Starting phenix.real_space_refine on Tue Apr 29 22:30:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b3j_7039/04_2025/6b3j_7039.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b3j_7039/04_2025/6b3j_7039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6b3j_7039/04_2025/6b3j_7039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b3j_7039/04_2025/6b3j_7039.map" model { file = "/net/cci-nas-00/data/ceres_data/6b3j_7039/04_2025/6b3j_7039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b3j_7039/04_2025/6b3j_7039.cif" } resolution = 3.3 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= 0.001 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5758 2.51 5 N 1560 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9034 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3134 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 364} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 254 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1654 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 4 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2595 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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} Time building chain proxies: 5.02, per 1000 atoms: 0.56 Number of scatterers: 9034 At special positions: 0 Unit cell: (82.68, 177.02, 98.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1662 8.00 N 1560 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.02 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 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=2.02 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 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 44.3% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 91 through 95 removed outlier: 3.577A pdb=" N SER R 94 " --> pdb=" O TRP R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 170 removed outlier: 4.006A pdb=" N ARG R 170 " --> pdb=" O LEU R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.535A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 211 Processing helix chain 'R' and resid 213 through 223 Processing helix chain 'R' and resid 225 through 257 removed outlier: 3.722A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 292 Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 296 through 300 removed outlier: 3.785A pdb=" N ARG R 299 " --> pdb=" O CYS R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.640A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 361 through 370 Processing helix chain 'R' and resid 372 through 376 removed outlier: 3.612A pdb=" N ARG R 376 " --> pdb=" O GLU R 373 " (cutoff:3.500A) Processing helix chain 'R' and resid 379 through 405 removed outlier: 4.307A pdb=" N LYS R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 Processing helix chain 'P' and resid 2 through 31 Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.126A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 4.112A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.832A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.987A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.734A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.632A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.759A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.532A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.584A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 83 through 84 removed outlier: 4.107A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL R 100 " --> pdb=" O VAL R 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.602A pdb=" N VAL A 217 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.715A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.608A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.354A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.724A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.892A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.583A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.792A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.111A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1380 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: 2.40 Time building geometry restraints manager: 2.44 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: 2888 1.34 - 1.46: 2116 1.46 - 1.58: 4163 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 9240 Sorted