraints weight = 28672.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.052370 restraints weight = 19421.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.053357 restraints weight = 14594.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054037 restraints weight = 11797.311| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11735 Z= 0.195 Angle : 0.622 13.303 15804 Z= 0.320 Chirality : 0.042 0.222 1759 Planarity : 0.003 0.038 2011 Dihedral : 7.114 171.193 1548 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.81 % Allowed : 16.73 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1411 helix: 1.25 (0.22), residues: 572 sheet: 0.79 (0.34), residues: 259 loop : -0.81 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 583 TYR 0.017 0.002 TYR A 457 PHE 0.019 0.001 PHE B 429 TRP 0.009 0.001 TRP B 289 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (11735) covalent geometry : angle 0.62164 / 0.32 (15804) hydrogen bonds : bond 0.03357 / 2.20 ( 547) hydrogen bonds : angle 4.58912 / 3.23 ( 1560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.9596 (mm-40) cc_final: 0.9362 (mt0) REVERT: A 38 ILE cc_start: 0.9381 (pp) cc_final: 0.8169 (pp) REVERT: A 42 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8317 (mm-30) REVERT: A 111 LYS cc_start: 0.9600 (ttmm) cc_final: 0.9385 (ttpt) REVERT: A 114 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.9111 (tmm) REVERT: A 200 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8838 (tm-30) REVERT: A 394 MET cc_start: 0.8808 (ptp) cc_final: 0.8520 (ptm) REVERT: A 430 TYR cc_start: 0.8560 (t80) cc_final: 0.8173 (t80) REVERT: A 499 PHE cc_start: 0.9402 (m-80) cc_final: 0.9163 (m-10) REVERT: A 513 MET cc_start: 0.8738 (mtt) cc_final: 0.8474 (mtt) REVERT: A 553 MET cc_start: 0.8554 (tpp) cc_final: 0.8328 (tmm) REVERT: A 567 MET cc_start: 0.9558 (mmm) cc_final: 0.9033 (mmm) REVERT: A 602 MET cc_start: 0.9451 (tpp) cc_final: 0.9156 (tpp) REVERT: A 606 MET cc_start: 0.9105 (ttm) cc_final: 0.8562 (tpt) REVERT: A 660 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8774 (mt-10) REVERT: B 93 MET cc_start: 0.8200 (ttp) cc_final: 0.7587 (tmm) REVERT: B 200 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8607 (tm-30) REVERT: B 311 ASP cc_start: 0.8890 (t0) cc_final: 0.8356 (t0) REVERT: B 328 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8134 (tm-30) REVERT: B 362 ILE cc_start: 0.9435 (mm) cc_final: 0.9137 (tp) REVERT: B 385 ASP cc_start: 0.9137 (t0) cc_final: 0.8454 (p0) REVERT: B 476 MET cc_start: 0.8419 (ttt) cc_final: 0.7932 (tpt) REVERT: B 513 MET cc_start: 0.7990 (mtm) cc_final: 0.7611 (mtm) REVERT: B 515 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8620 (mm-30) REVERT: B 553 MET cc_start: 0.9399 (tmm) cc_final: 0.8878 (ppp) REVERT: B 564 CYS cc_start: 0.9258 (m) cc_final: 0.8957 (m) REVERT: B 567 MET cc_start: 0.9308 (mtm) cc_final: 0.8927 (ptp) REVERT: B 584 LEU cc_start: 0.8821 (mp) cc_final: 0.8617 (mt) REVERT: B 590 CYS cc_start: 0.8106 (m) cc_final: 0.7449 (m) REVERT: B 602 MET cc_start: 0.9065 (tpp) cc_final: 0.8341 (tpp) REVERT: B 617 MET cc_start: 0.8782 (mtp) cc_final: 0.8420 (mmm) REVERT: B 627 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8326 (pm20) REVERT: B 681 TYR cc_start: 0.9132 (m-10) cc_final: 0.8668 (m-80) REVERT: C 40 PHE cc_start: 0.9193 (p90) cc_final: 0.8762 (p90) REVERT: C 45 MET cc_start: 0.9120 (mpp) cc_final: 0.8642 (mpp) REVERT: C 84 MET cc_start: 0.8564 (tpp) cc_final: 0.8296 (tpp) REVERT: C 95 ASP cc_start: 0.9161 (m-30) cc_final: 0.8714 (m-30) REVERT: C 102 TYR cc_start: 0.9118 (t80) cc_final: 0.8786 (t80) REVERT: C 139 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6058 (t80) outliers start: 36 outliers final: 22 residues processed: 196 average time/residue: 0.0864 time to fit residues: 25.8206 Evaluate side-chains 175 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 58 optimal weight: 0.0040 chunk 72 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.064765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049990 restraints weight = 50118.