Starting phenix.real_space_refine on Sun Mar 10 23:34:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m22_23629/03_2024/7m22_23629_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m22_23629/03_2024/7m22_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m22_23629/03_2024/7m22_23629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m22_23629/03_2024/7m22_23629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m22_23629/03_2024/7m22_23629_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m22_23629/03_2024/7m22_23629_neut.pdb" } 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 Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "N GLU 237": "OE1" <-> "OE2" Residue "N GLU 327": "OE1" <-> "OE2" Residue "N GLU 351": "OE1" <-> "OE2" Residue "N GLU 364": "OE1" <-> "OE2" Residue "N GLU 370": "OE1" <-> "OE2" Residue "N PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 457": "OE1" <-> "OE2" Residue "N GLU 550": "OE1" <-> "OE2" Residue "N GLU 576": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.84, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 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: 2.27 Conformation dependent library (CDL) restraints added in 1.2 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: 0.71 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: 1.85 Time building geometry restraints manager: 2.50 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: 99.96 - 106.79: 211 106.79 - 113.63: 3300 113.63 - 120.46: 2403 120.46 - 127.30: 2394 127.30 - 134.13: 85 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 2.520 nonbonded pdb=" NZ LYS D 154 " pdb=" OG1 THR D 156 " model vdw 2.213 2.520 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 2.440 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 ========== 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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.900 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.410 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- 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 6189 Z= 0.287 Angle : 0.827 7.420 8393 Z= 0.485 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 0.652 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: 0.2299 time to fit residues: 63.7643 Evaluate side-chains 211 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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: 0.6980 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.0050 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN 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 415 HIS N 436 ASN N 480 GLN ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6189 Z= 0.294 Angle : 0.699 6.582 8393 Z= 0.373 Chirality : 0.048 0.140 910 Planarity : 0.005 0.050 1082 Dihedral : 7.544 56.471 872 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.86 % Allowed : 11.53 % Favored : 83.61 % 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: -0.37 (0.29), residues: 732 helix: -0.89 (0.43), residues: 117 sheet: 1.44 (0.37), residues: 173 loop : -0.77 (0.28), residues: 442 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 0.012 0.002 PHE N 549 TYR 0.028 0.002 TYR C 130 ARG 0.006 0.001 ARG N 263 *********************** 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 232 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 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: 0.7531 (p90) cc_final: 0.6916 (p90) REVERT: C 48 MET cc_start: 0.7366 (pmm) cc_final: 0.7025 (pmm) REVERT: C 108 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7596 (mtm110) REVERT: D 111 ILE cc_start: 0.8357 (mm) cc_final: 0.7959 (mm) REVERT: D 125 MET cc_start: 0.7902 (ttm) cc_final: 0.7564 (ttp) REVERT: D 174 MET cc_start: 0.7967 (ttp) cc_final: 0.7742 (ttp) REVERT: E 77 LEU cc_start: 0.8587 (tp) cc_final: 0.8259 (tp) REVERT: N 151 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8294 (mtmt) REVERT: N 160 ILE cc_start: 0.8177 (tp) cc_final: 0.7834 (pt) REVERT: N 161 GLU cc_start: 0.7417 (pm20) cc_final: 0.7088 (pm20) REVERT: N 174 ASP cc_start: 0.7787 (t0) cc_final: 0.7242 (t0) REVERT: N 188 ILE cc_start: 0.8247 (mp) cc_final: 0.8012 (mt) REVERT: N 217 ASP cc_start: 0.7772 (t0) cc_final: 0.7568 (t0) REVERT: N 229 TYR cc_start: 0.7941 (m-80) cc_final: 0.7499 (m-80) REVERT: N 233 LYS cc_start: 0.7736 (mtpp) cc_final: 0.7480 (mtpp) REVERT: N 239 ARG cc_start: 0.7414 (mtt90) cc_final: 0.7150 (mtt-85) REVERT: N 332 ASP cc_start: 0.7669 (t0) cc_final: 0.7428 (t0) REVERT: N 339 LEU cc_start: 0.8276 (tp) cc_final: 0.7987 (mp) REVERT: N 362 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7657 (mtmm) REVERT: N 364 GLU cc_start: 0.6742 (tp30) cc_final: 0.6371 (tp30) REVERT: N 373 MET cc_start: 0.6963 (tmm) cc_final: 0.6585 (tmm) REVERT: N 376 ARG cc_start: 0.8146 (ptp-170) cc_final: 0.7758 (ptp-110) REVERT: N 456 GLN cc_start: 0.8008 (tm-30) cc_final: 0.6754 (tm-30) REVERT: N 457 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6993 (mm-30) REVERT: N 535 TRP cc_start: 0.7410 (m100) cc_final: 0.6828 (m100) REVERT: N 542 ARG cc_start: 0.5607 (OUTLIER) cc_final: 0.4532 (mmm160) REVERT: N 559 ASP cc_start: 0.7822 (t0) cc_final: 0.7432 (t0) REVERT: N 572 ARG cc_start: 0.6869 (mtt180) cc_final: 0.6101 (mtt180) REVERT: N 576 GLU cc_start: 0.6867 (mp0) cc_final: 0.6543 (mp0) outliers start: 32 outliers final: 23 residues processed: 209 average time/residue: 0.2417 time to fit residues: 62.0263 Evaluate side-chains 220 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 128 VAL Chi-restraints excluded: chain D residue 110 VAL 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 N residue 267 VAL Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 323 ASP 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 447 ASP 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6189 Z= 0.408 Angle : 0.713 6.925 8393 Z= 0.383 Chirality : 0.050 0.232 910 Planarity : 0.005 0.053 1082 Dihedral : 7.199 54.398 872 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.83 % Allowed : 12.75 % Favored : 80.42 % 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: -0.76 (0.29), residues: 732 helix: -0.91 (0.44), residues: 117 sheet: 1.03 (0.38), residues: 181 loop : -1.09 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP N 372 HIS 0.010 0.002 HIS C 38 PHE 0.015 0.002 PHE N 549 TYR 0.034 0.002 TYR C 130 ARG 0.006 0.001 ARG D 124 *********************** 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 249 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ILE cc_start: 0.8402 (mm) cc_final: 0.7980 (mm) REVERT: D 125 MET cc_start: 0.7816 (ttm) cc_final: 0.7435 (tmm) REVERT: D 164 ASN cc_start: 0.8149 (p0) cc_final: 0.7877 (p0) REVERT: E 51 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7657 (mmmt) REVERT: N 151 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8313 (mtmt) REVERT: N 153 PHE cc_start: 0.7439 (m-80) cc_final: 0.7181 (m-80) REVERT: N 160 ILE cc_start: 0.8189 (tp) cc_final: 0.7788 (pt) REVERT: N 161 GLU cc_start: 0.7420 (pm20) cc_final: 0.7045 (pm20) REVERT: N 174 ASP cc_start: 0.7838 (t0) cc_final: 0.7307 (t0) REVERT: N 186 GLU cc_start: 0.6698 (tp30) cc_final: 0.6199 (tp30) REVERT: N 188 ILE cc_start: 0.8277 (mp) cc_final: 0.8051 (mt) REVERT: N 226 ILE cc_start: 0.8744 (mt) cc_final: 0.8433 (mm) REVERT: N 229 TYR cc_start: 0.7929 (m-80) cc_final: 0.7463 (m-80) REVERT: N 332 ASP cc_start: 0.7853 (t0) cc_final: 0.7652 (t0) REVERT: N 339 LEU cc_start: 0.8238 (tp) cc_final: 0.7961 (mp) REVERT: N 362 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7677 (mtmm) REVERT: N 364 GLU cc_start: 0.6860 (tp30) cc_final: 0.6373 (tp30) REVERT: N 373 MET cc_start: 0.6896 (tmm) cc_final: 0.6614 (tmm) REVERT: N 375 TYR cc_start: 0.7308 (t80) cc_final: 0.6965 (t80) REVERT: N 376 ARG cc_start: 0.8168 (ptp-170) cc_final: 0.7687 (ptp-110) REVERT: N 456 GLN cc_start: 0.8010 (tm-30) cc_final: 0.6615 (tm-30) REVERT: N 457 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7113 (mm-30) REVERT: N 498 VAL cc_start: 0.8539 (t) cc_final: 0.8118 (m) REVERT: N 535 TRP cc_start: 0.7480 (m100) cc_final: 0.6892 (m100) REVERT: N 542 ARG cc_start: 0.5857 (OUTLIER) cc_final: 0.4915 (mmm160) REVERT: N 555 TYR cc_start: 0.7810 (p90) cc_final: 0.7532 (p90) REVERT: N 559 ASP cc_start: 0.7829 (t0) cc_final: 0.7423 (t0) REVERT: N 570 TYR cc_start: 0.6536 (m-80) cc_final: 0.6263 (m-80) REVERT: N 572 ARG cc_start: 0.6753 (mtt180) cc_final: 0.5976 (mtt180) REVERT: N 576 GLU cc_start: 0.6870 (mp0) cc_final: 0.6545 (mp0) outliers start: 45 outliers final: 35 residues processed: 222 average time/residue: 0.2351 time to fit residues: 64.8331 Evaluate side-chains 237 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 60 ASP 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 101 LEU 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 120 THR Chi-restraints excluded: chain D residue 141 VAL 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 48 THR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain N residue 172 ASN Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 296 SER Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 323 ASP 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 447 ASP 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 564 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6189 Z= 0.299 Angle : 0.652 7.361 8393 Z= 0.345 Chirality : 0.048 0.228 910 Planarity : 0.005 0.054 1082 Dihedral : 6.559 45.679 872 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 7.13 % Allowed : 15.17 % Favored : 77.69 % 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: -0.80 (0.29), residues: 732 helix: -0.69 (0.46), residues: 117 sheet: 1.00 (0.38), residues: 178 loop : -1.19 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 535 HIS 0.010 0.001 HIS C 38 PHE 0.011 0.002 PHE N 549 TYR 0.029 0.002 TYR C 130 ARG 0.005 0.000 ARG E 94 *********************** 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 238 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ILE cc_start: 0.8408 (mm) cc_final: 0.7971 (mm) REVERT: D 125 MET cc_start: 0.7836 (ttm) cc_final: 0.7439 (tmm) REVERT: D 164 ASN cc_start: 0.8267 (p0) cc_final: 0.8035 (p0) REVERT: E 51 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7630 (mmmt) REVERT: N 151 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8308 (mtmt) REVERT: N 153 PHE cc_start: 0.7411 (m-80) cc_final: 0.7190 (m-80) REVERT: N 160 ILE cc_start: 0.8191 (tp) cc_final: 0.7794 (pt) REVERT: N 161 GLU cc_start: 0.7321 (pm20) cc_final: 0.7005 (pm20) REVERT: N 174 ASP cc_start: 0.7783 (t0) cc_final: 0.7243 (t0) REVERT: N 188 ILE cc_start: 0.8309 (mp) cc_final: 0.8067 (mt) REVERT: N 226 ILE cc_start: 0.8721 (mt) cc_final: 0.8437 (mm) REVERT: N 229 TYR cc_start: 0.7845 (m-80) cc_final: 0.7423 (m-80) REVERT: N 339 LEU cc_start: 0.8222 (tp) cc_final: 0.7972 (mp) REVERT: N 362 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7706 (mtmm) REVERT: N 364 GLU cc_start: 0.6834 (tp30) cc_final: 0.6339 (tp30) REVERT: N 373 MET cc_start: 0.6903 (tmm) cc_final: 0.6616 (tmm) REVERT: N 376 ARG cc_start: 0.8156 (ptp-170) cc_final: 0.7612 (ptp-110) REVERT: N 456 GLN cc_start: 0.8030 (tm-30) cc_final: 0.6660 (tm-30) REVERT: N 457 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7168 (mm-30) REVERT: N 535 TRP cc_start: 0.7580 (m100) cc_final: 0.6895 (m100) REVERT: N 539 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: N 542 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5394 (mmm160) REVERT: N 559 ASP cc_start: 0.7879 (t0) cc_final: 0.7456 (t0) REVERT: N 570 TYR cc_start: 0.6545 (m-80) cc_final: 0.6198 (m-80) REVERT: N 572 ARG cc_start: 0.6776 (mtt180) cc_final: 0.5944 (mtt180) REVERT: N 576 GLU cc_start: 0.6947 (mp0) cc_final: 0.6540 (mp0) outliers start: 47 outliers final: 33 residues processed: 210 average time/residue: 0.2386 time to fit residues: 61.8745 Evaluate side-chains 222 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 187 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 56 LEU Chi-restraints excluded: chain C residue 60 ASP 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 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 87 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain N residue 172 ASN Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 296 SER Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 323 ASP 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 447 ASP Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 539 GLN Chi-restraints excluded: chain N residue 542 ARG Chi-restraints excluded: chain N residue 557 THR Chi-restraints