Starting phenix.real_space_refine on Fri Jul 25 23:21:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f54_31457/07_2025/7f54_31457.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f54_31457/07_2025/7f54_31457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f54_31457/07_2025/7f54_31457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f54_31457/07_2025/7f54_31457.map" model { file = "/net/cci-nas-00/data/ceres_data/7f54_31457/07_2025/7f54_31457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f54_31457/07_2025/7f54_31457.cif" } resolution = 3.0 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= 0.007 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 62 5.16 5 C 5155 2.51 5 N 1403 2.21 5 O 1513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8134 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1885 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2133 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain breaks: 2 Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 51 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 63 Classifications: {'peptide': 7} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "R" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 4.78, per 1000 atoms: 0.59 Number of scatterers: 8134 At special positions: 0 Unit cell: (86.19, 95.316, 122.694, 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 62 16.00 O 1513 8.00 N 1403 7.00 C 5155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.04 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DPN L 7 " - " HIS L 6 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 879.5 milliseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN L 7 " Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.1% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.837A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.527A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.457A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.557A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 47 through 71 removed outlier: 3.827A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 110 Processing helix chain 'R' and resid 117 through 153 Processing helix chain 'R' and resid 156 through 161 Processing helix chain 'R' and resid 162 through 187 Processing helix chain 'R' and resid 190 through 228 removed outlier: 3.919A pdb=" N ILE R 194 " --> pdb=" O SER R 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL R 228 " --> pdb=" O LYS R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 271 removed outlier: 3.734A pdb=" N PHE R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 274 through 282 removed outlier: 3.621A pdb=" N CYS R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 removed outlier: 3.920A pdb=" N ILE R 289 " --> pdb=" O ASN R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 302 removed outlier: 3.629A pdb=" N TYR R 302 " --> pdb=" O PRO R 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 299 through 302' Processing helix chain 'R' and resid 306 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.305A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.909A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.632A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.010A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.524A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.680A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.103A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.750A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.553A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.506A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1251 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: 2.27 Time building geometry restraints manager: 2.42 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: 2627 1.34 - 1.46: 1919 1.46 - 1.58: 3651 1.58 - 1.71: 0 1.71 - 1.83: 87 Bond restraints: 8284 Sorted by residual: bond pdb=" C PHE A 273 " pdb=" O PHE A 273 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.12e+00 bond