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051953 restraints weight = 28024.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053405 restraints weight = 19002.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.054384 restraints weight = 14151.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055117 restraints weight = 11415.926| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11735 Z= 0.128 Angle : 0.592 10.456 15804 Z= 0.302 Chirality : 0.043 0.309 1759 Planarity : 0.003 0.037 2011 Dihedral : 6.973 169.300 1547 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.19 % Allowed : 17.90 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1411 helix: 1.25 (0.22), residues: 572 sheet: 0.90 (0.34), residues: 259 loop : -0.84 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 583 TYR 0.015 0.001 TYR A 457 PHE 0.019 0.001 PHE B 429 TRP 0.007 0.001 TRP B 289 HIS 0.005 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (11735) covalent geometry : angle 0.59229 / 0.30 (15804) hydrogen bonds : bond 0.03175 / 2.09 ( 547) hydrogen bonds : angle 4.42346 / 3.12 ( 1560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.9335 (pp) cc_final: 0.8328 (pp) REVERT: A 42 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 51 LEU cc_start: 0.9510 (mt) cc_final: 0.9272 (mt) REVERT: A 111 LYS cc_start: 0.9578 (ttmm) cc_final: 0.9362 (ttpt) REVERT: A 183 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.8962 (pp) REVERT: A 200 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8841 (tm-30) REVERT: A 207 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8838 (tm-30) REVERT: A 430 TYR cc_start: 0.8524 (t80) cc_final: 0.8116 (t80) REVERT: A 451 LEU cc_start: 0.9401 (mt) cc_final: 0.9184 (mt) REVERT: A 457 TYR cc_start: 0.9070 (m-80) cc_final: 0.8860 (m-80) REVERT: A 499 PHE cc_start: 0.9390 (m-80) cc_final: 0.9138 (m-10) REVERT: A 513 MET cc_start: 0.8652 (mtt) cc_final: 0.8424 (mtt) REVERT: A 553 MET cc_start: 0.8492 (tpp) cc_final: 0.8280 (tmm) REVERT: A 567 MET cc_start: 0.9605 (mmm) cc_final: 0.9127 (mmm) REVERT: A 602 MET cc_start: 0.9461 (tpp) cc_final: 0.9112 (tpp) REVERT: A 606 MET cc_start: 0.9235 (ttm) cc_final: 0.8863 (tpt) REVERT: A 660 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8774 (mt-10) REVERT: B 49 ASP cc_start: 0.8927 (m-30) cc_final: 0.8690 (t0) REVERT: B 93 MET cc_start: 0.8071 (ttp) cc_final: 0.7663 (tmm) REVERT: B 125 MET cc_start: 0.8502 (mpp) cc_final: 0.8298 (mpp) REVERT: B 200 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8589 (tm-30) REVERT: B 311 ASP cc_start: 0.8889 (t0) cc_final: 0.8352 (t0) REVERT: B 328 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 362 ILE cc_start: 0.9467 (mm) cc_final: 0.9198 (tp) REVERT: B 385 ASP cc_start: 0.9094 (t0) cc_final: 0.8512 (p0) REVERT: B 476 MET cc_start: 0.8376 (ttt) cc_final: 0.8024 (tpt) REVERT: B 484 TYR cc_start: 0.9143 (m-80) cc_final: 0.8796 (m-10) REVERT: B 513 MET cc_start: 0.8035 (mtm) cc_final: 0.7684 (mtm) REVERT: B 515 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8615 (mm-30) REVERT: B 553 MET cc_start: 0.9374 (tmm) cc_final: 0.8834 (ppp) REVERT: B 567 MET cc_start: 0.9260 (mtm) cc_final: 0.8838 (mtm) REVERT: B 584 LEU cc_start: 0.8843 (mp) cc_final: 0.8603 (mt) REVERT: B 590 CYS cc_start: 0.8079 (m) cc_final: 0.7409 (m) REVERT: B 602 MET cc_start: 0.9099 (tpp) cc_final: 0.8394 (tpp) REVERT: B 617 MET cc_start: 0.8769 (mtp) cc_final: 0.8277 (mmm) REVERT: B 627 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8327 (pm20) REVERT: B 640 GLN cc_start: 0.9466 (mt0) cc_final: 0.9149 (tp-100) REVERT: B 681 TYR cc_start: 0.9248 (m-10) cc_final: 0.8645 (m-80) REVERT: C 21 ILE cc_start: 0.9103 (mm) cc_final: 0.8862 (mm) REVERT: C 45 MET cc_start: 0.9134 (mpp) cc_final: 0.8765 (mpp) REVERT: C 75 GLU cc_start: 0.9015 (pp20) cc_final: 0.8317 (mp0) REVERT: C 84 MET cc_start: 0.8543 (tpp) cc_final: 0.8203 (tpp) REVERT: C 95 ASP cc_start: 0.9094 (m-30) cc_final: 0.8597 (m-30) REVERT: C 102 TYR cc_start: 0.9136 (t80) cc_final: 0.8817 (t80) REVERT: C 139 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.6017 (t80) outliers start: 28 outliers final: 22 residues processed: 190 average time/residue: 0.0825 time to fit residues: 24.2472 Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 99 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.064985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.050261 restraints weight = 50079.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052280 restraints weight = 27905.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053706 restraints weight = 18712.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054692 restraints weight = 13992.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055419 restraints weight = 11289.172| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11735 Z= 0.127 Angle : 0.614 12.007 15804 Z= 0.307 Chirality : 0.042 0.314 1759 Planarity : 0.003 0.038 2011 Dihedral : 6.952 169.380 1547 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.35 % Allowed : 18.22 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1411 helix: 1.29 (0.22), residues: 570 sheet: 0.98 (0.34), residues: 261 loop : -0.90 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 682 TYR 0.013 0.001 TYR A 457 PHE 0.025 0.001 PHE C 40 TRP 0.018 0.001 TRP A 598 HIS 0.008 0.001 HIS C 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (11735) covalent geometry : angle 0.61422 / 0.31 (15804) hydrogen bonds : bond 0.03108 / 2.03 ( 547) hydrogen bonds : angle 4.41575 / 3.12 ( 1560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8418 (mm-30) REVERT: A 51 LEU cc_start: 0.9499 (mt) cc_final: 0.9257 (mt) REVERT: A 93 MET cc_start: 0.8352 (mtm) cc_final: 0.7686 (mpp) REVERT: A 111 LYS cc_start: 0.9570 (ttmm) cc_final: 0.9281 (ttpt) REVERT: A 183 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.8991 (pp) REVERT: A 200 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8847 (tm-30) REVERT: A 207 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8822 (tm-30) REVERT: A 304 PHE cc_start: 0.8735 (t80) cc_final: 0.8195 (t80) REVERT: A 476 MET cc_start: 0.8619 (ttt) cc_final: 0.7893 (tpp) REVERT: A 499 PHE cc_start: 0.9387 (m-80) cc_final: 0.9141 (m-10) REVERT: A 567 MET cc_start: 0.9637 (mmm) cc_final: 0.9151 (mmm) REVERT: A 602 MET cc_start: 0.9507 (tpp) cc_final: 0.9164 (tpp) REVERT: A 606 MET cc_start: 0.9187 (ttm) cc_final: 0.8840 (tpt) REVERT: A 621 MET cc_start: 0.8028 (tpp) cc_final: 0.7826 (mmp) REVERT: A 660 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8769 (mt-10) REVERT: A 671 GLU cc_start: 0.8900 (mp0) cc_final: 0.8511 (pm20) REVERT: A 679 ARG cc_start: 0.9046 (ttm110) cc_final: 0.8487 (mtt-85) REVERT: B 33 TYR cc_start: 0.8875 (m-80) cc_final: 0.8372 (m-80) REVERT: B 49 ASP cc_start: 0.8995 (m-30) cc_final: 0.8730 (t0) REVERT: B 93 MET cc_start: 0.8044 (ttp) cc_final: 0.7659 (tmm) REVERT: B 125 MET cc_start: 0.8569 (mpp) cc_final: 0.8356 (mpp) REVERT: B 200 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8595 (tm-30) REVERT: B 311 ASP cc_start: 0.8892 (t0) cc_final: 