excluded: chain N residue 564 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 0.0060 chunk 29 optimal weight: 0.6980 chunk 60 optimal weight: 0.0030 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 ASN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6189 Z= 0.226 Angle : 0.615 6.777 8393 Z= 0.322 Chirality : 0.046 0.185 910 Planarity : 0.004 0.052 1082 Dihedral : 5.999 39.809 872 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.77 % Allowed : 18.51 % Favored : 75.72 % 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: -0.73 (0.30), residues: 732 helix: -0.42 (0.48), residues: 117 sheet: 0.98 (0.37), residues: 188 loop : -1.24 (0.28), residues: 427 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 0.009 0.001 PHE D 190 TYR 0.028 0.001 TYR C 130 ARG 0.004 0.000 ARG E 32 *********************** 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 228 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 85 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8543 (p) REVERT: D 111 ILE cc_start: 0.8415 (mm) cc_final: 0.8001 (mm) REVERT: D 125 MET cc_start: 0.7833 (ttm) cc_final: 0.7454 (tmm) REVERT: D 164 ASN cc_start: 0.8215 (p0) cc_final: 0.7947 (p0) REVERT: N 151 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8328 (mtmt) REVERT: N 153 PHE cc_start: 0.7381 (m-80) cc_final: 0.7143 (m-80) REVERT: N 160 ILE cc_start: 0.8135 (tp) cc_final: 0.7793 (pt) REVERT: N 161 GLU cc_start: 0.7206 (pm20) cc_final: 0.6927 (pm20) REVERT: N 174 ASP cc_start: 0.7819 (t0) cc_final: 0.7288 (t0) REVERT: N 188 ILE cc_start: 0.8279 (mp) cc_final: 0.8058 (mt) REVERT: N 226 ILE cc_start: 0.8626 (mt) cc_final: 0.8353 (mm) REVERT: N 229 TYR cc_start: 0.7768 (m-80) cc_final: 0.7389 (m-80) REVERT: N 339 LEU cc_start: 0.8217 (tp) cc_final: 0.7999 (mp) REVERT: N 362 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7684 (mtmm) REVERT: N 364 GLU cc_start: 0.6850 (tp30) cc_final: 0.6370 (tp30) REVERT: N 373 MET cc_start: 0.6865 (tmm) cc_final: 0.6589 (tmm) REVERT: N 376 ARG cc_start: 0.8124 (ptp-170) cc_final: 0.7578 (ptp-110) REVERT: N 456 GLN cc_start: 0.8041 (tm-30) cc_final: 0.6735 (tm-30) REVERT: N 457 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7156 (mm-30) REVERT: N 498 VAL cc_start: 0.8546 (t) cc_final: 0.8121 (m) REVERT: N 504 GLN cc_start: 0.8160 (tt0) cc_final: 0.7747 (tt0) REVERT: N 559 ASP cc_start: 0.7882 (t0) cc_final: 0.7404 (t0) REVERT: N 572 ARG cc_start: 0.6744 (mtt180) cc_final: 0.5944 (mtt180) REVERT: N 576 GLU cc_start: 0.6974 (mp0) cc_final: 0.6650 (mp0) outliers start: 38 outliers final: 24 residues processed: 206 average time/residue: 0.2280 time to fit residues: 58.3696 Evaluate side-chains 213 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 85 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 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 106 THR Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 296 SER 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 447 ASP Chi-restraints excluded: chain N residue 450 ILE Chi-restraints excluded: chain N residue 469 SER Chi-restraints excluded: chain N residue 557 THR Chi-restraints excluded: chain N residue 564 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.0000 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 68 optimal weight: 0.9980 overall best weight: 0.2782 ------------------------------------------------------------------------------- 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 312 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6189 Z= 0.190 Angle : 0.599 8.407 8393 Z= 0.309 Chirality : 0.045 0.160 910 Planarity : 0.004 0.049 1082 Dihedral : 5.247 20.370 867 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 6.07 % Allowed : 18.82 % 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: -0.62 (0.30), residues: 732 helix: -0.25 (0.49), residues: 117 sheet: 1.19 (0.38), residues: 181 loop : -1.23 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 372 HIS 0.010 0.001 HIS C 38 PHE 0.010 0.001 PHE D 190 TYR 0.030 0.001 TYR C 130 ARG 0.005 0.000 ARG N 542 *********************** 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 233 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 