pdb=" C ARG R 147 " pdb=" O ARG R 147 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.17e-02 7.31e+03 3.10e+00 bond pdb=" C ALA R 144 " pdb=" O ALA R 144 " ideal model delta sigma weight residual 1.237 1.217 0.019 1.17e-02 7.31e+03 2.70e+00 bond pdb=" C LYS A 34 " pdb=" O LYS A 34 " ideal model delta sigma weight residual 1.237 1.218 0.018 1.17e-02 7.31e+03 2.44e+00 bond pdb=" C ALA R 70 " pdb=" N LYS R 71 " ideal model delta sigma weight residual 1.331 1.353 -0.023 1.48e-02 4.57e+03 2.36e+00 ... (remaining 8279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 10648 1.87 - 3.75: 479 3.75 - 5.62: 70 5.62 - 7.50: 10 7.50 - 9.37: 3 Bond angle restraints: 11210 Sorted by residual: angle pdb=" N LYS B 78 " pdb=" CA LYS B 78 " pdb=" C LYS B 78 " ideal model delta sigma weight residual 108.69 117.01 -8.32 1.77e+00 3.19e-01 2.21e+01 angle pdb=" N LEU R 286 " pdb=" CA LEU R 286 " pdb=" C LEU R 286 " ideal model delta sigma weight residual 113.41 107.78 5.63 1.22e+00 6.72e-01 2.13e+01 angle pdb=" C ILE R 143 " pdb=" CA ILE R 143 " pdb=" CB ILE R 143 " ideal model delta sigma weight residual 111.97 106.80 5.17 1.28e+00 6.10e-01 1.63e+01 angle pdb=" N CYS N 96 " pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 109.76 103.42 6.34 1.64e+00 3.72e-01 1.49e+01 angle pdb=" N LYS R 71 " pdb=" CA LYS R 71 " pdb=" C LYS R 71 " ideal model delta sigma weight residual 113.16 117.67 -4.51 1.24e+00 6.50e-01 1.33e+01 ... (remaining 11205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4657 17.58 - 35.16: 227 35.16 - 52.74: 49 52.74 - 70.32: 19 70.32 - 87.91: 5 Dihedral angle restraints: 4957 sinusoidal: 1950 harmonic: 3007 Sorted by residual: dihedral pdb=" CB CYS R 40 " pdb=" SG CYS R 40 " pdb=" SG CYS R 279 " pdb=" CB CYS R 279 " ideal model delta sinusoidal sigma weight residual -86.00 -35.53 -50.47 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CA TRP R 258 " pdb=" C TRP R 258 " pdb=" N ALA R 259 " pdb=" CA ALA R 259 " ideal model delta harmonic sigma weight residual -180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CB MET R 204 " pdb=" CG MET R 204 " pdb=" SD MET R 204 " pdb=" CE MET R 204 " ideal model delta sinusoidal sigma weight residual -180.00 -126.97 -53.03 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 4954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 967 0.055 - 0.111: 257 0.111 - 0.166: 46 0.166 - 0.222: 8 0.222 - 0.277: 2 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CA TYR R 157 " pdb=" N TYR R 157 " pdb=" C TYR R 157 " pdb=" CB TYR R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA HIS R 158 " pdb=" N HIS R 158 " pdb=" C HIS R 158 " pdb=" CB HIS R 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA GLU A 392 " pdb=" N GLU A 392 " pdb=" C GLU A 392 " pdb=" CB GLU A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 1277 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 382 " 0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ILE A 382 " -0.071 2.00e-02 2.50e+03 pdb=" O ILE A 382 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE A 383 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 13 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG A 13 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG A 13 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A 14 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 377 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C ASN A 377 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN A 377 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP A 378 " -0.021 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 678 2.74 - 3.28: 8125 3.28 - 3.82: 13191 3.82 - 4.36: 16492 4.36 - 4.90: 28408 Nonbonded interactions: 66894 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OD1 ASP B 163 " model vdw 2.194 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.216 3.040 nonbonded pdb=" OG SER R 58 " pdb=" OG SER R 94 " model vdw 2.244 3.040 nonbonded pdb=" OG SER R 116 " pdb=" N PHE R 117 " model vdw 2.259 3.120 nonbonded pdb=" OD2 ASP R 122 " pdb=" CG NLE L 4 " model vdw 2.302 3.440 ... (remaining 66889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.710 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:15.