Starting phenix.real_space_refine on Thu Jul 24 12:03:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m22_23629/07_2025/7m22_23629_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m22_23629/07_2025/7m22_23629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m22_23629/07_2025/7m22_23629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m22_23629/07_2025/7m22_23629.map" model { file = "/net/cci-nas-00/data/ceres_data/7m22_23629/07_2025/7m22_23629_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m22_23629/07_2025/7m22_23629_neut.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 35 5.16 5 C 3819 2.51 5 N 1069 2.21 5 O 1118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6042 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 852 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "D" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 905 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "E" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 893 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "N" Number of atoms: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3363 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 395} Chain breaks: 3 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.48, per 1000 atoms: 0.74 Number of scatterers: 6042 At special positions: 0 Unit cell: (94.424, 104.081, 120.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 35 16.00 O 1118 8.00 N 1069 7.00 C 3819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 49 " distance=2.03 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 111 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 207 " distance=2.02 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 40 " distance=2.03 Simple disulfide: pdb=" SG CYS N 149 " - pdb=" SG CYS N 175 " distance=2.03 Simple disulfide: pdb=" SG CYS N 208 " - pdb=" SG CYS N 230 " distance=2.03 Simple disulfide: pdb=" SG CYS N 277 " - pdb=" SG CYS N 427 " distance=2.04 Simple disulfide: pdb=" SG CYS N 434 " - pdb=" SG CYS N 592 " distance=2.04 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 Links applied NAG-ASN " NAG E 201 " - " ASN E 81 " " NAG N 701 " - " ASN N 157 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 10 sheets defined 19.7% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.203A pdb=" N GLY C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 85 through 92 removed outlier: 3.809A pdb=" N LYS C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.675A pdb=" N GLY D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 140 through 149 Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 45 through 69 removed outlier: 3.587A pdb=" N GLN E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'N' and resid 289 through 291 No H-bonds generated for 'chain 'N' and resid 289 through 291' Processing helix chain 'N' and resid 305 through 310 removed outlier: 3.590A pdb=" N GLN N 308 " --> pdb=" O THR N 305 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG N 310 " --> pdb=" O GLN N 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 428 through 432 removed outlier: 3.665A pdb=" N ALA N 432 " --> pdb=" O VAL N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 446 through 448 No H-bonds generated for 'chain 'N' and resid 446 through 448' Processing helix chain 'N' and resid 461 through 466 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AA3, first strand: chain 'C' and resid 130 through 133 removed outlier: 4.362A pdb=" N ARG D 160 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 118 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 152 through 153 removed outlier: 3.638A pdb=" N LEU N 180 " --> pdb=" O PHE N 153 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU N 213 " --> pdb=" O LYS N 228 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS N 228 " --> pdb=" O LEU N 213 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE N 215 " --> pdb=" O ILE N 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 158 through 161 removed outlier: 6.641A pdb=" N GLY N 259 " --> pdb=" O PHE N 194 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE N 194 " --> pdb=" O GLY N 259 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER N 261 " --> pdb=" O LEU N 192 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL N 267 " --> pdb=" O GLU N 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 279 through 280 removed outlier: 6.587A pdb=" N CYS N 427 " --> pdb=" O LEU N 339 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU N 339 " --> pdb=" O CYS N 427 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN N 330 " --> pdb=" O ARG N 408 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG N 408 " --> pdb=" O GLN N 330 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASP N 332 " --> pdb=" O PHE N 406 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE N 406 " --> pdb=" O ASP N 332 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ARG N 334 " --> pdb=" O THR N 404 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR N 404 " --> pdb=" O ARG N 334 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N LEU N 336 " --> pdb=" O LEU N 402 " (cutoff:3.500A) removed outlier: 10.964A pdb=" N LEU N 402 " --> pdb=" O LEU N 336 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N MET N 338 " --> pdb=" O ALA N 400 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N ALA N 400 " --> pdb=" O MET N 338 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR N 340 " --> pdb=" O LEU N 398 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER N 360 " --> pdb=" O GLN N 412 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP N 414 " --> pdb=" O VAL N 358 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL N 358 " --> pdb=" O TRP N 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 293 through 295 removed outlier: 6.698A pdb=" N GLN N 330 " --> pdb=" O ARG N 408 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG N 408 " --> pdb=" O GLN N 330 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASP N 332 " --> pdb=" O PHE N 406 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE N 406 " --> pdb=" O ASP N 332 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ARG N 334 " --> pdb=" O THR N 404 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR N 404 " --> pdb=" O ARG N 334 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N LEU N 336 " --> pdb=" O LEU N 402 " (cutoff:3.500A) removed outlier: 10.964A pdb=" N LEU N 402 " --> pdb=" O LEU N 336 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N MET N 338 " --> pdb=" O ALA N 400 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N ALA N 400 " --> pdb=" O MET N 338 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR N 340 " --> pdb=" O LEU N 398 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER N 360 " --> pdb=" O GLN N 412 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP N 414 " --> pdb=" O VAL N 358 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL N 358 " --> pdb=" O TRP N 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 347 through 348 Processing sheet with id=AA9, first strand: chain 'N' and resid 436 through 437 removed outlier: 6.513A pdb=" N CYS N 592 " --> pdb=" O VAL N 498 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL N 498 " --> pdb=" O CYS N 592 " (cutoff:3.500A) removed outlier: 13.427A pdb=" N LEU N 488 " --> pdb=" O GLU N 576 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N GLU N 576 " --> pdb=" O LEU N 488 " (cutoff:3.500A) removed outlier: 12.666A pdb=" N VAL N 490 " --> pdb=" O TYR N 574 " (cutoff:3.500A) removed outlier: 11.314A pdb=" N TYR N 574 " --> pdb=" O VAL N 490 " (cutoff:3.500A) removed outlier: 11.439A pdb=" N LEU N 492 " --> pdb=" O ARG N 572 " (cutoff:3.500A) removed outlier: 12.351A pdb=" N ARG N 572 " --> pdb=" O LEU N 492 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR N 494 " --> pdb=" O TYR N 570 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR N 570 " --> pdb=" O THR N 494 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY N 500 " --> pdb=" O ASP N 564 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N ASP N 564 " --> pdb=" O GLY N 500 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N ILE N 502 " --> pdb=" O ARG N 562 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N ARG N 562 " --> pdb=" O ILE N 502 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N GLN N 504 " --> pdb=" O ILE N 560 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N ILE N 560 " --> pdb=" O GLN N 504 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS N 523 " --> pdb=" O GLU N 576 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP N 578 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL N 521 " --> pdb=" O TRP N 578 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 450 through 452 removed outlier: 13.427A pdb=" N LEU N 488 " --> pdb=" O GLU N 576 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N GLU N 576 " --> pdb=" O LEU N 488 " (cutoff:3.500A) removed outlier: 12.666A pdb=" N VAL N 490 " --> pdb=" O TYR N 574 " (cutoff:3.500A) removed outlier: 11.314A pdb=" N TYR N 574 " --> pdb=" O VAL N 490 " (cutoff:3.500A) removed outlier: 11.439A pdb=" N LEU N 492 " --> pdb=" O ARG N 572 " (cutoff:3.500A) removed outlier: 12.351A pdb=" N ARG N 572 " --> pdb=" O LEU N 492 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N THR N 494 " --> pdb=" O TYR N 570 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR N 570 " --> pdb=" O THR N 494 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY N 500 " --> pdb=" O ASP N 564 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N ASP N 564 " --> pdb=" O GLY N 500 " (cutoff:3.500A) removed outlier: 9.922A pdb=" N ILE N 502 " --> pdb=" O ARG N 562 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N ARG N 562 " --> pdb=" O ILE N 502 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N GLN N 504 " --> pdb=" O ILE N 560 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N ILE N 560 " --> pdb=" O GLN N 504 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS N 523 " --> pdb=" O GLU N 576 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP N 578 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL N 521 " --> pdb=" O TRP N 578 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 597 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: 1.81 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1984 1.34 - 1.46: 1481 1.46 - 1.58: 2674 1.58 - 1.70: 0 1.70 - 1.83: 50 Bond restraints: 6189 Sorted by residual: bond pdb=" C5 NAG N 701 " pdb=" O5 NAG N 701 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" N ILE N 538 " pdb=" CA ILE N 538 " ideal model delta sigma weight residual 1.474 1.456 0.019 1.57e-02 4.06e+03 1.43e+00 bond pdb=" CB ASP N 540 " pdb=" CG ASP N 540 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CB CYS C 30 " pdb=" SG CYS C 30 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB CYS N 230 " pdb=" SG CYS N 230 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.16e+00 ... (remaining 6184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 7777 1.48 - 2.97: 522 2.97 - 4.45: 74 4.45 - 5.94: 16 5.94 - 7.42: 4 Bond angle restraints: 8393 Sorted by residual: angle pdb=" C GLN N 544 " pdb=" N GLN N 545 " pdb=" CA GLN N 545 " ideal model delta sigma weight residual 122.26 115.25 7.01 1.60e+00 3.91e-01 1.92e+01 angle pdb=" N LEU N 467 " pdb=" CA LEU N 467 " pdb=" C LEU N 467 " ideal model delta sigma weight residual 111.28 116.02 -4.74 1.09e+00 8.42e-01 1.89e+01 angle pdb=" N GLN N 544 " pdb=" CA GLN N 544 " pdb=" C GLN N 544 " ideal model delta sigma weight residual 111.28 114.80 -3.52 1.09e+00 8.42e-01 1.04e+01 angle pdb=" C LEU N 467 " pdb=" N VAL N 468 " pdb=" CA VAL N 468 " ideal model delta sigma weight residual 121.97 116.89 5.08 1.80e+00 3.09e-01 7.95e+00 angle pdb=" C ARG N 466 " pdb=" N LEU N 467 " pdb=" CA LEU N 467 " ideal model delta sigma weight residual 120.28 123.93 -3.65 1.34e+00 5.57e-01 7.40e+00 ... (remaining 8388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3405 17.89 - 35.78: 274 35.78 - 53.67: 47 53.67 - 71.56: 13 71.56 - 89.44: 8 Dihedral angle restraints: 3747 sinusoidal: 1567 harmonic: 2180 Sorted by residual: dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 111 " pdb=" CB CYS C 111 " ideal model delta sinusoidal sigma weight residual 93.00 162.30 -69.30 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CA ARG N 421 " pdb=" C ARG N 421 " pdb=" N LEU N 422 " pdb=" CA LEU N 422 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA LEU N 420 " pdb=" C LEU N 420 " pdb=" N ARG N 421 " pdb=" CA ARG N 421 " ideal model delta harmonic sigma weight residual 180.00 152.39 27.61 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 3744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 509 0.037 - 0.074: 245 0.074 - 0.111: 119 0.111 - 0.149: 33 0.149 - 0.186: 4 Chirality restraints: 910 Sorted by residual: chirality pdb=" CB THR N 154 " pdb=" CA THR N 154 " pdb=" OG1 THR N 154 " pdb=" CG2 THR N 154 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA CYS C 49 " pdb=" N CYS C 49 " pdb=" C CYS C 49 " pdb=" CB CYS C 49 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB VAL N 468 " pdb=" CA VAL N 468 " pdb=" CG1 VAL N 468 " pdb=" CG2 VAL N 468 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 907 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 561 " -0.092 9.50e-02 1.11e+02 5.41e-02 1.64e+01 pdb=" NE ARG N 561 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG N 561 " -0.067 2.00e-02 2.50e+03 pdb=" NH1 ARG N 561 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG N 