85 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8587 (p) REVERT: D 111 ILE cc_start: 0.8416 (mm) cc_final: 0.7992 (mm) REVERT: D 125 MET cc_start: 0.7824 (ttm) cc_final: 0.7448 (tmm) REVERT: D 164 ASN cc_start: 0.8161 (p0) cc_final: 0.7935 (p0) REVERT: D 170 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: N 151 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8301 (mtmt) REVERT: N 153 PHE cc_start: 0.7400 (m-80) cc_final: 0.7164 (m-80) REVERT: N 160 ILE cc_start: 0.8108 (tp) cc_final: 0.7718 (pt) REVERT: N 161 GLU cc_start: 0.7187 (pm20) cc_final: 0.6922 (pm20) REVERT: N 174 ASP cc_start: 0.7786 (t0) cc_final: 0.7216 (t0) REVERT: N 188 ILE cc_start: 0.8272 (mp) cc_final: 0.8057 (mt) REVERT: N 226 ILE cc_start: 0.8612 (mt) cc_final: 0.8335 (mm) REVERT: N 229 TYR cc_start: 0.7771 (m-80) cc_final: 0.7311 (m-80) REVERT: N 339 LEU cc_start: 0.8209 (tp) cc_final: 0.7991 (mp) REVERT: N 362 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7681 (mtmm) REVERT: N 364 GLU cc_start: 0.6892 (tp30) cc_final: 0.6276 (tp30) REVERT: N 373 MET cc_start: 0.6880 (tmm) cc_final: 0.6627 (tmm) REVERT: N 376 ARG cc_start: 0.8084 (ptp-170) cc_final: 0.7570 (ptp-110) REVERT: N 405 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7722 (ttt180) REVERT: N 440 MET cc_start: 0.7951 (tpp) cc_final: 0.7722 (tpp) REVERT: N 456 GLN cc_start: 0.8022 (tm-30) cc_final: 0.6793 (tm-30) REVERT: N 457 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7171 (mm-30) REVERT: N 498 VAL cc_start: 0.8553 (t) cc_final: 0.8130 (m) REVERT: N 504 GLN cc_start: 0.7987 (tt0) cc_final: 0.7638 (tt0) REVERT: N 572 ARG cc_start: 0.6764 (mtt180) cc_final: 0.5892 (mtt180) REVERT: N 576 GLU cc_start: 0.6974 (mp0) cc_final: 0.6621 (mp0) outliers start: 40 outliers final: 27 residues processed: 211 average time/residue: 0.2322 time to fit residues: 60.5865 Evaluate side-chains 222 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 60 ASP Chi-restraints excluded: chain C residue 85 THR 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 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 106 THR Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 296 SER Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 323 ASP 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 447 ASP 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 557 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 0.0970 chunk 70 optimal weight: 0.2980 chunk 44 optimal weight: 0.4980 chunk 42 optimal weight: 0.2980 chunk 32 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 overall best weight: 0.2778 ------------------------------------------------------------------------------- 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** N 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6189 Z= 0.191 Angle : 0.591 8.394 8393 Z= 0.305 Chirality : 0.045 0.147 910 Planarity : 0.004 0.048 1082 Dihedral : 5.111 20.858 867 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.07 % Allowed : 19.88 % 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: -0.56 (0.30), residues: 732 helix: -0.20 (0.49), residues: 117 sheet: 1.39 (0.38), residues: 176 loop : -1.23 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 372 HIS 0.010 0.001 HIS C 38 PHE 0.009 0.001 PHE D 190 TYR 0.034 0.001 TYR C 130 ARG 0.005 0.000 ARG E 32 *********************** 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 228 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 85 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8619 (p) REVERT: D 111 ILE cc_start: 0.8419 (mm) cc_final: 0.7996 (mm) REVERT: D 125 MET cc_start: 0.7810 (ttm) cc_final: 0.7458 (tmm) REVERT: D 170 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: N 151 LYS cc_start: 0.8504 (mtmt) cc_final: 0.8293 (mtmt) REVERT: N 153 PHE cc_start: 0.7403 (m-80) cc_final: 0.7148 (m-80) REVERT: N 160 ILE cc_start: 0.8111 (tp) cc_final: 0.7707 (pt) REVERT: N 161 GLU cc_start: 0.7180 (pm20) cc_final: 0.6925 (pm20) REVERT: N 174 ASP cc_start: 0.7759 (t0) cc_final: 0.7232 (t0) REVERT: N 188 ILE cc_start: 0.8281 (mp) cc_final: 0.8065 (mt) REVERT: N 226 ILE cc_start: 0.8577 (mt) cc_final: 0.8324 (mm) REVERT: N 229 TYR cc_start: 0.7737 (m-80) cc_final: 0.7192 (m-80) REVERT: N 339 LEU cc_start: 0.8218 (tp) cc_final: 0.7979 (mp) REVERT: N 362 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7658 (mtmm) REVERT: N 364 GLU cc_start: 0.6885 (tp30) cc_final: 0.6349 (tp30) REVERT: N 376 ARG cc_start: 0.8137 (ptp-170) cc_final: 0.7656 (ptp-110) REVERT: N 405 ARG cc_start: 0.8066 (ttt180) cc_final: 0.7782 (ttt180) REVERT: N 440 MET cc_start: 0.7906 (tpp) cc_final: 0.7632 (tpp) REVERT: N 456 GLN cc_start: 0.8016 (tm-30) cc_final: 0.6798 (tm-30) REVERT: N 457 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7152 (mm-30) REVERT: N 498 VAL cc_start: 0.8559 (t) cc_final: 0.8143 (m) REVERT: N 504 GLN cc_start: 0.8016 (tt0) cc_final: 0.7644 (tt0) REVERT: N 559 ASP cc_start: 0.8134 (t0) cc_final: 0.7677 (t0) REVERT: N 572 ARG cc_start: 0.6834 (mtt180) cc_final: 0.6584 (mtt180) REVERT: N 576 GLU cc_start: 0.6967 (mp0) cc_final: 0.6619 (mp0) outliers start: 40 outliers final: 32 residues processed: 208 average time/residue: 0.2313 time to fit residues: 59.3917 Evaluate side-chains 220 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 60 ASP Chi-restraints excluded: chain C residue 85 THR 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 46 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 296 SER Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 323 ASP 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 447 ASP 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 557 THR Chi-restraints excluded: chain N residue 564 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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** N 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6189 Z= 0.296 Angle : 0.663 12.264 8393 Z= 0.340 Chirality : 0.047 0.174 910 Planarity : 0.005 0.050 1082 Dihedral : 5.426 20.639 867 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 6.07 % Allowed : 19.88 % 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: -0.75 (0.30), residues: 732 helix: -0.32 (0.48), residues: 117 sheet: 1.29 (0.39), residues: 176 loop : -1.38 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 372 HIS 0.010 0.001 HIS C 38 PHE 0.011 0.002 PHE E 122 TYR 0.041 0.002 TYR C 130 ARG 0.008 0.001 ARG N 562 *********************** 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 238 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7170 (t) REVERT: C 78 THR cc_start: 0.7294 (OUTLIER) cc_final: 0.7027 (t) REVERT: C 85 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8601 (p) REVERT: D 111 ILE cc_start: 0.8464 (mm) cc_final: 0.8050 (mm) REVERT: D 125 MET cc_start: 0.7808 (ttm) cc_final: 0.7448 (tmm) REVERT: D 164 ASN cc_start: 0.7959 (p0) cc_final: 0.7750 (p0) REVERT: D 170 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: N 151 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8288 (mtmt) REVERT: N 153 PHE cc_start: 0.7454 (m-80) cc_final: 0.7231 (m-80) REVERT: N 174 ASP cc_start: 0.7766 (t0) cc_final: 0.7231 (t0) REVERT: N 188 ILE cc_start: 0.8286 (mp) cc_final: 0.8062 (mt) REVERT: N 226 ILE cc_start: 0.8629 (mt) cc_final: 0.8367 (mm) REVERT: N 229 TYR cc_start: 0.7809 (m-80) cc_final: 0.7381 (m-80) REVERT: N 339 LEU cc_start: 0.8242 (tp) cc_final: 0.7969 (mp) REVERT: N 362 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7569 (mtmm) REVERT: N 364 GLU cc_start: 0.6957 (tp30) cc_final: 0.6386 (tp30) REVERT: N 376 ARG cc_start: 0.8104 (ptp-170) cc_final: 0.7625 (ptp-110) REVERT: N 405 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7786 (ttt180) REVERT: N 440 MET cc_start: 0.7959 (tpp) cc_final: 0.7729 (tpp) REVERT: N 456 GLN cc_start: 0.7999 (tm-30) cc_final: 0.6642 (tm-30) REVERT: N 457 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7204 (mm-30) REVERT: N 498 VAL cc_start: 0.8620 (t) cc_final: 0.8194 (m) REVERT: N 504 GLN cc_start: 0.8136 (tt0) cc_final: 0.7702 (tt0) REVERT: N 535 TRP cc_start: 0.7591 (m100) cc_final: 0.6895 (m100) REVERT: N 536 GLU cc_start: 0.6563 (tp30) cc_final: 0.6218 (tp30) REVERT: N 559 ASP cc_start: 0.8056 (t0) cc_final: 0.7658 (t0) REVERT: N 572 ARG cc_start: 0.6762 (mtt180) cc_final: 0.6000 (mtt180) REVERT: N 576 GLU cc_start: 0.6934 (mp0) cc_final: 0.6594 (mp0) outliers start: 40 outliers