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 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 0.039 8289 Z= 0.233 Angle : 0.895 9.374 11221 Z= 0.555 Chirality : 0.053 0.277 1280 Planarity : 0.006 0.041 1423 Dihedral : 11.933 87.906 2994 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.89 % Favored : 97.91 % Rotamer: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.26), residues: 1006 helix: 0.98 (0.24), residues: 413 sheet: 0.79 (0.35), residues: 223 loop : 0.75 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 99 HIS 0.008 0.002 HIS B 183 PHE 0.025 0.003 PHE B 199 TYR 0.016 0.002 TYR A 339 ARG 0.023 0.002 ARG N 98 Details of bonding type rmsd link_TRANS : bond 0.00506 ( 1) link_TRANS : angle 0.63596 ( 3) hydrogen bonds : bond 0.14710 ( 441) hydrogen bonds : angle 6.27302 ( 1251) SS BOND : bond 0.00655 ( 4) SS BOND : angle 3.16046 ( 8) covalent geometry : bond 0.00443 ( 8284) covalent geometry : angle 0.89157 (11210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7460 (tt0) cc_final: 0.7157 (tp-100) REVERT: A 293 LYS cc_start: 0.8370 (mttt) cc_final: 0.7755 (tmtt) REVERT: B 20 ASP cc_start: 0.6349 (m-30) cc_final: 0.5819 (p0) REVERT: B 265 SER cc_start: 0.7898 (p) cc_final: 0.7538 (m) REVERT: R 145 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7668 (t) REVERT: R 204 MET cc_start: 0.6074 (mtt) cc_final: 0.5602 (mmt) outliers start: 2 outliers final: 1 residues processed: 239 average time/residue: 1.0630 time to fit residues: 270.9963 Evaluate side-chains 151 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 226 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 176 GLN B 259 GLN G 24 ASN R 72 ASN R 264 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.197874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.155738 restraints weight = 8685.645| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 2.57 r_work: 0.3989 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8289 Z= 0.150 Angle : 0.603 7.653 11221 Z= 0.328 Chirality : 0.043 0.149 1280 Planarity : 0.004 0.035 1423 Dihedral : 4.287 16.445 1125 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.48 % Allowed : 13.71 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.93 (0.26), residues: 1006 helix: 2.17 (0.24), residues: 412 sheet: 1.13 (0.33), residues: 220 loop : 0.46 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.009 0.002 HIS R 264 PHE 0.017 0.002 PHE N 68 TYR 0.014 0.002 TYR R 80 ARG 0.007 0.001 ARG B 197 Details of bonding type rmsd link_TRANS : bond 0.00071 ( 1) link_TRANS : angle 0.27163 ( 3) hydrogen bonds : bond 0.05240 ( 441) hydrogen bonds : angle 4.59156 ( 1251) SS BOND : bond 0.00339 ( 4) SS BOND : angle 0.63607 ( 8) covalent geometry : bond 0.00319 ( 8284) covalent geometry : angle 0.60332 (11210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6833 (tp-100) REVERT: A 293 LYS cc_start: 0.8484 (mttt) cc_final: 0.7218 (tmtt) REVERT: A 346 LEU cc_start: 0.7477 (mt) cc_final: 0.7202 (mt) REVERT: A 364 THR cc_start: 0.6817 (p) cc_final: 0.6476 (t) REVERT: A 374 ARG cc_start: 0.8210 (mtt180) cc_final: 0.8000 (mtm-85) REVERT: B 20 ASP cc_start: 0.6693 (m-30) cc_final: 0.6005 (p0) REVERT: B 186 ASP cc_start: 0.5816 (OUTLIER) cc_final: 0.5530 (m-30) REVERT: B 217 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7114 (ptm) REVERT: B 234 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.7336 (OUTLIER) REVERT: B 251 ARG cc_start: 0.7258 (mtm-85) cc_final: 0.6943 (mtm-85) REVERT: B 265 SER cc_start: 0.7820 (p) cc_final: 0.7617 (m) REVERT: B 280 LYS cc_start: 0.8278 (tttt) cc_final: 0.7999 (tttt) REVERT: G 16 VAL cc_start: 0.7049 (m) cc_final: 0.6838 (t) REVERT: G 44 HIS cc_start: 0.5920 (m170) cc_final: 0.5160 (t-170) REVERT: N 77 ASN cc_start: 0.7816 (m-40) cc_final: 0.7533 (t0) outliers start: 31 outliers final: 10 residues processed: 181 average time/residue: 1.1621 time to fit residues: 225.5300 Evaluate