by residual: bond pdb=" CB TRP B 169 " pdb=" CG TRP B 169 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.30e+00 bond pdb=" C VAL R 276 " pdb=" N PRO R 277 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.36e-02 5.41e+03 3.30e+00 bond pdb=" N LYS R 113 " pdb=" CA LYS R 113 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.16e+00 bond pdb=" N ILE R 357 " pdb=" CA ILE R 357 " ideal model delta sigma weight residual 1.464 1.484 -0.020 1.23e-02 6.61e+03 2.53e+00 bond pdb=" CB MET P 15 " pdb=" CG MET P 15 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.35e+00 ... (remaining 9235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 12250 2.80 - 5.59: 242 5.59 - 8.39: 19 8.39 - 11.18: 12 11.18 - 13.98: 1 Bond angle restraints: 12524 Sorted by residual: angle pdb=" C LYS N 76 " pdb=" N ASN N 77 " pdb=" CA ASN N 77 " ideal model delta sigma weight residual 121.54 132.25 -10.71 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C GLU A 330 " pdb=" N ASP A 331 " pdb=" CA ASP A 331 " ideal model delta sigma weight residual 121.59 135.57 -13.98 3.54e+00 7.98e-02 1.56e+01 angle pdb=" N GLY R 168 " pdb=" CA GLY R 168 " pdb=" C GLY R 168 " ideal model delta sigma weight residual 112.73 117.15 -4.42 1.20e+00 6.94e-01 1.35e+01 ... (remaining 12519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 5186 15.66 - 31.33: 216 31.33 - 46.99: 52 46.99 - 62.65: 3 62.65 - 78.32: 7 Dihedral angle restraints: 5464 sinusoidal: 2178 harmonic: 3286 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 171.32 -78.32 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CA ALA R 57 " pdb=" C ALA R 57 " pdb=" N THR R 58 " pdb=" CA THR R 58 " ideal model delta harmonic sigma weight residual 180.00 144.49 35.51 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CA SER R 261 " pdb=" C SER R 261 " pdb=" N GLU R 262 " pdb=" CA GLU R 262 " ideal model delta harmonic sigma weight residual -180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1068 0.069 - 0.138: 264 0.138 - 0.207: 37 0.207 - 0.276: 5 0.276 - 0.345: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CB VAL R 276 " pdb=" CA VAL R 276 " pdb=" CG1 VAL R 276 " pdb=" CG2 VAL R 276 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE R 317 " pdb=" CA ILE R 317 " pdb=" CG1 ILE R 317 " pdb=" CG2 ILE R 317 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1373 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 272 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C ILE R 272 " -0.069 2.00e-02 2.50e+03 pdb=" O ILE R 272 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY R 273 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 361 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.025 2.00e-02 2.50e+03 1.96e-02 7.65e+00 pdb=" CG TYR B 105 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.001 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1328 2.76 - 3.30: 8363 3.30 - 3.83: 14711 3.83 - 4.37: 16344 4.37 - 4.90: 29559 Nonbonded interactions: 70305 Sorted by model distance: nonbonded pdb=" OG1 THR N 91 " pdb=" O VAL N 124 " model vdw 2.229 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR R 105 " pdb=" O LEU R 109 " model vdw 2.276 3.040 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.300 3.040 ... (remaining 70300 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: 0.530 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.780 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.007 0.075 9246 Z= 0.310 Angle : 1.005 13.976 12536 Z= 0.569 Chirality : 0.061 0.345 1376 Planarity : 0.007 0.089 1597 Dihedral : 9.888 77.618 3320 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1105 helix: 2.60 (0.22), residues: 451 sheet: 0.58 (0.37), residues: 196 loop : -2.12 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP R 72 HIS 0.010 0.002 HIS R 171 PHE 0.026 0.003 PHE R 367 TYR 0.048 0.004 TYR B 105 ARG 0.010 0.001 ARG R 64 Details of bonding type rmsd hydrogen bonds : bond 0.15739 ( 477) hydrogen bonds : angle 6.42273 ( 1380) SS BOND : bond 0.00582 ( 6) SS BOND : angle 2.08567 ( 12) covalent geometry : bond 0.00692 ( 9240) covalent geometry : angle 1.00377 (12524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4130 (p0) cc_final: 0.3885 (m-30) REVERT: R 123 LEU cc_start: 0.4851 (pp) cc_final: 0.4611 (tp) REVERT: R 127 GLU cc_start: 0.6915 (tp30) cc_final: 0.6556 (mt-10) REVERT: R 182 ASN cc_start: 0.8973 (m-40) cc_final: 0.8719 (m110) REVERT: R 211 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7910 (tt0) REVERT: R 242 TYR cc_start: 0.8440 (m-80) cc_final: 0.8026 (m-80) REVERT: R 305 TYR cc_start: 0.7486 (m-10) cc_final: 0.7153 (m-10) REVERT: R 351 LYS cc_start: 0.8633 (tttt) cc_final: 0.8249 (mmtt) REVERT: R 367 PHE cc_start: 0.8126 (m-80) cc_final: 0.7925 (m-10) REVERT: R 370 VAL cc_start: 0.7561 (t) cc_final: 0.7265 (t) REVERT: R 393 PHE cc_start: 0.8134 (m-10) cc_final: 0.7760 (m-10) REVERT: R 404 PHE cc_start: 0.4434 (t80) cc_final: 0.3359 (m-80) REVERT: R 408 GLU cc_start: 0.8503 (pt0) cc_final: 0.8124 (pt0) REVERT: P 21 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8192 (mmm-85) REVERT: A 286 SER cc_start: 0.9165 (m) cc_final: 0.8717 (p) REVERT: B 23 LYS cc_start: 0.8236 (tttp) cc_final: 0.7512 (mmtt) REVERT: B 46 ARG cc_start: 0.7053 (tpt-90) cc_final: 0.6555 (mtp-110) REVERT: B 71 VAL cc_start: 0.8702 (t) cc_final: 0.8438 (p) REVERT: B 82 TRP cc_start: 0.8855 (m100) cc_final: 0.8629 (m100) REVERT: B 111 TYR cc_start: 0.8655 (m-80) cc_final: 0.8453 (m-80) REVERT: B 154 ASP cc_start: 0.7964 (m-30) cc_final: 0.7611 (t0) REVERT: B 189 SER cc_start: 0.9163 (t) cc_final: 0.8883 (p) REVERT: B 191 SER cc_start: 0.8693 (t) cc_final: 0.8425 (p) REVERT: B 217 MET cc_start: 0.7812 (ptp) cc_final: 0.7320 (tpt) REVERT: G 14 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7309 (tttp) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2847 time to fit residues: 90.4703 Evaluate side-chains 124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 115 ASN R 263 GLN R 407 ASN P 5 ASN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 155 ASN B 266 HIS G 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.117581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.103782 restraints weight = 23069.755| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.42 r_work: 0.3664 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9246 Z= 0.140 Angle : 0.637 9.034 12536 Z= 0.342 Chirality : 0.043 0.173 1376 Planarity : 0.004 0.052 1597 Dihedral : 5.501 50.400 1233 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.85 % Allowed : 8.44 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.18 % 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: 1.00 (0.25), residues: 1105 helix: 2.92 (0.23), residues: 451 sheet: 0.46 (0.36), residues: 203 loop : -1.73 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 33 HIS 0.004 0.001 HIS G 44 PHE 0.026 0.002 PHE R 230 TYR 0.018 0.002 TYR R 402 ARG 0.006 0.001 ARG R 299 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 477) hydrogen bonds : angle 5.02461 ( 1380) SS BOND : bond 0.00400 ( 6) SS BOND : angle 3.76414 ( 12) covalent geometry : bond 0.00303 ( 9240) covalent geometry : angle 0.62686 (12524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.119 Fit side-chains REVERT: R 67 ASP cc_start: 0.5023 (p0) cc_final: 0.4064 (m-30) REVERT: R 305 TYR cc_start: 0.7437 (m-10) cc_final: 0.7205 (m-10) REVERT: R 354 LEU cc_start: 0.8268 (mt) cc_final: 0.8039 (tt) REVERT: R 404 PHE cc_start: 0.4595 (t80) cc_final: 0.3801 (m-80) REVERT: A 318 TYR cc_start: 0.5970 (t80) cc_final: 0.5433 (t80) REVERT: B 23 LYS cc_start: 0.8144 (tttp) cc_final: 0.7717 (mmtt) REVERT: B 82 TRP cc_start: 0.8696 (m100) cc_final: 0.8362 (m100) REVERT: B 270 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8327 (pp) REVERT: G 14 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7618 (tttp) outliers start: 18 outliers final: 11 residues processed: 154 average time/residue: 0.2213 time to fit residues: 47.2011 Evaluate side-chains 128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.113660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.099074 restraints weight = 23497.931| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.80 r_work: 0.3573 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9246 Z= 0.199 Angle : 0.648 9.361 12536 Z= 0.347 Chirality : 0.044 0.176 1376 Planarity : 0.005 0.057 1597 Dihedral : 5.416 43.474 1233 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.40 % Allowed : 9.99 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.18 % 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: 0.92 (0.25), residues: 1105 helix: 2.80 (0.23), residues: 445 sheet: 0.27 (0.36), residues: 204 loop : -1.57 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 243 HIS 0.005 0.001 HIS A 357 PHE 0.029 