561 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 350 " -0.077 9.50e-02 1.11e+02 4.61e-02 1.22e+01 pdb=" NE ARG N 350 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG N 350 " -0.058 2.00e-02 2.50e+03 pdb=" NH1 ARG N 350 " 0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG N 350 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 408 " 0.076 9.50e-02 1.11e+02 4.25e-02 8.92e+00 pdb=" NE ARG N 408 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG N 408 " 0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG N 408 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG N 408 " -0.014 2.00e-02 2.50e+03 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 281 2.71 - 3.26: 6108 3.26 - 3.81: 9313 3.81 - 4.35: 11638 4.35 - 4.90: 19539 Nonbonded interactions: 46879 Sorted by model distance: nonbonded pdb=" NZ LYS C 47 " pdb=" OD2 ASP N 252 " model vdw 2.168 3.120 nonbonded pdb=" NZ LYS D 154 " pdb=" OG1 THR D 156 " model vdw 2.213 3.120 nonbonded pdb=" O VAL N 255 " pdb="CA CA N 700 " model vdw 2.228 2.510 nonbonded pdb=" OH TYR N 169 " pdb=" OD2 ASP N 211 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP N 211 " pdb="CA CA N 700 " model vdw 2.240 2.510 ... (remaining 46874 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.130 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 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 0.036 6201 Z= 0.206 Angle : 0.838 7.819 8419 Z= 0.488 Chirality : 0.052 0.186 910 Planarity : 0.006 0.054 1082 Dihedral : 14.155 89.444 2311 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.61 % Allowed : 5.16 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.28), residues: 732 helix: -1.78 (0.39), residues: 111 sheet: 1.09 (0.35), residues: 186 loop : -0.91 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP N 535 HIS 0.006 0.001 HIS C 90 PHE 0.012 0.002 PHE D 190 TYR 0.025 0.005 TYR N 357 ARG 0.068 0.008 ARG N 561 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 2) link_NAG-ASN : angle 3.04091 ( 6) hydrogen bonds : bond 0.17122 ( 206) hydrogen bonds : angle 7.79682 ( 597) SS BOND : bond 0.00416 ( 10) SS BOND : angle 2.33297 ( 20) covalent geometry : bond 0.00436 ( 6189) covalent geometry : angle 0.82728 ( 8393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 221 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 TYR cc_start: 0.7380 (p90) cc_final: 0.6664 (p90) REVERT: C 48 MET cc_start: 0.7326 (pmm) cc_final: 0.7013 (pmm) REVERT: C 116 ASP cc_start: 0.7754 (m-30) cc_final: 0.7193 (m-30) REVERT: D 111 ILE cc_start: 0.8318 (mm) cc_final: 0.7917 (mm) REVERT: D 125 MET cc_start: 0.8095 (ttm) cc_final: 0.7784 (ttm) REVERT: D 154 LYS cc_start: 0.8140 (tptp) cc_final: 0.7707 (tptp) REVERT: D 178 SER cc_start: 0.8348 (p) cc_final: 0.8052 (p) REVERT: D 188 VAL cc_start: 0.8545 (m) cc_final: 0.8200 (p) REVERT: E 51 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7476 (mmmt) REVERT: E 91 ASP cc_start: 0.7903 (t0) cc_final: 0.7695 (t0) REVERT: N 151 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8240 (mtmt) REVERT: N 160 ILE cc_start: 0.8071 (tp) cc_final: 0.7680 (pt) REVERT: N 161 GLU cc_start: 0.7323 (pm20) cc_final: 0.6998 (pm20) REVERT: N 174 ASP cc_start: 0.7711 (t0) cc_final: 0.7315 (t0) REVERT: N 186 GLU cc_start: 0.6907 (tp30) cc_final: 0.6252 (tp30) REVERT: N 188 ILE cc_start: 0.8164 (mp) cc_final: 0.7821 (mt) REVERT: N 212 TRP cc_start: 0.8535 (p90) cc_final: 0.8323 (p90) REVERT: N 226 ILE cc_start: 0.8829 (mt) cc_final: 0.8505 (mm) REVERT: N 229 TYR cc_start: 0.7965 (m-80) cc_final: 0.7622 (m-80) REVERT: N 238 LEU cc_start: 0.8468 (pt) cc_final: 0.8201 (pp) REVERT: N 239 ARG cc_start: 0.7441 (mtt90) cc_final: 0.7063 (mtt-85) REVERT: N 278 ASN cc_start: 0.6584 (m-40) cc_final: 0.6321 (m-40) REVERT: N 339 LEU cc_start: 0.7946 (tp) cc_final: 0.7725 (mp) REVERT: N 364 GLU cc_start: 0.6716 (tp30) cc_final: 0.6425 (tp30) REVERT: N 373 MET cc_start: 0.6995 (tmm) cc_final: 0.6704 (tmm) REVERT: N 376 ARG cc_start: 0.8098 (ptp-170) cc_final: 0.7844 (ptp-110) REVERT: N 423 GLU cc_start: 0.6904 (tp30) cc_final: 0.6686 (tp30) REVERT: N 456 GLN cc_start: 0.7737 (tm-30) cc_final: 0.6616 (tm-30) REVERT: N 457 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6735 (mm-30) REVERT: N 460 TRP cc_start: 0.7725 (t-100) cc_final: 0.7108 (t-100) REVERT: N 498 VAL cc_start: 0.8365 (t) cc_final: 0.7955 (m) REVERT: N 535 TRP cc_start: 0.7304 (m100) cc_final: 0.6626 (m100) REVERT: N 555 TYR cc_start: 0.7522 (p90) cc_final: 0.7283 (p90) REVERT: N 559 ASP cc_start: 0.7477 (t0) cc_final: 0.7237 (t0) REVERT: N 572 ARG cc_start: 0.7108 (mtt180) cc_final: 0.6364 (mtt180) outliers start: 4 outliers final: 2 residues processed: 225 average time/residue: 0.2263 time to fit residues: 62.7343 Evaluate side-chains 211 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain N residue 542 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 90 HIS C 91 ASN D 119 GLN D 138 GLN D 181 HIS D 211 ASN N 171 HIS N 172 ASN N 250 HIS N 292 GLN N 385 GLN N 396 ASN N 415 HIS N 436 ASN N 480 GLN ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112225 restraints weight = 10283.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116036 restraints weight = 5276.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118569 restraints weight = 3208.886| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6201 Z= 0.231 Angle : 0.736 6.410 8419 Z= 0.393 Chirality : 0.050 0.141 910 Planarity : 0.005 0.054 1082 Dihedral : 7.525 57.131 872 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.86 % Allowed : 10.77 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.29), residues: 732 helix: -0.73 (0.44), residues: 111 sheet: 1.31 (0.37), residues: 172 loop : -0.92 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 535 HIS 0.010 0.002 HIS C 38 PHE 0.015 0.002 PHE N 549 TYR 0.028 0.002 TYR C 130 ARG 0.006 0.001 ARG N 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00891 ( 2) link_NAG-ASN : angle 2.86631 ( 6) hydrogen bonds : bond 0.05206 ( 206) hydrogen bonds : angle 5.89538 ( 597) SS BOND : bond 0.00537 ( 10) SS BOND : angle 1.56295 ( 20) covalent geometry : bond 0.00515 ( 6189) covalent geometry : angle 0.72962 ( 8393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 TYR cc_start: 0.7712 (p90) cc_final: 0.7138 (p90) REVERT: C 48 MET cc_start: 0.7461 (pmm) cc_final: 0.7051 (pmm) REVERT: C 132 TRP cc_start: 0.7783 (m100) cc_final: 0.7566 (m100) REVERT: D 111 ILE cc_start: 0.8401 (mm) cc_final: 0.8001 (mm) REVERT: D 174 MET cc_start: 0.7987 (ttp) cc_final: 0.7754 (ttp) REVERT: D 178 SER cc_start: 0.8355 (p) cc_final: 0.8138 (p) REVERT: E 77 LEU cc_start: 0.8605 (tp) cc_final: 0.8297 (tp) REVERT: E 91 ASP cc_start: 0.7930 (t0) cc_final: 0.7683 (t0) REVERT: N 151 LYS cc_start: 0.8604 (mtmt) cc_final: 0.8289 (mtmt) REVERT: N 160 ILE