side-chains 143 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN G 24 ASN R 72 ASN R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.194926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.152921 restraints weight = 8871.183| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.60 r_work: 0.3953 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8289 Z= 0.128 Angle : 0.551 7.546 11221 Z= 0.297 Chirality : 0.042 0.139 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.161 18.392 1122 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.93 % Allowed : 16.40 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.95 (0.26), residues: 1006 helix: 2.37 (0.25), residues: 411 sheet: 1.13 (0.32), residues: 222 loop : 0.24 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.008 0.001 HIS R 264 PHE 0.028 0.002 PHE B 241 TYR 0.014 0.001 TYR R 268 ARG 0.005 0.000 ARG A 380 Details of bonding type rmsd link_TRANS : bond 0.00032 ( 1) link_TRANS : angle 0.35618 ( 3) hydrogen bonds : bond 0.04633 ( 441) hydrogen bonds : angle 4.26703 ( 1251) SS BOND : bond 0.00289 ( 4) SS BOND : angle 0.55340 ( 8) covalent geometry : bond 0.00270 ( 8284) covalent geometry : angle 0.55136 (11210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6709 (tppt) REVERT: A 35 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6737 (tm-30) REVERT: A 293 LYS cc_start: 0.8465 (mttt) cc_final: 0.7070 (tmtt) REVERT: A 342 ARG cc_start: 0.6886 (ttp-170) cc_final: 0.6117 (ttm-80) REVERT: A 346 LEU cc_start: 0.7490 (mt) cc_final: 0.7219 (mt) REVERT: A 364 THR cc_start: 0.6917 (p) cc_final: 0.6669 (t) REVERT: A 374 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7994 (mtm-85) REVERT: B 20 ASP cc_start: 0.6773 (m-30) cc_final: 0.6237 (p0) REVERT: B 175 GLN cc_start: 0.6743 (tp40) cc_final: 0.6421 (mm-40) REVERT: B 186 ASP cc_start: 0.5740 (OUTLIER) cc_final: 0.5489 (m-30) REVERT: B 217 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7170 (ptm) REVERT: G 44 HIS cc_start: 0.6009 (m170) cc_final: 0.5471 (t-170) outliers start: 35 outliers final: 13 residues processed: 170 average time/residue: 1.0083 time to fit residues: 184.3041 Evaluate side-chains 146 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 65 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 292 ASN A 390 GLN R 76 HIS R 264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.192616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.150615 restraints weight = 8823.250| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.56 r_work: 0.3896 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8289 Z= 0.152 Angle : 0.574 7.832 11221 Z= 0.308 Chirality : 0.043 0.149 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.314 21.841 1122 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.16 % Allowed : 17.30 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.85 (0.26), residues: 1006 helix: 2.35 (0.25), residues: 406 sheet: 1.16 (0.34), residues: 204 loop : 0.13 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.006 0.002 HIS R 264 PHE 0.016 0.002 PHE B 199 TYR 0.014 0.002 TYR N 95 ARG 0.006 0.000 ARG N 98 Details of bonding type rmsd link_TRANS : bond 0.00014 ( 1) link_TRANS : angle 0.43296 ( 3) hydrogen bonds : bond 0.04797 ( 441) hydrogen bonds : angle 4.31574 ( 1251) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.61618 ( 8) covalent geometry : bond 0.00339 ( 8284) covalent geometry : angle 0.57434 (11210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6923 (tppt) REVERT: A 267 GLN cc_start: 0.7894 (tp40) cc_final: 0.7434 (tm-30) REVERT: A 293 LYS cc_start: 0.8337 (mttt) cc_final: 0.7011 (tmtt) REVERT: A 342 ARG cc_start: 0.6928 (ttp-170) cc_final: 0.6133 (ttm-80) REVERT: A 346 LEU cc_start: 0.7565 (mt) cc_final: 0.7286 (mt) REVERT: A 358 TYR cc_start: 0.7766 (m-80) cc_final: 0.7540 (m-10) REVERT: A 364 THR cc_start: 0.6969 (p) cc_final: 0.6695 (t) REVERT: B 59 TYR cc_start: 0.6279 (m-80) cc_final: 0.6037 (m-80) REVERT: B 175 GLN cc_start: 0.7019 (tp40) cc_final: 0.6663 (mm-40) REVERT: B 186 ASP cc_start: 