0.8353 (t0) REVERT: B 328 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 362 ILE cc_start: 0.9472 (mm) cc_final: 0.9183 (tp) REVERT: B 384 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: B 385 ASP cc_start: 0.9064 (t0) cc_final: 0.8555 (p0) REVERT: B 476 MET cc_start: 0.8325 (ttt) cc_final: 0.7960 (tpt) REVERT: B 484 TYR cc_start: 0.9170 (m-80) cc_final: 0.8767 (m-10) REVERT: B 513 MET cc_start: 0.8147 (mtm) cc_final: 0.7896 (mtm) REVERT: B 515 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8615 (mm-30) REVERT: B 553 MET cc_start: 0.9348 (tmm) cc_final: 0.8815 (ppp) REVERT: B 567 MET cc_start: 0.9293 (mtm) cc_final: 0.8920 (mtm) REVERT: B 584 LEU cc_start: 0.8930 (mp) cc_final: 0.8556 (mt) REVERT: B 590 CYS cc_start: 0.8149 (m) cc_final: 0.7322 (m) REVERT: B 602 MET cc_start: 0.9081 (tpp) cc_final: 0.8357 (tpp) REVERT: B 617 MET cc_start: 0.8754 (mtp) cc_final: 0.8277 (mmm) REVERT: B 627 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8341 (pm20) REVERT: B 640 GLN cc_start: 0.9459 (mt0) cc_final: 0.9158 (tp-100) REVERT: B 681 TYR cc_start: 0.9239 (m-10) cc_final: 0.8656 (m-80) REVERT: C 21 ILE cc_start: 0.9048 (mm) cc_final: 0.8800 (mm) REVERT: C 45 MET cc_start: 0.9149 (mpp) cc_final: 0.8746 (mpp) REVERT: C 75 GLU cc_start: 0.9040 (pp20) cc_final: 0.8304 (mp0) REVERT: C 84 MET cc_start: 0.8550 (tpp) cc_final: 0.8197 (tpp) REVERT: C 95 ASP cc_start: 0.9199 (m-30) cc_final: 0.8767 (m-30) REVERT: C 139 TYR cc_start: 0.6682 (OUTLIER) cc_final: 0.5994 (t80) outliers start: 30 outliers final: 24 residues processed: 187 average time/residue: 0.0812 time to fit residues: 23.6746 Evaluate side-chains 186 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 402 LYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 126 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.062526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.048110 restraints weight = 51407.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.050008 restraints weight = 29196.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051320 restraints weight = 19816.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052302 restraints weight = 14961.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052978 restraints weight = 12079.009| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11735 Z= 0.272 Angle : 0.711 13.637 15804 Z= 0.367 Chirality : 0.044 0.299 1759 Planarity : 0.004 0.036 2011 Dihedral : 7.292 173.250 1547 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.35 % Allowed : 18.53 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1411 helix: 1.04 (0.22), residues: 570 sheet: 0.92 (0.34), residues: 258 loop : -1.02 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 583 TYR 0.025 0.002 TYR A 457 PHE 0.022 0.002 PHE B 429 TRP 0.010 0.002 TRP A 598 HIS 0.007 0.001 HIS C 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.27 (11735) covalent geometry : angle 0.71071 / 0.37 (15804) hydrogen bonds : bond 0.03646 / 2.35 ( 547) hydrogen bonds : angle 4.84662 / 3.42 ( 1560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.467 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: A 38 ILE cc_start: 0.9411 (pp) cc_final: 0.8342 (pp) REVERT: A 42 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8471 (mm-30) REVERT: A 125 MET cc_start: 0.9076 (pmm) cc_final: 0.8796 (pmm) REVERT: A 200 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8846 (tm-30) REVERT: A 207 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8769 (tm-30) REVERT: A 430 TYR cc_start: 0.8568 (t80) cc_final: 0.8345 (t80) REVERT: A 466 MET cc_start: 0.9408 (mmm) cc_final: 0.9085 (mmm) REVERT: A 499 PHE cc_start: 0.9460 (m-80) cc_final: 0.9247 (m-10) REVERT: A 