cc_start: 0.8179 (tp) cc_final: 0.7857 (pt) REVERT: N 161 GLU cc_start: 0.7334 (pm20) cc_final: 0.7104 (pm20) REVERT: N 174 ASP cc_start: 0.7765 (t0) cc_final: 0.7213 (t0) REVERT: N 188 ILE cc_start: 0.8298 (mp) cc_final: 0.7922 (mt) REVERT: N 228 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7500 (mtpp) REVERT: N 229 TYR cc_start: 0.8054 (m-80) cc_final: 0.7486 (m-80) REVERT: N 233 LYS cc_start: 0.7781 (mtpp) cc_final: 0.7510 (mtpp) REVERT: N 239 ARG cc_start: 0.7389 (mtt90) cc_final: 0.7046 (mtt-85) REVERT: N 278 ASN cc_start: 0.6351 (m-40) cc_final: 0.6134 (m110) REVERT: N 288 ILE cc_start: 0.8305 (mt) cc_final: 0.8091 (mt) REVERT: N 332 ASP cc_start: 0.7746 (t0) cc_final: 0.7499 (t0) REVERT: N 339 LEU cc_start: 0.8218 (tp) cc_final: 0.7958 (mp) REVERT: N 362 LYS cc_start: 0.7957 (mtmt) cc_final: 0.7680 (mtmm) REVERT: N 364 GLU cc_start: 0.6811 (tp30) cc_final: 0.6340 (tp30) REVERT: N 373 MET cc_start: 0.6964 (tmm) cc_final: 0.6655 (tmm) REVERT: N 376 ARG cc_start: 0.8137 (ptp-170) cc_final: 0.7759 (ptp-110) REVERT: N 440 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7461 (tpp) REVERT: N 456 GLN cc_start: 0.8034 (tm-30) cc_final: 0.6747 (tm-30) REVERT: N 457 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7053 (mm-30) REVERT: N 535 TRP cc_start: 0.7450 (m100) cc_final: 0.6854 (m100) REVERT: N 542 ARG cc_start: 0.5732 (OUTLIER) cc_final: 0.4434 (mmm160) REVERT: N 559 ASP cc_start: 0.7807 (t0) cc_final: 0.7458 (t0) REVERT: N 572 ARG cc_start: 0.6999 (mtt180) cc_final: 0.6296 (mtt180) REVERT: N 576 GLU cc_start: 0.6775 (mp0) cc_final: 0.6464 (mp0) outliers start: 32 outliers final: 24 residues processed: 209 average time/residue: 0.2667 time to fit residues: 69.5607 Evaluate side-chains 222 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 438 LEU Chi-restraints excluded: chain N residue 440 MET Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 488 LEU Chi-restraints excluded: chain N residue 542 ARG Chi-restraints excluded: chain N residue 550 GLU Chi-restraints excluded: chain N residue 557 THR Chi-restraints excluded: chain N residue 585 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112342 restraints weight = 10347.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116170 restraints weight = 5285.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118666 restraints weight = 3183.762| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6201 Z= 0.212 Angle : 0.683 7.107 8419 Z= 0.362 Chirality : 0.049 0.239 910 Planarity : 0.005 0.053 1082 Dihedral : 7.041 58.535 872 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.46 % Allowed : 12.75 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.30), residues: 732 helix: -0.70 (0.46), residues: 117 sheet: 1.18 (0.38), residues: 176 loop : -1.02 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 535 HIS 0.010 0.001 HIS C 38 PHE 0.012 0.002 PHE N 549 TYR 0.029 0.002 TYR C 130 ARG 0.005 0.000 ARG E 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00752 ( 2) link_NAG-ASN : angle 2.61353 ( 6) hydrogen bonds : bond 0.04864 ( 206) hydrogen bonds : angle 5.69033 ( 597) SS BOND : bond 0.00529 ( 10) SS BOND : angle 1.58195 ( 20) covalent geometry : bond 0.00472 ( 6189) covalent geometry : angle 0.67624 ( 8393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 TYR cc_start: 0.7818 (p90) cc_final: 0.7385 (p90) REVERT: C 48 MET cc_start: 0.7425 (pmm) cc_final: 0.7030 (pmm) REVERT: C 132 TRP cc_start: 0.7815 (m100) cc_final: 0.7543 (m100) REVERT: D 111 ILE cc_start: 0.8406 (mm) cc_final: 0.7970 (mm) REVERT: D 164 ASN cc_start: 0.8129 (p0) cc_final: 0.7878 (p0) REVERT: D 174 MET cc_start: 0.7990 (ttp) cc_final: 0.7784 (ttp) REVERT: E 51 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7628 (mmmt) REVERT: E 91 ASP cc_start: 0.7954 (t0) cc_final: 0.7721 (t0) REVERT: N 151 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8254 (mtmt) REVERT: N 153 PHE cc_start: 0.7444 (m-80) cc_final: 0.7206 (m-80) REVERT: N 160 ILE cc_start: 0.8179 (tp) cc_final: 0.7833 (pt) REVERT: N 174 ASP cc_start: 0.7843 (t0) cc_final: 0.7255 (t0) REVERT: N 186 GLU cc_start: 0.6605 (tp30) cc_final: 0.6145 (tp30) REVERT: N 188 ILE cc_start: 0.8332 (mp) cc_final: 0.8105 (mt) REVERT: N 228 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7343 (mtpp) REVERT: N 229 TYR cc_start: 0.8049 (m-80) cc_final: 0.7492 (m-80) REVERT: N 233 LYS cc_start: 0.7777 (mtpp) cc_final: 0.7569 (mtpp) REVERT: N 278 ASN cc_start: 0.6436 (m-40) cc_final: 0.6214 (m110) REVERT: N 288 ILE cc_start: 0.8343 (mt) cc_final: 0.8118 (mt) REVERT: N 332 ASP cc_start: 0.7848 (t0) cc_final: 0.7627 (t0) REVERT: N 339 LEU cc_start: 0.8197 (tp) cc_final: 0.7942 (mp) REVERT: N 362 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7683 (mtmm) REVERT: N 364 GLU cc_start: 0.6845 (tp30) cc_final: 0.6310 (tp30) REVERT: N 372 TRP cc_start: 0.7801 (m100) cc_final: 0.7554 (m100) REVERT: N 373 MET cc_start: 0.6925 (tmm) cc_final: 0.6651 (tmm) REVERT: N 376 ARG cc_start: 0.8121 (ptp-170) cc_final: 0.7634 (ptp-110) REVERT: N 456 GLN cc_start: 0.8044 (tm-30) cc_final: 0.6720 (tm-30) REVERT: N 457 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7098 (mm-30) REVERT: N 498 VAL cc_start: 0.8505 (t) cc_final: 0.8072 (m) REVERT: N 535 TRP cc_start: 0.7488 (m100) cc_final: 0.6931 (m100) REVERT: N 542 ARG cc_start: 0.5619 (OUTLIER) cc_final: 0.4613 (mmm160) REVERT: N 559 ASP cc_start: 0.7812 (t0) cc_final: 0.7563 (t0) REVERT: N 570 TYR cc_start: 0.6492 (m-80) cc_final: 0.6201 (m-80) REVERT: N 572 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6226 (mtt180) REVERT: N 576 GLU cc_start: 0.6829 (mp0) cc_final: 0.6525 (mp0) outliers start: 36 outliers final: 23 residues processed: 209 average time/residue: 0.2346 time to fit residues: 60.6778 Evaluate side-chains 219 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain N residue 172 ASN Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 279 VAL Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 337 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 438 LEU Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 488 LEU Chi-restraints excluded: chain N residue 542 ARG Chi-restraints excluded: chain N residue 557 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.0040 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 39 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.0050 overall best weight: 0.2406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.131658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.114787 restraints weight = 10412.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118486 restraints weight = 5323.