final: 34 residues processed: 214 average time/residue: 0.2494 time to fit residues: 65.3657 Evaluate side-chains 234 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 60 ASP 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 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 171 MET 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 94 ARG Chi-restraints excluded: chain E residue 106 THR 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 296 SER Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 323 ASP 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 447 ASP 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 557 THR Chi-restraints excluded: chain N residue 564 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** N 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6189 Z= 0.288 Angle : 0.675 10.778 8393 Z= 0.343 Chirality : 0.047 0.180 910 Planarity : 0.005 0.052 1082 Dihedral : 5.476 21.672 867 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 6.53 % Allowed : 20.33 % Favored : 73.14 % 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: -0.87 (0.30), residues: 732 helix: -0.42 (0.48), residues: 117 sheet: 1.13 (0.38), residues: 178 loop : -1.43 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 372 HIS 0.010 0.001 HIS C 38 PHE 0.012 0.002 PHE N 425 TYR 0.040 0.002 TYR C 130 ARG 0.008 0.001 ARG N 562 *********************** 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 243 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7162 (t) REVERT: C 78 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.7022 (t) REVERT: C 85 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8612 (p) REVERT: D 111 ILE cc_start: 0.8459 (mm) cc_final: 0.8038 (mm) REVERT: D 125 MET cc_start: 0.7868 (ttm) cc_final: 0.7471 (tmm) REVERT: D 170 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: N 151 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8288 (mtmt) REVERT: N 153 PHE cc_start: 0.7442 (m-80) cc_final: 0.7215 (m-80) REVERT: N 174 ASP cc_start: 0.7750 (t0) cc_final: 0.7215 (t0) REVERT: N 188 ILE cc_start: 0.8285 (mp) cc_final: 0.8059 (mt) REVERT: N 226 ILE cc_start: 0.8620 (mt) cc_final: 0.8362 (mm) REVERT: N 229 TYR cc_start: 0.7833 (m-80) cc_final: 0.7381 (m-80) REVERT: N 339 LEU cc_start: 0.8251 (tp) cc_final: 0.7974 (mp) REVERT: N 362 LYS cc_start: 0.8053 (mtmt) cc_final: 0.7511 (mtmm) REVERT: N 364 GLU cc_start: 0.7013 (tp30) cc_final: 0.6431 (tp30) REVERT: N 373 MET cc_start: 0.6919 (tmm) cc_final: 0.6529 (tmm) REVERT: N 376 ARG cc_start: 0.8109 (ptp-170) cc_final: 0.7647 (ptp-110) REVERT: N 405 ARG cc_start: 0.8094 (ttt180) cc_final: 0.7874 (ttt180) REVERT: N 440 MET cc_start: 0.7943 (tpp) cc_final: 0.7740 (tpp) REVERT: N 456 GLN cc_start: 0.7964 (tm-30) cc_final: 0.6401 (tm-30) REVERT: N 457 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7211 (mm-30) REVERT: N 498 VAL cc_start: 0.8599 (t) cc_final: 0.8161 (m) REVERT: N 504 GLN cc_start: 0.8103 (tt0) cc_final: 0.7694 (tt0) REVERT: N 536 GLU cc_start: 0.6559 (tp30) cc_final: 0.6200 (tp30) REVERT: N 542 ARG cc_start: 0.5883 (mmm160) cc_final: 0.5661 (mmm160) REVERT: N 559 ASP cc_start: 0.8106 (t0) cc_final: 0.7694 (t0) REVERT: N 572 ARG cc_start: 0.6743 (mtt180) cc_final: 0.5992 (mtt180) REVERT: N 576 GLU cc_start: 0.6921 (mp0) cc_final: 0.6571 (mp0) outliers start: 43 outliers final: 34 residues processed: 218 average time/residue: 0.2393 time to fit residues: 63.8243 Evaluate side-chains 232 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 60 ASP 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 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 171 MET 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 106 THR 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 296 SER Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 323 ASP 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 447 ASP 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 557 THR Chi-restraints excluded: chain N residue 564 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6189 Z= 0.283 Angle : 0.676 10.357 8393 Z= 0.345 Chirality : 0.047 0.169 910 Planarity : 0.005 0.071 1082 Dihedral : 5.488 21.522 867 