567 MET cc_start: 0.9620 (mmm) cc_final: 0.9133 (mmm) REVERT: A 584 LEU cc_start: 0.9188 (mp) cc_final: 0.8691 (tp) REVERT: A 602 MET cc_start: 0.9538 (tpp) cc_final: 0.9240 (tpp) REVERT: A 606 MET cc_start: 0.9172 (ttm) cc_final: 0.8896 (tpt) REVERT: A 660 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8773 (mt-10) REVERT: B 25 MET cc_start: 0.9542 (tpp) cc_final: 0.9281 (tpp) REVERT: B 49 ASP cc_start: 0.9102 (m-30) cc_final: 0.8785 (t0) REVERT: B 93 MET cc_start: 0.8308 (ttp) cc_final: 0.7582 (tmm) REVERT: B 311 ASP cc_start: 0.8968 (t0) cc_final: 0.8516 (t0) REVERT: B 328 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8274 (tm-30) REVERT: B 385 ASP cc_start: 0.9156 (t0) cc_final: 0.8810 (p0) REVERT: B 476 MET cc_start: 0.8376 (ttt) cc_final: 0.7685 (tpt) REVERT: B 513 MET cc_start: 0.8091 (mtm) cc_final: 0.7682 (mtm) REVERT: B 515 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8671 (mm-30) REVERT: B 553 MET cc_start: 0.9353 (tmm) cc_final: 0.8858 (ppp) REVERT: B 567 MET cc_start: 0.9339 (mtm) cc_final: 0.8958 (mtt) REVERT: B 584 LEU cc_start: 0.8837 (mp) cc_final: 0.8095 (tp) REVERT: B 602 MET cc_start: 0.9048 (tpp) cc_final: 0.8275 (tpp) REVERT: B 617 MET cc_start: 0.8757 (mtp) cc_final: 0.8411 (mmm) REVERT: B 627 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8639 (mt-10) REVERT: B 640 GLN cc_start: 0.9455 (mt0) cc_final: 0.9135 (tp-100) REVERT: B 681 TYR cc_start: 0.9263 (m-10) cc_final: 0.8805 (m-80) REVERT: C 45 MET cc_start: 0.9113 (mpp) cc_final: 0.8663 (mpp) REVERT: C 55 ASP cc_start: 0.8075 (m-30) cc_final: 0.7566 (p0) REVERT: C 75 GLU cc_start: 0.9034 (pp20) cc_final: 0.8244 (mp0) REVERT: C 95 ASP cc_start: 0.9214 (m-30) cc_final: 0.8736 (m-30) REVERT: C 139 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.6024 (t80) outliers start: 30 outliers final: 26 residues processed: 185 average time/residue: 0.0854 time to fit residues: 24.2894 Evaluate side-chains 176 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 28 optimal weight: 5.9990 chunk 123 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 47 optimal weight: 0.0270 chunk 52 optimal weight: 0.0020 chunk 102 optimal weight: 0.8980 overall best weight: 0.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.051750 restraints weight = 49509.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053832 restraints weight = 27270.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055249 restraints weight = 18158.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056280 restraints weight = 13548.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056935 restraints weight = 10883.285| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11735 Z= 0.119 Angle : 0.702 14.521 15804 Z= 0.339 Chirality : 0.044 0.322 1759 Planarity : 0.003 0.037 2011 Dihedral : 6.877 163.172 1547 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.64 % Allowed : 19.94 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1411 helix: 1.06 (0.22), residues: 570 sheet: 1.01 (0.34), residues: 269 loop : -0.93 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 682 TYR 0.020 0.001 TYR A 457 PHE 0.023 0.001 PHE C 154 TRP 0.016 0.002 TRP A 598 HIS 0.006 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (11735) covalent geometry : angle 0.70240 / 0.34 (15804) hydrogen bonds : bond 0.03255 / 2.15 ( 547) hydrogen bonds : angle 4.48522 / 3.19 ( 1560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.8329 (mtm) cc_final: 0.7562 (mpp) REVERT: A 125 MET cc_start: 0.8907 (pmm) cc_final: 0.8662 (pmm) REVERT: A 183 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9059 (pp) REVERT: A 200 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8842 (tm-30) REVERT: A 457 TYR