0.5783 (OUTLIER) cc_final: 0.5556 (m-30) REVERT: B 217 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7252 (ptm) REVERT: B 275 SER cc_start: 0.7043 (m) cc_final: 0.6680 (p) REVERT: B 336 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8048 (mt) REVERT: G 44 HIS cc_start: 0.6340 (m170) cc_final: 0.5768 (t-170) REVERT: N 38 ARG cc_start: 0.7047 (ttm170) cc_final: 0.6739 (ttp80) REVERT: R 297 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6676 (tp) outliers start: 37 outliers final: 20 residues processed: 169 average time/residue: 1.0985 time to fit residues: 198.7322 Evaluate side-chains 152 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 253 VAL Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 292 ASN R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.193998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.152619 restraints weight = 8652.536| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.55 r_work: 0.3928 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8289 Z= 0.124 Angle : 0.547 8.898 11221 Z= 0.290 Chirality : 0.042 0.149 1280 Planarity : 0.004 0.035 1423 Dihedral : 4.159 16.836 1122 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.71 % Allowed : 19.78 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.26), residues: 1006 helix: 2.42 (0.25), residues: 406 sheet: 1.18 (0.36), residues: 192 loop : 0.11 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.009 0.001 HIS R 264 PHE 0.013 0.001 PHE B 199 TYR 0.014 0.001 TYR N 95 ARG 0.004 0.000 ARG A 380 Details of bonding type rmsd link_TRANS : bond 0.00016 ( 1) link_TRANS : angle 0.42109 ( 3) hydrogen bonds : bond 0.04359 ( 441) hydrogen bonds : angle 4.16803 ( 1251) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.52842 ( 8) covalent geometry : bond 0.00268 ( 8284) covalent geometry : angle 0.54707 (11210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6521 (tppp) REVERT: A 267 GLN cc_start: 0.7851 (tp40) cc_final: 0.7355 (tm-30) REVERT: A 293 LYS cc_start: 0.8323 (mttt) cc_final: 0.6958 (tmtt) REVERT: A 342 ARG cc_start: 0.6758 (ttp-170) cc_final: 0.6021 (ttm-80) REVERT: A 346 LEU cc_start: 0.7647 (mt) cc_final: 0.7355 (mt) REVERT: B 175 GLN cc_start: 0.7142 (tp40) cc_final: 0.6823 (mm-40) REVERT: B 186 ASP cc_start: 0.5443 (OUTLIER) cc_final: 0.5222 (m-30) REVERT: B 217 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7202 (ptm) REVERT: B 226 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7243 (mt-10) REVERT: B 239 ASN cc_start: 0.7175 (m110) cc_final: 0.6231 (t0) REVERT: B 275 SER cc_start: 0.7095 (m) cc_final: 0.6733 (p) REVERT: G 44 HIS cc_start: 0.6393 (m170) cc_final: 0.5761 (t-170) REVERT: R 273 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6823 (mp10) REVERT: R 281 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7901 (mpt) REVERT: R 292 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6434 (mtt) outliers start: 33 outliers final: 16 residues processed: 161 average time/residue: 0.9348 time to fit residues: 162.2630 Evaluate side-chains 150 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 227 GLN A 236 GLN R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.190006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.147403 restraints weight = 8783.641| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.70 r_work: 0.3847 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8289 Z= 0.173 Angle : 0.615 12.275 11221 Z= 0.325 Chirality : 0.044 0.159 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.354 16.616 1122 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.16 % Allowed : 19.66 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.60 (0.26), residues: 1006 helix: 2.23 (0.25), residues: 409 sheet: 0.94 (0.36), residues: 194 loop : -0.05 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP R 258 HIS 0.012 0.002 HIS R 264 PHE 0.018 0.002 PHE B 335 TYR 0.016 0.002 TYR N 95 ARG 0.005 0.000 ARG N 38 Details of bonding type rmsd link_TRANS : bond 0.00028 ( 1) link_TRANS : angle 0.56205 ( 3) hydrogen bonds : bond 0.04879 ( 