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120942 restraints weight = 3223.762| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6201 Z= 0.123 Angle : 0.626 7.666 8419 Z= 0.322 Chirality : 0.045 0.184 910 Planarity : 0.004 0.049 1082 Dihedral : 6.194 52.172 872 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.86 % Allowed : 16.24 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.30), residues: 732 helix: -0.53 (0.47), residues: 117 sheet: 1.33 (0.38), residues: 179 loop : -0.95 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 179 HIS 0.010 0.001 HIS C 38 PHE 0.011 0.001 PHE D 190 TYR 0.028 0.001 TYR C 130 ARG 0.006 0.000 ARG E 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 2) link_NAG-ASN : angle 2.01785 ( 6) hydrogen bonds : bond 0.03984 ( 206) hydrogen bonds : angle 5.32425 ( 597) SS BOND : bond 0.00350 ( 10) SS BOND : angle 1.08837 ( 20) covalent geometry : bond 0.00274 ( 6189) covalent geometry : angle 0.62205 ( 8393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 TYR cc_start: 0.7812 (p90) cc_final: 0.7357 (p90) REVERT: C 48 MET cc_start: 0.7289 (pmm) cc_final: 0.6896 (pmm) REVERT: C 101 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7008 (pp) REVERT: C 132 TRP cc_start: 0.7737 (m100) cc_final: 0.7347 (m100) REVERT: D 111 ILE cc_start: 0.8367 (mm) cc_final: 0.7964 (mm) REVERT: D 124 ARG cc_start: 0.6709 (mtm180) cc_final: 0.6494 (mtm180) REVERT: D 125 MET cc_start: 0.7685 (ttp) cc_final: 0.7026 (ttp) REVERT: D 164 ASN cc_start: 0.8168 (p0) cc_final: 0.7945 (p0) REVERT: D 174 MET cc_start: 0.7973 (ttp) cc_final: 0.7740 (ttp) REVERT: E 61 LEU cc_start: 0.7348 (tp) cc_final: 0.7039 (mt) REVERT: E 91 ASP cc_start: 0.7887 (t0) cc_final: 0.7635 (t0) REVERT: N 151 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8172 (mtmt) REVERT: N 153 PHE cc_start: 0.7388 (m-80) cc_final: 0.7168 (m-80) REVERT: N 174 ASP cc_start: 0.7757 (t0) cc_final: 0.7254 (t0) REVERT: N 188 ILE cc_start: 0.8342 (mp) cc_final: 0.8108 (mt) REVERT: N 229 TYR cc_start: 0.8010 (m-80) cc_final: 0.7479 (m-80) REVERT: N 239 ARG cc_start: 0.7388 (mtt90) cc_final: 0.7093 (mtt90) REVERT: N 288 ILE cc_start: 0.8345 (mt) cc_final: 0.8120 (mt) REVERT: N 339 LEU cc_start: 0.8193 (tp) cc_final: 0.7961 (mp) REVERT: N 362 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7681 (mtmm) REVERT: N 364 GLU cc_start: 0.6779 (tp30) cc_final: 0.6221 (tp30) REVERT: N 372 TRP cc_start: 0.7686 (m100) cc_final: 0.7337 (m100) REVERT: N 373 MET cc_start: 0.6886 (tmm) cc_final: 0.6604 (tmm) REVERT: N 376 ARG cc_start: 0.8068 (ptp-170) cc_final: 0.7585 (ptp-110) REVERT: N 440 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7383 (tpp) REVERT: N 456 GLN cc_start: 0.8070 (tm-30) cc_final: 0.6807 (tm-30) REVERT: N 457 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7176 (mm-30) REVERT: N 498 VAL cc_start: 0.8402 (t) cc_final: 0.8019 (m) REVERT: N 535 TRP cc_start: 0.7475 (m100) cc_final: 0.6986 (m100) REVERT: N 542 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.5218 (mmm160) REVERT: N 559 ASP cc_start: 0.7901 (t0) cc_final: 0.7579 (t0) REVERT: N 570 TYR cc_start: 0.6461 (m-80) cc_final: 0.6210 (m-80) REVERT: N 572 ARG cc_start: 0.7001 (mtt180) cc_final: 0.6263 (mtt180) REVERT: N 576 GLU cc_start: 0.6878 (mp0) cc_final: 0.6510 (mp0) outliers start: 32 outliers final: 18 residues processed: 205 average time/residue: 0.2559 time to fit residues: 64.3551 Evaluate side-chains 212 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 337 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 438 LEU Chi-restraints excluded: chain N residue 440 MET Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 542 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 0.0470 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 544 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114335 restraints weight = 10309.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118010 restraints weight = 5299.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120446 restraints weight = 3216.174| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6201 Z= 0.145 Angle : 0.620 7.388 8419 Z= 0.321 Chirality : 0.046 0.167 910 Planarity : 0.004 0.048 1082 Dihedral : 5.994 49.046 872 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.70 % Allowed : 18.51 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.30), residues: 732 helix: -0.47 (0.47), residues: 117 sheet: 1.14 (0.38), residues: 184 loop : -0.99 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 179 HIS 0.010 0.001 HIS C 38 PHE 0.011 0.001 PHE E 122 TYR 0.033 0.001 TYR C 130 ARG 0.007 0.000 ARG N 562 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 2) link_NAG-ASN : angle 2.01985 ( 6) hydrogen bonds : bond 0.04072 ( 206) hydrogen bonds : angle 5.27165 ( 597) SS BOND : bond 0.00391 ( 10) SS BOND : angle 0.97581 ( 20) covalent geometry : bond 0.00326 ( 6189) covalent geometry : angle 0.61694 ( 8393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: C 44 TYR cc_start: 0.7914 (p90) cc_final: 0.7408 (p90) REVERT: C 48 MET cc_start: 0.7286 (pmm) cc_final: 0.6883 (pmm) REVERT: C 78 THR cc_start: 0.7182 (OUTLIER) cc_final: 0.6960 (t) REVERT: C 101 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7111 (pp) REVERT: D 111 ILE cc_start: 0.8390 (mm) cc_final: 0.7964 (mm) REVERT: D 164 ASN cc_start: 0.8162 (p0) cc_final: 0.7958 (p0) REVERT: E 91 ASP cc_start: 0.7899 (t0) cc_final: 0.7650 (t0) REVERT: N 151 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8185 (mtmt) REVERT: N 153 PHE cc_start: 0.7446 (m-80) cc_final: 0.7208 (m-80) REVERT: N 174 ASP cc_start: 0.7794 (t0) cc_final: 0.7250 (t0) REVERT: N 188 ILE cc_start: 0.8351 (mp) cc_final: 0.8103 (mt) REVERT: N 228 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7590 (mtpp) REVERT: N 229 TYR cc_start: 0.8124 (m-80) cc_final: 0.7486 (m-80) REVERT: N 239 ARG cc_start: 0.7387 (mtt90) cc_final: 0.7110 (mtt90) REVERT: N 288 ILE cc_start: 0.8337 (mt) cc_final: 0.8114 (mt) REVERT: N 339 LEU cc_start: 0.8194 (tp) cc_final: 0.7943 (mp) REVERT: N 362 LYS cc_start: 0.8055 (mtmt) cc_final: 0.7703 (mtmm) REVERT: N 364 GLU cc_start: 0.6942 (tp30) cc_final: 0.6310 (tp30) REVERT: N 372 TRP cc_start: 0.7721 (m100) cc_final: 0.7376 (m100) REVERT: N 373 MET cc_start: 0.6919 (tmm) cc_final: 0.6665 (tmm) REVERT: N 376 ARG cc_start: 0.8113 (ptp-170) cc_final: 0.7556 (ptp-110) REVERT: N 440 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7284 (tpp) REVERT: N 456 GLN cc_start: 0.8065 (tm-30) cc_final: 0.6850 (tm-30) REVERT: N 457 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7198 (mm-30) REVERT: N 498 VAL cc_start: 0.8467 (t) cc_final: 0.8068 (m) REVERT: N 535 TRP cc_start: 0.7506 (m100) cc_final: 0.6890 (m100) REVERT: N 542 ARG cc_start: 0.5581 (OUTLIER) cc_final: 0.5350 (mmm160) REVERT: N 555 TYR cc_start: 0.7883 (p90) cc_final: 0.7636 (p90) REVERT: N 559 ASP cc_start: 0.7875 (t0) cc_final: 0.7554 (t0) REVERT: N 572 ARG cc_start: 0.6977 (mtt180) cc_final: 0.6233 (mtt180) REVERT: N 576 GLU cc_start: 0.6861 (mp0) cc_final: 0.6475 (mp0) outliers start: 31 outliers final: 21 residues processed: 203 average time/residue: 0.2296 time to fit residues: 57.1904 Evaluate side-chains 219 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 337 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 438 LEU Chi-restraints excluded: chain N residue 440 MET Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 542 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 29 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 22 optimal weight: 0.0570 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 345 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 = 0.3705 r_free = 0.3705 target = 0.131700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.114879 restraints weight = 10196.