0.002 PHE R 385 TYR 0.022 0.002 TYR R 402 ARG 0.005 0.001 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 477) hydrogen bonds : angle 4.84458 ( 1380) SS BOND : bond 0.00378 ( 6) SS BOND : angle 3.21071 ( 12) covalent geometry : bond 0.00455 ( 9240) covalent geometry : angle 0.64082 (12524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 1.070 Fit side-chains REVERT: R 67 ASP cc_start: 0.4582 (p0) cc_final: 0.3997 (m-30) REVERT: R 139 GLU cc_start: 0.7054 (tt0) cc_final: 0.6378 (pm20) REVERT: R 354 LEU cc_start: 0.8377 (mt) cc_final: 0.8079 (tt) REVERT: R 404 PHE cc_start: 0.4518 (t80) cc_final: 0.3733 (m-80) REVERT: A 27 GLU cc_start: 0.7650 (pp20) cc_final: 0.7403 (pp20) REVERT: A 318 TYR cc_start: 0.6103 (t80) cc_final: 0.5561 (t80) REVERT: B 23 LYS cc_start: 0.8469 (tttp) cc_final: 0.7753 (mmtt) REVERT: B 82 TRP cc_start: 0.8833 (m100) cc_final: 0.8591 (m100) REVERT: G 14 LYS cc_start: 0.7894 (mmmt) cc_final: 0.7445 (tttp) REVERT: G 51 LEU cc_start: 0.7126 (tp) cc_final: 0.6827 (mt) outliers start: 33 outliers final: 19 residues processed: 141 average time/residue: 0.1927 time to fit residues: 39.1066 Evaluate side-chains 117 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.115698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.101316 restraints weight = 23280.010| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.84 r_work: 0.3610 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9246 Z= 0.117 Angle : 0.555 7.138 12536 Z= 0.298 Chirality : 0.041 0.155 1376 Planarity : 0.004 0.053 1597 Dihedral : 5.022 39.324 1233 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.37 % Allowed : 12.05 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.18 % 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: 1.04 (0.25), residues: 1105 helix: 2.89 (0.24), residues: 447 sheet: 0.17 (0.36), residues: 201 loop : -1.40 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.001 PHE R 385 TYR 0.016 0.001 TYR N 60 ARG 0.005 0.000 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 477) hydrogen bonds : angle 4.49030 ( 1380) SS BOND : bond 0.00253 ( 6) SS BOND : angle 2.50813 ( 12) covalent geometry : bond 0.00250 ( 9240) covalent geometry : angle 0.54963 (12524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4470 (p0) cc_final: 0.4019 (m-30) REVERT: R 120 TRP cc_start: 0.5998 (t60) cc_final: 0.5787 (t60) REVERT: R 121 ARG cc_start: 0.5609 (OUTLIER) cc_final: 0.5308 (mtm180) REVERT: R 139 GLU cc_start: 0.7061 (tt0) cc_final: 0.6448 (pm20) REVERT: R 269 TYR cc_start: 0.8444 (m-10) cc_final: 0.8032 (m-80) REVERT: R 298 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8015 (t) REVERT: R 404 PHE cc_start: 0.4467 (t80) cc_final: 0.3661 (m-80) REVERT: A 27 GLU cc_start: 0.7632 (pp20) cc_final: 0.7383 (pp20) REVERT: A 318 TYR cc_start: 0.5966 (t80) cc_final: 0.5424 (t80) REVERT: B 23 LYS cc_start: 0.8397 (tttp) cc_final: 0.7745 (mmtt) REVERT: B 82 TRP cc_start: 0.8807 (m100) cc_final: 0.8536 (m100) REVERT: B 170 ASP cc_start: 0.7266 (t0) cc_final: 0.7019 (t0) REVERT: B 270 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8445 (pp) REVERT: G 14 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7515 (tttp) outliers start: 23 outliers final: 16 residues processed: 136 average time/residue: 0.1901 time to fit residues: 37.2540 Evaluate side-chains 127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.115711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101286 restraints weight = 23316.717| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.84 r_work: 0.3612 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9246 Z= 0.116 Angle : 0.537 6.584 12536 Z= 0.287 Chirality : 0.041 0.156 1376 Planarity : 0.004 0.052 1597 Dihedral : 4.742 37.279 1233 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.99 % Allowed : 12.56 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.18 % 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: 1.09 (0.26), residues: 1105 helix: 2.91 (0.24), residues: 447 sheet: 0.15 (0.36), residues: 201 loop : -1.33 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE R 385 TYR 0.016 0.001 TYR R 69 ARG 0.006 0.000 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 477) hydrogen bonds : angle 4.35453 ( 1380) SS BOND : bond 0.00228 ( 6) SS BOND : angle 2.36165 ( 12) covalent geometry : bond 0.00250 ( 9240) covalent geometry : angle 0.53208 (12524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.962 Fit side-chains REVERT: R 67 ASP cc_start: 0.4495 (p0) cc_final: 0.4023 (m-30) REVERT: R 120 TRP cc_start: 0.5935 (t60) cc_final: 0.5686 (t60) REVERT: R 139 GLU cc_start: 0.7189 (tt0) cc_final: 0.6428 (pm20) REVERT: R 269 TYR cc_start: 0.8478 (m-10) cc_final: 0.7997 (m-80) REVERT: R 298 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8032 (t) REVERT: R 404 PHE cc_start: 0.4400 (t80) cc_final: 0.3697 (m-80) REVERT: A 27 GLU cc_start: 0.7669 (pp20) cc_final: 0.7386 (pp20) REVERT: A 318 TYR cc_start: 0.5958 (t80) cc_final: 0.5509 (t80) REVERT: B 23 LYS cc_start: 0.8421 (tttp) cc_final: 0.7761 (mmtt) REVERT: B 61 MET cc_start: 0.9056 (ppp) cc_final: 0.8850 (ptm) REVERT: B 82 TRP cc_start: 0.8818 (m100) cc_final: 0.8548 (m100) REVERT: B 170 ASP cc_start: 0.7277 (t0) cc_final: 0.7023 (t0) REVERT: B 270 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8413 (pp) REVERT: G 14 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7507 (tttp) outliers start: 29 outliers final: 18 residues processed: 136 average time/residue: 0.1896 time to fit residues: 36.8280 Evaluate side-chains 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.111204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.097020 restraints weight = 23785.189| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.78 r_work: 0.3534 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9246 Z= 0.255 Angle : 0.684 10.958 12536 Z= 0.365 Chirality : 0.045 0.180 1376 Planarity : 0.005 0.050 1597 Dihedral : 5.332 38.598 1233 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.40 % Allowed : 13.59 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.18 % 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: 0.70 (0.25), residues: 1105 helix: 2.72 (0.23), residues: 436 sheet: -0.18 (0.33), residues: 230 loop : -1.59 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 110 HIS 0.006 0.001 HIS A 357 PHE 0.024 0.002 PHE A 246 TYR 0.020 0.002 TYR R 242 ARG 0.006 0.001 ARG R 64 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 477) hydrogen bonds : angle 4.77309 ( 1380) SS BOND : bond 0.00396 ( 6) SS BOND : angle 2.94543 ( 12) covalent geometry : bond 0.00583 ( 9240) covalent geometry : angle 0.67819 (12524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 1.016 Fit side-chains REVERT: R 67 ASP cc_start: 0.4425 (p0) cc_final: 0.3954 (m-30) REVERT: R 120 TRP cc_start: 0.6051 (t60) cc_final: 0.5783 (t60) REVERT: R 139 GLU cc_start: 0.7092 (tt0) cc_final: 0.6406 (pm20) REVERT: R 247 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8110 (tp30) REVERT: R 298 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8240 (t) REVERT: R 354 LEU cc_start: 0.8386 (mt) cc_final: 0.8147 (tt) REVERT: R 404 PHE cc_start: 0.4410 (t80) cc_final: 0.3696 (m-80) REVERT: A 27 GLU cc_start: 0.7767 (pp20) cc_final: 0.7444 (pp20) REVERT: A 318 TYR cc_start: 0.6168 (t80) cc_final: 0.5664 (t80) REVERT: B 23 LYS cc_start: 0.8689 (tttp) cc_final: 0.7916 (mmtt) REVERT: B 45 MET cc_start: 0.7672 (mmp) cc_final: 0.7444 (mmp) REVERT: G 14 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7481 (tttp) outliers start: 33 outliers final: 26 residues processed: 135 average time/residue: 0.1889 time to fit residues: 36.9241 Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 27 optimal weight: 0.0470 chunk 82 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.114557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.100063 restraints weight = 23726.629| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.84 r_work: 0.3583 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9246 Z= 0.116 Angle : 0.551 7.280 12536 Z= 0.295 Chirality : 0.040 0.156 1376 Planarity : 0.004 0.050 1597 Dihedral : 4.859 36.638 1233 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.57 % Allowed : 14.21 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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 (0.26), residues: 1105 helix: 2.92 (0.24), residues: 439 sheet: -0.16 (0.34), residues: 219 loop : -1.47 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE R 381 TYR 0.017 0.001 TYR R 69 ARG 0.002 0.000 ARG R 64 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 477) hydrogen bonds : angle 4.40328 ( 1380) SS BOND : bond 0.00279 ( 6) SS BOND : angle 2.44966 ( 12) covalent geometry : bond 0.00249 ( 9240) covalent geometry : angle 0.54620 (12524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4490 (p0) cc_final: 0.4101 (m-30) REVERT: R 120 TRP cc_start: 0.5957 (t60) cc_final: 0.5641 (t60) REVERT: R 139 GLU cc_start: 0.7131 (tt0) cc_final: 0.6434 (pm20) REVERT: R 269 TYR cc_start: 0.8495 (m-80) cc_final: 0.8287 (m-80) REVERT: R 354 LEU cc_start: 0.8345 (mt) cc_final: 0.8081 (tt) REVERT: R 404 PHE cc_start: 0.4436 (t80) cc_final: 0.3762 (m-80) REVERT: A 27 GLU cc_start: 0.7778 (pp20) cc_final: 0.7448 (pp20) REVERT: A 318 TYR cc_start: 0.5857 (t80) cc_final: 0.5450 (t80) REVERT: B 23 LYS cc_start: 0.8558 (tttp) cc_final: 0.7806 (mmtt) REVERT: B 234 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7583 (t80) REVERT: B 270 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8384 (pp) REVERT: G 14 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7458 (tttp) REVERT: N 60 TYR cc_start: 0.8641 (m-80) cc_final: 0.8439 (m-80) outliers start: 25 outliers final: 19 residues processed: 126 average time/residue: 0.1763 time to fit residues: 32.5541 Evaluate side-chains 121 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.112225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.097936 restraints weight = 24141.298| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.83 r_work: 0.3547 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9246 Z= 0.196 Angle : 0.631 8.643 12536 Z= 0.336 Chirality : 0.043 0.170 1376 Planarity : 0.004 0.049 1597 Dihedral : 5.060 37.291 1233 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.19 % Allowed : 13.80 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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: 0.79 (0.25), residues: 1105 helix: 2.80 (0.24), residues: 436 sheet: -0.25 (0.33), residues: 232 loop : -1.49 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 110 HIS 0.005 0.001 HIS A 357 PHE 0.023 0.002 PHE N 29 TYR 0.015 0.002 TYR R 220 ARG 0.004 0.000 ARG R 64 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 477) hydrogen bonds : angle 4.54841 ( 1380) SS BOND : bond 0.00348 ( 6) SS BOND : angle 2.72175 ( 12) covalent geometry : bond 0.00447 ( 9240) covalent geometry : angle 0.62598 (12524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4656 (p0) cc_final: 0.4110 (m-30) REVERT: R 120 TRP cc_start: 0.6078 (t60) cc_final: 0.5733 (t60) REVERT: R 139 GLU cc_start: 0.7058 (tt0) cc_final: 0.6332 (pm20) REVERT: R 247 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8083 (tp30) REVERT: R 354 LEU cc_start: 0.8521 (mt) cc_final: 0.8251 (tt) REVERT: R 404 PHE cc_start: 0.4390 (t80) cc_final: 0.3713 (m-80) REVERT: A 27 GLU cc_start: 0.7862 (pp20) cc_final: 0.7508 (pp20) REVERT: A 318 TYR cc_start: 0.6069 (t80) cc_final: 0.5593 (t80) REVERT: B 23 LYS cc_start: 0.8675 (tttp) cc_final: 0.7915 (mmtt) REVERT: B 45 MET cc_start: 0.7706 (mmp) cc_final: 0.7448 (mmp) REVERT: B 234 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.7586 (t80) REVERT: G 14 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7508 (tttp) outliers start: 31 outliers final: 27 residues processed: 125 average time/residue: 0.1800 time to fit residues: 33.2976 Evaluate side-chains 127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.114294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099715 restraints weight = 23494.667| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.85 r_work: 0.3582 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9246 Z= 0.124 Angle : 0.579 7.767 12536 Z= 0.306 Chirality : 0.041 0.156 1376 Planarity : 0.004 0.049 1597 Dihedral : 4.824 36.087 1233 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.99 % Allowed : 13.70 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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: 0.85 (0.26), residues: 1105 helix: 2.89 (0.24), residues: 436 sheet: -0.28 (0.33), residues: 225 loop : -1.44 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 39 HIS 0.005 0.001 HIS A 357 PHE 0.023 0.002 PHE R 381 TYR 0.020 0.001 TYR R 269 ARG 0.003 0.000 ARG R 64 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 477) hydrogen bonds : angle 4.38286 ( 1380) SS BOND : bond 0.00277 ( 6) SS BOND : angle 2.47094 ( 12) covalent geometry : bond 0.00274 ( 9240) covalent geometry : angle 0.57370 (12524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4532 (p0) cc_final: 0.4029 (m-30) REVERT: R 120 TRP cc_start: 0.6041 (t60) cc_final: 0.5722 (t60) REVERT: R 139 GLU cc_start: 