441) hydrogen bonds : angle 4.38839 ( 1251) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.69712 ( 8) covalent geometry : bond 0.00399 ( 8284) covalent geometry : angle 0.61515 (11210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6546 (tppp) REVERT: A 289 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7669 (tt) REVERT: A 293 LYS cc_start: 0.8283 (mttt) cc_final: 0.6905 (tmtt) REVERT: A 342 ARG cc_start: 0.6916 (ttp-170) cc_final: 0.6201 (ttm-80) REVERT: A 346 LEU cc_start: 0.7708 (mt) cc_final: 0.7393 (mt) REVERT: B 16 ASN cc_start: 0.7721 (m-40) cc_final: 0.6758 (t160) REVERT: B 44 GLN cc_start: 0.8156 (tp40) cc_final: 0.7839 (tm-30) REVERT: B 45 MET cc_start: 0.7890 (mpt) cc_final: 0.7611 (mtm) REVERT: B 175 GLN cc_start: 0.7295 (tp40) cc_final: 0.6886 (mm-40) REVERT: B 217 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7305 (ptm) REVERT: B 239 ASN cc_start: 0.7287 (m110) cc_final: 0.6426 (t0) REVERT: B 275 SER cc_start: 0.7029 (m) cc_final: 0.6754 (p) REVERT: G 44 HIS cc_start: 0.6561 (m170) cc_final: 0.5790 (t-170) REVERT: R 281 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7733 (mpt) REVERT: R 292 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6333 (mtt) REVERT: R 297 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.6825 (tp) outliers start: 37 outliers final: 18 residues processed: 162 average time/residue: 0.9053 time to fit residues: 158.0464 Evaluate side-chains 158 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain R residue 292 MET Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 90 optimal weight: 0.0980 chunk 97 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 357 HIS R 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.193013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.151587 restraints weight = 8737.821| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.55 r_work: 0.3908 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8289 Z= 0.125 Angle : 0.586 11.782 11221 Z= 0.307 Chirality : 0.042 0.139 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.171 20.315 1122 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.71 % Allowed : 20.67 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.26), residues: 1006 helix: 2.40 (0.25), residues: 406 sheet: 1.08 (0.37), residues: 190 loop : -0.04 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.011 0.001 HIS R 264 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.007 0.000 ARG N 38 Details of bonding type rmsd link_TRANS : bond 0.00045 ( 1) link_TRANS : angle 0.45256 ( 3) hydrogen bonds : bond 0.04286 ( 441) hydrogen bonds : angle 4.24015 ( 1251) SS BOND : bond 0.00231 ( 4) SS BOND : angle 0.49282 ( 8) covalent geometry : bond 0.00275 ( 8284) covalent geometry : angle 0.58625 (11210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6500 (tppp) REVERT: A 267 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7222 (tm-30) REVERT: A 293 LYS cc_start: 0.8251 (mttt) cc_final: 0.6893 (tmtt) REVERT: A 299 GLU cc_start: 0.8170 (pp20) cc_final: 0.7899 (pm20) REVERT: A 342 ARG cc_start: 0.6828 (ttp-170) cc_final: 0.6168 (ttm-80) REVERT: B 16 ASN cc_start: 0.7640 (m-40) cc_final: 0.6713 (t160) REVERT: B 45 MET cc_start: 0.7958 (mpt) cc_final: 0.7619 (mtm) REVERT: B 175 GLN cc_start: 0.7259 (tp40) cc_final: 0.6900 (mm-40) REVERT: B 186 ASP cc_start: 0.5376 (OUTLIER) cc_final: 0.5156 (m-30) REVERT: B 217 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7292 (ptm) REVERT: B 239 ASN cc_start: 0.7055 (m110) cc_final: 0.6245 (t0) REVERT: B 325 MET cc_start: 0.8390 (tpp) cc_final: 0.8179 (tpp) REVERT: G 44 HIS cc_start: 0.6453 (m170) cc_final: 0.5795 (t-170) REVERT: R 297 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6515 (tp) outliers start: 33 outliers final: 15 residues processed: 156 average time/residue: 0.9941 time to fit residues: 167.3238 Evaluate side-chains 146 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 236 GLN R 264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.192048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.150731 