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118534 restraints weight = 5258.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120938 restraints weight = 3192.251| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6201 Z= 0.130 Angle : 0.606 8.248 8419 Z= 0.312 Chirality : 0.045 0.193 910 Planarity : 0.004 0.049 1082 Dihedral : 5.768 45.411 872 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.16 % Allowed : 19.58 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.30), residues: 732 helix: -0.23 (0.49), residues: 111 sheet: 1.16 (0.38), residues: 184 loop : -0.99 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 179 HIS 0.010 0.001 HIS C 38 PHE 0.010 0.001 PHE E 122 TYR 0.034 0.001 TYR C 130 ARG 0.008 0.000 ARG E 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 2) link_NAG-ASN : angle 1.93308 ( 6) hydrogen bonds : bond 0.03940 ( 206) hydrogen bonds : angle 5.21189 ( 597) SS BOND : bond 0.00336 ( 10) SS BOND : angle 0.90899 ( 20) covalent geometry : bond 0.00291 ( 6189) covalent geometry : angle 0.60338 ( 8393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 TYR cc_start: 0.7940 (p90) cc_final: 0.7377 (p90) REVERT: C 48 MET cc_start: 0.7336 (pmm) cc_final: 0.6909 (pmm) REVERT: C 78 THR cc_start: 0.7124 (OUTLIER) cc_final: 0.6913 (t) REVERT: C 101 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7123 (pp) REVERT: C 104 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: D 111 ILE cc_start: 0.8412 (mm) cc_final: 0.7990 (mm) REVERT: D 154 LYS cc_start: 0.8318 (tptp) cc_final: 0.7986 (tptp) REVERT: D 170 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: E 32 ARG cc_start: 0.8469 (mmt90) cc_final: 0.8156 (mmt90) REVERT: E 91 ASP cc_start: 0.7884 (t0) cc_final: 0.7639 (t0) REVERT: N 151 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8139 (mtmt) REVERT: N 153 PHE cc_start: 0.7456 (m-80) cc_final: 0.7254 (m-80) REVERT: N 174 ASP cc_start: 0.7756 (t0) cc_final: 0.7220 (t0) REVERT: N 188 ILE cc_start: 0.8349 (mp) cc_final: 0.8103 (mt) REVERT: N 228 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7581 (ttmm) REVERT: N 229 TYR cc_start: 0.8058 (m-80) cc_final: 0.7582 (m-80) REVERT: N 239 ARG cc_start: 0.7374 (mtt90) cc_final: 0.7119 (mtt90) REVERT: N 288 ILE cc_start: 0.8328 (mt) cc_final: 0.8105 (mt) REVERT: N 339 LEU cc_start: 0.8204 (tp) cc_final: 0.7948 (mp) REVERT: N 362 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7715 (mtmm) REVERT: N 364 GLU cc_start: 0.6908 (tp30) cc_final: 0.6333 (tp30) REVERT: N 372 TRP cc_start: 0.7714 (m100) cc_final: 0.7370 (m100) REVERT: N 373 MET cc_start: 0.6913 (tmm) cc_final: 0.6670 (tmm) REVERT: N 376 ARG cc_start: 0.8079 (ptp-170) cc_final: 0.7600 (ptp-110) REVERT: N 456 GLN cc_start: 0.8037 (tm-30) cc_final: 0.6833 (tm-30) REVERT: N 457 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7187 (mm-30) REVERT: N 535 TRP cc_start: 0.7535 (m100) cc_final: 0.6973 (m100) REVERT: N 542 ARG cc_start: 0.5619 (OUTLIER) cc_final: 0.5221 (mmm160) REVERT: N 555 TYR cc_start: 0.7892 (p90) cc_final: 0.7626 (p90) REVERT: N 559 ASP cc_start: 0.7864 (t0) cc_final: 0.7551 (t0) REVERT: N 572 ARG cc_start: 0.6987 (mtt180) cc_final: 0.6261 (mtt180) REVERT: N 576 GLU cc_start: 0.6879 (mp0) cc_final: 0.6468 (mp0) outliers start: 34 outliers final: 20 residues processed: 205 average time/residue: 0.2604 time to fit residues: 66.0903 Evaluate side-chains 216 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 337 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 488 LEU Chi-restraints excluded: chain N residue 501 VAL Chi-restraints excluded: chain N residue 542 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 0.0060 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113654 restraints weight = 10252.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117293 restraints weight = 5287.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119704 restraints weight = 3212.844| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6201 Z= 0.171 Angle : 0.627 7.756 8419 Z= 0.326 Chirality : 0.047 0.162 910 Planarity : 0.005 0.049 1082 Dihedral : 5.789 42.581 871 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.46 % Allowed : 19.42 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.30), residues: 732 helix: -0.29 (0.49), residues: 111 sheet: 1.11 (0.37), residues: 193 loop : -1.06 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 179 HIS 0.010 0.001 HIS C 38 PHE 0.010 0.001 PHE E 122 TYR 0.040 0.002 TYR C 130 ARG 0.007 0.001 ARG E 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 2) link_NAG-ASN : angle 2.24474 ( 6) hydrogen bonds : bond 0.04239 ( 206) hydrogen bonds : angle 5.25459 ( 597) SS BOND : bond 0.00356 ( 10) SS BOND : angle 0.97201 ( 20) covalent geometry : bond 0.00382 ( 6189) covalent geometry : angle 0.62308 ( 8393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: C 44 TYR cc_start: 0.7964 (p90) cc_final: 0.7432 (p90) REVERT: C 48 MET cc_start: 0.7398 (pmm) cc_final: 0.7016 (pmm) REVERT: C 78 THR cc_start: 0.7177 (OUTLIER) cc_final: 0.6937 (t) REVERT: D 111 ILE cc_start: 0.8474 (mm) cc_final: 0.8047 (mm) REVERT: D 154 LYS cc_start: 0.8306 (tptp) cc_final: 0.7979 (tptp) REVERT: D 164 ASN cc_start: 0.8023 (p0) cc_final: 0.7821 (p0) REVERT: D 170 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8198 (mt0) REVERT: E 32 ARG cc_start: 0.8506 (mmt90) cc_final: 0.8118 (mmt90) REVERT: E 91 ASP cc_start: 0.7906 (t0) cc_final: 0.7661 (t0) REVERT: N 151 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8188 (mtmt) REVERT: N 153 PHE cc_start: 0.7489 (m-80) cc_final: 0.7258 (m-80) REVERT: N 168 LYS cc_start: 0.6351 (mttp) cc_final: 0.6125 (mmmm) REVERT: N 174 ASP cc_start: 0.7736 (t0) cc_final: 0.7172 (t0) REVERT: N 188 ILE cc_start: 0.8382 (mp) cc_final: 0.8143 (mt) REVERT: N 228 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7476 (mtpp) REVERT: N 229 TYR cc_start: 0.8074 (m-80) cc_final: 0.7558 (m-80) REVERT: N 239 ARG cc_start: 0.7394 (mtt90) cc_final: 0.7161 (mtt90) REVERT: N 288 