cc_start: 0.8964 (m-80) cc_final: 0.8603 (m-80) REVERT: A 466 MET cc_start: 0.9305 (mmm) cc_final: 0.8852 (mmm) REVERT: A 476 MET cc_start: 0.8639 (ttt) cc_final: 0.7897 (tpp) REVERT: A 499 PHE cc_start: 0.9353 (m-80) cc_final: 0.9128 (m-10) REVERT: A 513 MET cc_start: 0.8289 (mtt) cc_final: 0.8089 (mtt) REVERT: A 567 MET cc_start: 0.9682 (mmm) cc_final: 0.9173 (mmm) REVERT: A 602 MET cc_start: 0.9542 (tpp) cc_final: 0.9216 (tpp) REVERT: A 606 MET cc_start: 0.9142 (ttm) cc_final: 0.8725 (tpt) REVERT: A 612 ARG cc_start: 0.8238 (ppt170) cc_final: 0.7592 (ppt170) REVERT: A 660 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8923 (mt-10) REVERT: B 49 ASP cc_start: 0.8974 (m-30) cc_final: 0.8585 (t0) REVERT: B 311 ASP cc_start: 0.8918 (t0) cc_final: 0.8502 (t0) REVERT: B 328 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8170 (tm-30) REVERT: B 385 ASP cc_start: 0.8989 (t0) cc_final: 0.8603 (p0) REVERT: B 476 MET cc_start: 0.8387 (ttt) cc_final: 0.8029 (tpt) REVERT: B 484 TYR cc_start: 0.9100 (m-80) cc_final: 0.8818 (m-10) REVERT: B 513 MET cc_start: 0.8147 (mtm) cc_final: 0.7860 (mtm) REVERT: B 553 MET cc_start: 0.9423 (tmm) cc_final: 0.8824 (ppp) REVERT: B 567 MET cc_start: 0.9308 (mtm) cc_final: 0.8772 (mtm) REVERT: B 589 CYS cc_start: 0.9118 (m) cc_final: 0.8702 (m) REVERT: B 602 MET cc_start: 0.9044 (tpp) cc_final: 0.8317 (tpp) REVERT: B 617 MET cc_start: 0.8729 (mtp) cc_final: 0.8270 (mmm) REVERT: B 627 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8114 (pm20) REVERT: B 640 GLN cc_start: 0.9436 (mt0) cc_final: 0.9140 (tp-100) REVERT: B 681 TYR cc_start: 0.9267 (m-10) cc_final: 0.8690 (m-80) REVERT: C 21 ILE cc_start: 0.8984 (mm) cc_final: 0.8690 (mm) REVERT: C 55 ASP cc_start: 0.8113 (m-30) cc_final: 0.7609 (p0) REVERT: C 75 GLU cc_start: 0.8985 (pp20) cc_final: 0.8247 (mp0) REVERT: C 84 MET cc_start: 0.8180 (tpp) cc_final: 0.7780 (tpp) REVERT: C 95 ASP cc_start: 0.9178 (m-30) cc_final: 0.8753 (m-30) REVERT: C 139 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.6030 (t80) outliers start: 21 outliers final: 19 residues processed: 186 average time/residue: 0.0764 time to fit residues: 22.3685 Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 LYS Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 109 optimal weight: 0.0060 chunk 74 optimal weight: 0.0980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.066247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.051551 restraints weight = 49898.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.053594 restraints weight = 27897.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055011 restraints weight = 18699.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056021 restraints weight = 13990.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.056793 restraints weight = 11250.478| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11735 Z= 0.115 Angle : 0.709 13.747 15804 Z= 0.343 Chirality : 0.043 0.337 1759 Planarity : 0.003 0.057 2011 Dihedral : 6.836 166.428 1545 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.64 % Allowed : 20.72 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.23), residues: 1411 helix: 1.02 (0.22), residues: 571 sheet: 0.98 (0.34), residues: 273 loop : -1.05 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 682 TYR 0.028 0.001 TYR C 102 PHE 0.028 0.001 PHE C 154 TRP 0.013 0.001 TRP B 157 HIS 0.005 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11735) covalent geometry : angle 0.70892 / 0.34 (15804) hydrogen bonds : bond 0.03111 / 2.04 ( 547) hydrogen bonds : angle 4.45843 / 3.16 ( 1560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.48 seconds wall clock time: 34 minutes 7.40 seconds (2047.40 seconds total)