restraints weight = 8817.255| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.55 r_work: 0.3908 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8289 Z= 0.135 Angle : 0.614 13.535 11221 Z= 0.317 Chirality : 0.042 0.166 1280 Planarity : 0.004 0.033 1423 Dihedral : 4.152 19.928 1122 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.15 % Allowed : 21.91 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.26), residues: 1006 helix: 2.40 (0.25), residues: 406 sheet: 1.00 (0.37), residues: 192 loop : -0.03 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 339 HIS 0.012 0.001 HIS R 264 PHE 0.020 0.002 PHE B 241 TYR 0.016 0.001 TYR B 111 ARG 0.006 0.000 ARG N 38 Details of bonding type rmsd link_TRANS : bond 0.00019 ( 1) link_TRANS : angle 0.49490 ( 3) hydrogen bonds : bond 0.04341 ( 441) hydrogen bonds : angle 4.31387 ( 1251) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.52880 ( 8) covalent geometry : bond 0.00307 ( 8284) covalent geometry : angle 0.61382 (11210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6496 (tppp) REVERT: A 267 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7334 (tm-30) REVERT: A 293 LYS cc_start: 0.8220 (mttt) cc_final: 0.6883 (tmtt) REVERT: A 299 GLU cc_start: 0.8189 (pp20) cc_final: 0.7902 (pm20) REVERT: B 16 ASN cc_start: 0.7667 (m-40) cc_final: 0.6762 (t160) REVERT: B 45 MET cc_start: 0.7999 (mpt) cc_final: 0.7729 (mtm) REVERT: B 59 TYR cc_start: 0.5704 (m-80) cc_final: 0.5418 (m-80) REVERT: B 175 GLN cc_start: 0.7367 (tp40) cc_final: 0.7038 (mm-40) REVERT: B 186 ASP cc_start: 0.5364 (OUTLIER) cc_final: 0.5163 (m-30) REVERT: B 239 ASN cc_start: 0.7055 (m110) cc_final: 0.6257 (t0) REVERT: B 251 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7801 (mtt90) REVERT: G 44 HIS cc_start: 0.6374 (m170) cc_final: 0.5778 (t-170) REVERT: R 273 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6765 (mp10) REVERT: R 297 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6774 (tp) outliers start: 28 outliers final: 15 residues processed: 157 average time/residue: 1.3437 time to fit residues: 228.4199 Evaluate side-chains 153 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 236 GLN A 292 ASN B 176 GLN R 264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.195375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.153951 restraints weight = 8907.119| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.59 r_work: 0.3943 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8289 Z= 0.124 Angle : 0.616 12.758 11221 Z= 0.319 Chirality : 0.042 0.157 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.093 20.899 1122 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.92 % Allowed : 22.58 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.26), residues: 1006 helix: 2.46 (0.25), residues: 402 sheet: 1.03 (0.37), residues: 192 loop : 0.01 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 339 HIS 0.012 0.001 HIS R 264 PHE 0.022 0.001 PHE B 241 TYR 0.012 0.001 TYR R 268 ARG 0.007 0.000 ARG A 20 Details of bonding type rmsd link_TRANS : bond 0.00010 ( 1) link_TRANS : angle 0.43980 ( 3) hydrogen bonds : bond 0.04143 ( 441) hydrogen bonds : angle 4.24577 ( 1251) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.46465 ( 8) covalent geometry : bond 0.00274 ( 8284) covalent geometry : angle 0.61580 (11210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6811 (tppt) REVERT: A 221 MET cc_start: 0.8085 (ttp) cc_final: 0.7829 (tpp) REVERT: A 267 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7281 (tm-30) REVERT: A 293 LYS cc_start: 0.8229 (mttt) cc_final: 0.6893 (tmtt) REVERT: A 299 GLU cc_start: 0.8197 (pp20) cc_final: 0.7960 (pm20) REVERT: B 16 ASN cc_start: 0.7800 (m-40) cc_final: 0.6743 (t0) REVERT: B 175 GLN cc_start: 0.7406 (tp40) cc_final: 0.7131 (mm-40) REVERT: B 217 MET cc_start: 0.7647 (ptm) cc_final: 0.7372 (ppp) REVERT: B 239 ASN cc_start: 0.6939 (m110) cc_final: 0.6237 (t0) REVERT: B 251 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7745 (mtt90) REVERT: G 44 HIS cc_start: 0.6306 (m170) cc_final: 