ILE cc_start: 0.8302 (mt) cc_final: 0.8094 (mt) REVERT: N 339 LEU cc_start: 0.8205 (tp) cc_final: 0.7951 (mp) REVERT: N 362 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7724 (mtmm) REVERT: N 364 GLU cc_start: 0.6931 (tp30) cc_final: 0.6332 (tp30) REVERT: N 372 TRP cc_start: 0.7788 (m100) cc_final: 0.7469 (m100) REVERT: N 373 MET cc_start: 0.6952 (tmm) cc_final: 0.6712 (tmm) REVERT: N 376 ARG cc_start: 0.8086 (ptp-170) cc_final: 0.7603 (ptp-110) REVERT: N 456 GLN cc_start: 0.8020 (tm-30) cc_final: 0.6865 (tm-30) REVERT: N 457 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7203 (mm-30) REVERT: N 535 TRP cc_start: 0.7568 (m100) cc_final: 0.7045 (m100) REVERT: N 542 ARG cc_start: 0.5776 (OUTLIER) cc_final: 0.5311 (mmm160) REVERT: N 555 TYR cc_start: 0.7892 (p90) cc_final: 0.7638 (p90) REVERT: N 559 ASP cc_start: 0.7831 (t0) cc_final: 0.7567 (t0) REVERT: N 572 ARG cc_start: 0.6974 (mtt180) cc_final: 0.6270 (mtt180) REVERT: N 576 GLU cc_start: 0.6847 (mp0) cc_final: 0.6436 (mp0) outliers start: 36 outliers final: 24 residues processed: 204 average time/residue: 0.2354 time to fit residues: 59.4723 Evaluate side-chains 216 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 337 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 488 LEU Chi-restraints excluded: chain N residue 501 VAL Chi-restraints excluded: chain N residue 542 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 22 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.0070 chunk 16 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113484 restraints weight = 10286.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.117130 restraints weight = 5319.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119567 restraints weight = 3236.483| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6201 Z= 0.177 Angle : 0.640 8.281 8419 Z= 0.331 Chirality : 0.047 0.174 910 Planarity : 0.005 0.049 1082 Dihedral : 5.814 41.972 871 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.46 % Allowed : 20.33 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.30), residues: 732 helix: -0.34 (0.49), residues: 111 sheet: 1.05 (0.37), residues: 193 loop : -1.14 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 179 HIS 0.010 0.001 HIS C 38 PHE 0.011 0.001 PHE E 122 TYR 0.040 0.001 TYR C 130 ARG 0.007 0.000 ARG E 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 2) link_NAG-ASN : angle 2.28925 ( 6) hydrogen bonds : bond 0.04275 ( 206) hydrogen bonds : angle 5.22398 ( 597) SS BOND : bond 0.00382 ( 10) SS BOND : angle 1.07710 ( 20) covalent geometry : bond 0.00397 ( 6189) covalent geometry : angle 0.63573 ( 8393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: C 48 MET cc_start: 0.7399 (pmm) cc_final: 0.6999 (pmm) REVERT: C 78 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6908 (t) REVERT: D 111 ILE cc_start: 0.8489 (mm) cc_final: 0.8048 (mm) REVERT: D 154 LYS cc_start: 0.8305 (tptp) cc_final: 0.7981 (tptp) REVERT: D 170 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8216 (mt0) REVERT: E 32 ARG cc_start: 0.8513 (mmt90) cc_final: 0.8121 (mmt90) REVERT: E 91 ASP cc_start: 0.7920 (t0) cc_final: 0.7664 (t0) REVERT: N 151 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8173 (mtmt) REVERT: N 153 PHE cc_start: 0.7507 (m-80) cc_final: 0.7301 (m-80) REVERT: N 174 ASP cc_start: 0.7730 (t0) cc_final: 0.7186 (t0) REVERT: N 188 ILE cc_start: 0.8364 (mp) cc_final: 0.8141 (mt) REVERT: N 229 TYR cc_start: 0.8110 (m-80) cc_final: 0.7640 (m-80) REVERT: N 239 ARG cc_start: 0.7410 (mtt90) cc_final: 0.7174 (mtt90) REVERT: N 288 ILE cc_start: 0.8295 (mt) cc_final: 0.8028 (mt) REVERT: N 339 LEU cc_start: 0.8202 (tp) cc_final: 0.7953 (mp) REVERT: N 362 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7718 (mtmm) REVERT: N 364 GLU cc_start: 0.6955 (tp30) cc_final: 0.6337 (tp30) REVERT: N 372 TRP cc_start: 0.7795 (m100) cc_final: 0.7531 (m100) REVERT: N 373 MET cc_start: 0.6937 (tmm) cc_final: 0.6719 (tmm) REVERT: N 376 ARG cc_start: 0.8088 (ptp-170) cc_final: 0.7608 (ptp-110) REVERT: N 456 GLN cc_start: 0.8012 (tm-30) cc_final: 0.6813 (tm-30) REVERT: N 457 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7223 (mm-30) REVERT: N 535 TRP cc_start: 0.7562 (m100) cc_final: 0.7018 (m100) REVERT: N 542 ARG cc_start: 0.5827 (OUTLIER) cc_final: 0.5459 (mmm160) REVERT: N 555 TYR cc_start: 0.7894 (p90) cc_final: 0.7635 (p90) REVERT: N 559 ASP cc_start: 0.7794 (t0) cc_final: 0.7552 (t0) REVERT: N 572 ARG cc_start: 0.6924 (mtt180) cc_final: 0.6254 (mtt180) REVERT: N 576 GLU cc_start: 0.6850 (mp0) cc_final: 0.6489 (mp0) outliers start: 36 outliers final: 28 residues processed: 203 average time/residue: 0.2436 time to fit residues: 60.9738 Evaluate side-chains 219 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain N residue 172 ASN Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain N residue 337 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 438 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 488 LEU Chi-restraints excluded: chain N residue 501 VAL Chi-restraints excluded: chain N residue 542 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.0170 chunk 67 optimal weight: 0.2980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.130300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.113424 restraints weight = 10265.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117032 restraints weight = 5314.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119448 restraints weight = 3241.268| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6201 Z= 0.174 Angle : 0.646 8.859 8419 Z= 0.332 Chirality : 0.046 0.148 910 Planarity : 0.005 0.051 1082 Dihedral : 5.799 42.368 871 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.86 % Allowed : 21.09 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.30), residues: 732 helix: -0.35 (0.49), residues: 111 sheet: 0.98 (0.37), residues: 193 loop : -1.22 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 216 HIS 0.010 0.001 HIS C 38 PHE 0.011 0.002 PHE E 122 TYR 0.039 0.001 TYR C 130 ARG 0.006 0.000 ARG E 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 2) link_NAG-ASN : angle 2.28028 ( 6) hydrogen bonds : bond 0.04206 ( 206) hydrogen bonds : angle 5.28722 ( 597) SS BOND : bond 0.00375 ( 10) SS BOND : angle 1.07376 ( 20) covalent geometry : bond 0.00391 ( 6189) covalent geometry : angle 0.64180 ( 8393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.7436 (pmm) cc_final: 0.7031 (pmm) REVERT: C 78 THR cc_start: 0.7164 (OUTLIER) cc_final: 0.6936 (t) REVERT: D 111 ILE cc_start: 0.8482 (mm) cc_final: 0.8034 (mm) REVERT: D 154 LYS cc_start: 0.8310 (tptp) cc_final: 0.7985 (tptp) REVERT: D 170 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8226 (mt0) REVERT: E 32 ARG cc_start: 0.8501 (mmt90) cc_final: 0.8101 (mmt90) REVERT: E 65 TYR