0.7161 (tt0) cc_final: 0.6420 (pm20) REVERT: R 247 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: R 354 LEU cc_start: 0.8484 (mt) cc_final: 0.8180 (tt) REVERT: R 404 PHE cc_start: 0.4411 (t80) cc_final: 0.3746 (m-80) REVERT: A 27 GLU cc_start: 0.7826 (pp20) cc_final: 0.7484 (pp20) REVERT: A 318 TYR cc_start: 0.5883 (t80) cc_final: 0.5485 (t80) REVERT: B 23 LYS cc_start: 0.8562 (tttp) cc_final: 0.7793 (mmtt) REVERT: B 45 MET cc_start: 0.7700 (mmp) cc_final: 0.7483 (mmp) REVERT: B 234 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7575 (t80) REVERT: B 270 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8322 (pp) REVERT: G 14 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7453 (tttp) outliers start: 29 outliers final: 23 residues processed: 124 average time/residue: 0.1829 time to fit residues: 33.2418 Evaluate side-chains 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 90 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.115191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.100644 restraints weight = 23541.568| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.86 r_work: 0.3595 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9246 Z= 0.121 Angle : 0.575 8.686 12536 Z= 0.302 Chirality : 0.041 0.153 1376 Planarity : 0.004 0.049 1597 Dihedral : 4.668 35.282 1233 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 14.11 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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: 0.94 (0.26), residues: 1105 helix: 2.93 (0.24), residues: 437 sheet: -0.17 (0.34), residues: 213 loop : -1.38 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 39 HIS 0.004 0.001 HIS A 357 PHE 0.022 0.001 PHE R 385 TYR 0.013 0.001 TYR N 60 ARG 0.002 0.000 ARG R 64 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 477) hydrogen bonds : angle 4.28398 ( 1380) SS BOND : bond 0.00284 ( 6) SS BOND : angle 2.35878 ( 12) covalent geometry : bond 0.00269 ( 9240) covalent geometry : angle 0.57045 (12524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4492 (p0) cc_final: 0.3923 (m-30) REVERT: R 120 TRP cc_start: 0.6054 (t60) cc_final: 0.5754 (t60) REVERT: R 139 GLU cc_start: 0.7042 (tt0) cc_final: 0.6382 (pm20) REVERT: R 242 TYR cc_start: 0.8561 (m-80) cc_final: 0.8266 (m-80) REVERT: R 247 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: R 354 LEU cc_start: 0.8470 (mt) cc_final: 0.8168 (tt) REVERT: R 404 PHE cc_start: 0.4606 (t80) cc_final: 0.3788 (m-80) REVERT: P 10 ASP cc_start: 0.8115 (t0) cc_final: 0.7884 (t0) REVERT: A 27 GLU cc_start: 0.7869 (pp20) cc_final: 0.7560 (pp20) REVERT: A 318 TYR cc_start: 0.5893 (t80) cc_final: 0.5507 (t80) REVERT: B 23 LYS cc_start: 0.8557 (tttp) cc_final: 0.7799 (mmtt) REVERT: B 45 MET cc_start: 0.7720 (mmp) cc_final: 0.7509 (mmp) REVERT: B 270 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8314 (pp) REVERT: G 14 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7503 (tttp) outliers start: 25 outliers final: 21 residues processed: 126 average time/residue: 0.1965 time to fit residues: 35.5861 Evaluate side-chains 125 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 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 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.114178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099698 restraints weight = 23537.348| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.84 r_work: 0.3585 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9246 Z= 0.142 Angle : 0.592 8.160 12536 Z= 0.312 Chirality : 0.041 0.157 1376 Planarity : 0.004 0.049 1597 Dihedral : 4.719 35.585 1233 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.68 % Allowed : 14.01 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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: 0.88 (0.26), residues: 1105 helix: 2.85 (0.24), residues: 438 sheet: -0.23 (0.33), residues: 219 loop : -1.38 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.023 0.002 PHE R 381 TYR 0.013 0.002 TYR R 242 ARG 0.003 0.000 ARG R 64 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 477) hydrogen bonds : angle 4.32291 ( 1380) SS BOND : bond 0.00321 ( 6) SS BOND : angle 2.44775 ( 12) covalent geometry : bond 0.00321 ( 9240) covalent geometry : angle 0.58764 (12524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4072.47 seconds wall clock time: 71 minutes 5.80 seconds (4265.80 seconds total)