0.5811 (t-170) REVERT: R 204 MET cc_start: 0.5672 (mtp) cc_final: 0.5160 (pp-130) REVERT: R 273 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6755 (mp10) outliers start: 26 outliers final: 16 residues processed: 155 average time/residue: 0.9962 time to fit residues: 165.7600 Evaluate side-chains 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 236 GLN A 292 ASN R 264 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.194889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.153352 restraints weight = 8772.488| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.58 r_work: 0.3955 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8289 Z= 0.126 Angle : 0.628 11.077 11221 Z= 0.325 Chirality : 0.043 0.172 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.128 20.903 1122 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.02 % Allowed : 23.82 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.75 (0.26), residues: 1006 helix: 2.45 (0.25), residues: 405 sheet: 1.03 (0.37), residues: 186 loop : -0.05 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 339 HIS 0.012 0.001 HIS R 264 PHE 0.021 0.001 PHE B 241 TYR 0.023 0.001 TYR B 59 ARG 0.009 0.000 ARG A 232 Details of bonding type rmsd link_TRANS : bond 0.00022 ( 1) link_TRANS : angle 0.46664 ( 3) hydrogen bonds : bond 0.04111 ( 441) hydrogen bonds : angle 4.26534 ( 1251) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.44063 ( 8) covalent geometry : bond 0.00282 ( 8284) covalent geometry : angle 0.62798 (11210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6840 (tppt) REVERT: A 221 MET cc_start: 0.8098 (ttp) cc_final: 0.7779 (tpp) REVERT: A 267 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7321 (tm-30) REVERT: A 293 LYS cc_start: 0.8260 (mttt) cc_final: 0.6925 (tmtt) REVERT: A 342 ARG cc_start: 0.6670 (ttp-170) cc_final: 0.6131 (ttm-80) REVERT: B 16 ASN cc_start: 0.7949 (m-40) cc_final: 0.6950 (t0) REVERT: B 175 GLN cc_start: 0.7383 (tp40) cc_final: 0.7130 (mm-40) REVERT: B 217 MET cc_start: 0.7621 (ptm) cc_final: 0.7350 (ppp) REVERT: B 239 ASN cc_start: 0.6824 (m110) cc_final: 0.6180 (t0) REVERT: B 251 ARG cc_start: 0.7976 (mtt180) cc_final: 0.7519 (mtm-85) REVERT: B 274 THR cc_start: 0.6904 (OUTLIER) cc_final: 0.6284 (p) REVERT: G 44 HIS cc_start: 0.6232 (m170) cc_final: 0.5985 (t-170) REVERT: R 204 MET cc_start: 0.5561 (mtp) cc_final: 0.5235 (pp-130) REVERT: R 273 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6803 (mp10) outliers start: 18 outliers final: 15 residues processed: 151 average time/residue: 0.8991 time to fit residues: 146.4948 Evaluate side-chains 147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 146 ASP Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 273 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 236 GLN A 292 ASN B 75 GLN R 264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.190567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.149314 restraints weight = 8877.180| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.60 r_work: 0.3891 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8289 Z= 0.156 Angle : 0.668 11.304 11221 Z= 0.346 Chirality : 0.044 0.174 1280 Planarity : 0.004 0.034 1423 Dihedral : 4.257 19.197 1122 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.58 % Allowed : 23.37 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.26), residues: 1006 helix: 2.41 (0.25), residues: 400 sheet: 0.91 (0.37), residues: 194 loop : -0.14 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 339 HIS 0.013 0.001 HIS R 264 PHE 0.024 0.002 PHE B 241 TYR 0.015 0.002 TYR A 339 ARG 0.008 0.000 ARG A 232 Details of bonding type rmsd link_TRANS : bond 0.00040 ( 1) link_TRANS : angle 0.50987 ( 3) hydrogen bonds : bond 0.04602 ( 441) hydrogen bonds : angle 4.42343 ( 1251) SS BOND : bond 0.00268 ( 4) SS BOND : angle 0.55300 ( 8) covalent geometry : bond 0.00357 ( 8284) covalent geometry : angle 0.66816 (11210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6917.81 seconds wall clock time: 121 minutes 45.66 seconds (7305.66 seconds total)