cc_start: 0.7904 (t80) cc_final: 0.7637 (t80) REVERT: E 91 ASP cc_start: 0.7923 (t0) cc_final: 0.7662 (t0) REVERT: N 151 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8176 (mtmt) REVERT: N 168 LYS cc_start: 0.6392 (mttp) cc_final: 0.6129 (mmmm) REVERT: N 174 ASP cc_start: 0.7739 (t0) cc_final: 0.7177 (t0) REVERT: N 188 ILE cc_start: 0.8367 (mp) cc_final: 0.8125 (mt) REVERT: N 229 TYR cc_start: 0.8063 (m-80) cc_final: 0.7661 (m-80) REVERT: N 288 ILE cc_start: 0.8291 (mt) cc_final: 0.8021 (mt) REVERT: N 339 LEU cc_start: 0.8204 (tp) cc_final: 0.7964 (mp) REVERT: N 362 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7608 (mtmm) REVERT: N 364 GLU cc_start: 0.6954 (tp30) cc_final: 0.6278 (tp30) REVERT: N 372 TRP cc_start: 0.7785 (m100) cc_final: 0.7541 (m100) REVERT: N 376 ARG cc_start: 0.8078 (ptp-170) cc_final: 0.7598 (ptp-110) REVERT: N 456 GLN cc_start: 0.7995 (tm-30) cc_final: 0.6727 (tm-30) REVERT: N 457 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7210 (mm-30) REVERT: N 542 ARG cc_start: 0.5881 (OUTLIER) cc_final: 0.5545 (mmm160) REVERT: N 555 TYR cc_start: 0.7885 (p90) cc_final: 0.7626 (p90) REVERT: N 559 ASP cc_start: 0.7802 (t0) cc_final: 0.7563 (t0) REVERT: N 572 ARG cc_start: 0.6919 (mtt180) cc_final: 0.6232 (mtt180) REVERT: N 576 GLU cc_start: 0.6852 (mp0) cc_final: 0.6486 (mp0) outliers start: 32 outliers final: 27 residues processed: 206 average time/residue: 0.3575 time to fit residues: 92.3732 Evaluate side-chains 223 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 324 SER Chi-restraints excluded: chain N residue 337 THR Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 438 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 501 VAL Chi-restraints excluded: chain N residue 542 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.0970 chunk 56 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 0.0050 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114396 restraints weight = 10418.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118004 restraints weight = 5338.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120437 restraints weight = 3242.664| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6201 Z= 0.139 Angle : 0.653 13.289 8419 Z= 0.329 Chirality : 0.046 0.146 910 Planarity : 0.005 0.050 1082 Dihedral : 5.624 40.981 871 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.70 % Allowed : 21.40 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.30), residues: 732 helix: -0.25 (0.50), residues: 111 sheet: 1.11 (0.37), residues: 195 loop : -1.20 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 212 HIS 0.010 0.001 HIS C 38 PHE 0.009 0.001 PHE D 190 TYR 0.037 0.001 TYR C 130 ARG 0.006 0.000 ARG D 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 2) link_NAG-ASN : angle 2.13146 ( 6) hydrogen bonds : bond 0.03953 ( 206) hydrogen bonds : angle 5.16148 ( 597) SS BOND : bond 0.00365 ( 10) SS BOND : angle 1.03096 ( 20) covalent geometry : bond 0.00316 ( 6189) covalent geometry : angle 0.64950 ( 8393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.7380 (pmm) cc_final: 0.6965 (pmm) REVERT: C 78 THR cc_start: 0.7128 (OUTLIER) cc_final: 0.6915 (t) REVERT: D 111 ILE cc_start: 0.8464 (mm) cc_final: 0.8033 (mm) REVERT: D 154 LYS cc_start: 0.8279 (tptp) cc_final: 0.7965 (tptp) REVERT: D 170 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: E 32 ARG cc_start: 0.8408 (mmt90) cc_final: 0.8051 (mmt90) REVERT: E 79 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.8094 (mtm-85) REVERT: E 91 ASP cc_start: 0.7905 (t0) cc_final: 0.7632 (t0) REVERT: N 151 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8061 (mtpp) REVERT: N 168 LYS cc_start: 0.6333 (mttp) cc_final: 0.6077 (mmmm) REVERT: N 174 ASP cc_start: 0.7725 (t0) cc_final: 0.7161 (t0) REVERT: N 188 ILE cc_start: 0.8363 (mp) cc_final: 0.8132 (mt) REVERT: N 229 TYR cc_start: 0.8059 (m-80) cc_final: 0.7579 (m-80) REVERT: N 288 ILE cc_start: 0.8329 (mt) cc_final: 0.8055 (mt) REVERT: N 339 LEU cc_start: 0.8210 (tp) cc_final: 0.7989 (mp) REVERT: N 362 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7591 (mtmm) REVERT: N 364 GLU cc_start: 0.6941 (tp30) cc_final: 0.6399 (tp30) REVERT: N 366 SER cc_start: 0.8483 (t) cc_final: 0.8243 (t) REVERT: N 372 TRP cc_start: 0.7742 (m100) cc_final: 0.7234 (m100) REVERT: N 376 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7497 (ptp-110) REVERT: N 456 GLN cc_start: 0.7966 (tm-30) cc_final: 0.6750 (tm-30) REVERT: N 457 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7229 (mm-30) REVERT: N 542 ARG cc_start: 0.5771 (OUTLIER) cc_final: 0.5510 (mmm160) REVERT: N 555 TYR cc_start: 0.7905 (p90) cc_final: 0.7636 (p90) REVERT: N 559 ASP cc_start: 0.7794 (t0) cc_final: 0.7569 (t0) REVERT: N 572 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6295 (mtt180) REVERT: N 576 GLU cc_start: 0.6881 (mp0) cc_final: 0.6515 (mp0) outliers start: 31 outliers final: 25 residues processed: 205 average time/residue: 0.2851 time to fit residues: 71.5462 Evaluate side-chains 219 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain N residue 180 LEU Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain N residue 438 LEU Chi-restraints excluded: chain N residue 444 LEU Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 501 VAL Chi-restraints excluded: chain N residue 542 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 0.0470 chunk 26 optimal weight: 0.0040 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 554 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.132998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.115942 restraints weight = 10487.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119553 restraints weight = 5397.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122066 restraints weight = 3302.345| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6201 Z= 0.115 Angle : 0.636 14.312 8419 Z= 0.318 Chirality : 0.044 0.149 910 Planarity : 0.005 0.049 1082 Dihedral : 5.302 38.587 871 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.64 % Allowed : 22.61 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.30), residues: 732 helix: -0.09 (0.50), residues: 111 sheet: 1.19 (0.37), residues: 196 loop : -1.17 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 212 HIS 0.010 0.001 HIS C 38 PHE 0.010 0.001 PHE D 190 TYR 0.032 0.001 TYR C 130 ARG 0.006 0.000 ARG E 32 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 2) link_NAG-ASN : angle 1.76925 ( 6) hydrogen bonds : bond 0.03553 ( 206) hydrogen bonds : angle 4.96771 ( 597) SS BOND : bond 0.00270 ( 10) SS BOND : angle 0.97826 ( 20) covalent geometry : bond 0.00261 ( 6189) covalent geometry : angle 0.63329 ( 8393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2937.19 seconds wall clock time: 52 minutes 42.02 seconds (3162.02 seconds total)