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 6.37 % Allowed : 20.64 % Favored : 72.99 % 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: -0.89 (0.29), residues: 732 helix: -0.39 (0.48), residues: 117 sheet: 1.12 (0.38), residues: 178 loop : -1.46 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 372 HIS 0.010 0.001 HIS C 38 PHE 0.010 0.002 PHE E 122 TYR 0.041 0.002 TYR C 130 ARG 0.013 0.001 ARG E 32 ********************** 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 244 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 202 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7158 (t) REVERT: C 78 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.7012 (t) REVERT: C 85 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8609 (p) REVERT: D 111 ILE cc_start: 0.8476 (mm) cc_final: 0.8055 (mm) REVERT: D 125 MET cc_start: 0.7848 (ttm) cc_final: 0.7472 (tmm) REVERT: D 170 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: N 151 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8284 (mtmt) REVERT: N 153 PHE cc_start: 0.7427 (m-80) cc_final: 0.7206 (m-80) REVERT: N 174 ASP cc_start: 0.7742 (t0) cc_final: 0.7198 (t0) REVERT: N 188 ILE cc_start: 0.8270 (mp) cc_final: 0.8042 (mt) REVERT: N 226 ILE cc_start: 0.8625 (mt) cc_final: 0.8361 (mm) REVERT: N 229 TYR cc_start: 0.7809 (m-80) cc_final: 0.7393 (m-80) REVERT: N 339 LEU cc_start: 0.8235 (tp) cc_final: 0.7981 (mp) REVERT: N 362 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7500 (mtmm) REVERT: N 364 GLU cc_start: 0.7018 (tp30) cc_final: 0.6439 (tp30) REVERT: N 373 MET cc_start: 0.6964 (tmm) cc_final: 0.6522 (tmm) REVERT: N 376 ARG cc_start: 0.8125 (ptp-170) cc_final: 0.7664 (ptp-110) REVERT: N 456 GLN cc_start: 0.7945 (tm-30) cc_final: 0.6215 (tm-30) REVERT: N 457 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7254 (mm-30) REVERT: N 498 VAL cc_start: 0.8592 (t) cc_final: 0.8150 (m) REVERT: N 504 GLN cc_start: 0.8078 (tt0) cc_final: 0.7676 (tt0) REVERT: N 536 GLU cc_start: 0.6567 (tp30) cc_final: 0.6198 (tp30) REVERT: N 559 ASP cc_start: 0.8054 (t0) cc_final: 0.7684 (t0) REVERT: N 572 ARG cc_start: 0.6681 (mtt180) cc_final: 0.5925 (mtt180) REVERT: N 576 GLU cc_start: 0.6919 (mp0) cc_final: 0.6568 (mp0) outliers start: 42 outliers final: 34 residues processed: 220 average time/residue: 0.2404 time to fit residues: 65.1804 Evaluate side-chains 239 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 201 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 60 ASP 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 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 171 MET 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 94 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 296 SER Chi-restraints excluded: chain N residue 312 HIS Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 323 ASP 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 447 ASP 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 557 THR Chi-restraints excluded: chain N residue 564 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 HIS E 116 HIS N 190 GLN ** N 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 554 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.129565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113157 restraints weight = 10255.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116637 restraints weight = 5355.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118989 restraints weight = 3285.552| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6189 Z= 0.300 Angle : 0.690 10.348 8393 Z= 0.352 Chirality : 0.047 0.166 910 Planarity : 0.005 0.071 1082 Dihedral : 5.538 22.558 867 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.92 % Allowed : 20.79 % Favored : 73.29 % 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: -0.91 (0.29), residues: 732 helix: -0.40 (0.47), residues: 117 sheet: 1.08 (0.38), residues: 178 loop : -1.47 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 372 HIS 0.010 0.001 HIS C 38 PHE 0.011 0.002 PHE E 122 TYR 0.041 0.002 TYR C 130 ARG 0.012 0.001 ARG E 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2087.24 seconds wall clock time: 38 minutes 21.75 seconds (2301.75 seconds total)