Starting phenix.real_space_refine on Wed Sep 17 15:02:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw3_39621/09_2025/8yw3_39621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw3_39621/09_2025/8yw3_39621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw3_39621/09_2025/8yw3_39621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw3_39621/09_2025/8yw3_39621.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw3_39621/09_2025/8yw3_39621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw3_39621/09_2025/8yw3_39621.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 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 5887 2.51 5 N 1596 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9231 Number of models: 1 Model: "" Number of chains: 6 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: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2588 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1884 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Chain: "R" Number of atoms: 3125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3125 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 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: "P" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 237 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'AIB:plan-1': 2, '2ML:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.98, per 1000 atoms: 0.21 Number of scatterers: 9231 At special positions: 0 Unit cell: (80.325, 98.532, 174.573, 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 1694 8.00 N 1596 7.00 C 5887 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 98 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 109 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 367.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 42.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'N' and resid 30 through 34 Processing helix chain 'N' and resid 89 through 93 removed outlier: 3.608A pdb=" N THR N 93 " --> pdb=" O PRO N 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 30 removed outlier: 3.646A pdb=" N GLU B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.989A pdb=" N ASN B 137 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.967A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 39 removed outlier: 3.854A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.586A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.793A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.895A pdb=" N ASP R 53 " --> pdb=" O SER R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 169 removed outlier: 3.653A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.926A pdb=" N LYS R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 216 Processing helix chain 'R' and resid 224 through 256 removed outlier: 4.367A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 removed outlier: 3.859A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 279 Processing helix chain 'R' and resid 280 through 292 Processing helix chain 'R' and resid 294 through 298 removed outlier: 3.840A pdb=" N TRP R 297 " --> pdb=" O GLU R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.817A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.327A 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 346 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 365 Processing helix chain 'R' and resid 376 through 403 removed outlier: 3.529A pdb=" N ARG R 380 " --> pdb=" O ARG R 376 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.793A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'P' and resid 2 through 28 removed outlier: 3.812A pdb=" N GLU P 28 " --> pdb=" O GLU P 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'N' and resid 60 through 62 removed outlier: 3.733A pdb=" N SER N 61 " --> pdb=" O ASP N 52 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP N 38 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP N 52 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N MET N 36 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.753A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.545A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.052A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 156 removed outlier: 4.104A pdb=" N ILE B 162 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.960A pdb=" N SER B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.818A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.782A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.474A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 removed outlier: 3.703A pdb=" N THR R 65 " --> pdb=" O TRP R 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 82 through 83 471 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2125 1.33 - 1.45: 2110 1.45 - 1.57: 5129 1.57 - 1.69: 2 1.69 - 1.81: 73 Bond restraints: 9439 Sorted by residual: bond pdb=" N AIB P 2 " pdb=" CA AIB P 2 " ideal model delta sigma weight residual 1.458 1.570 -0.112 1.90e-02 2.77e+03 3.45e+01 bond pdb=" CA 2ML P 13 " pdb=" C 2ML P 13 " ideal model delta sigma weight residual 1.525 1.583 -0.058 2.10e-02 2.27e+03 7.74e+00 bond pdb=" CA AIB P 2 " pdb=" C AIB P 2 " ideal model delta sigma weight residual 1.525 1.581 -0.056 2.10e-02 2.27e+03 7.17e+00 bond pdb=" N GLU R 139 " pdb=" CA GLU R 139 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.16e-02 7.43e+03 5.64e+00 bond pdb=" N GLU R 127 " pdb=" CA GLU R 127 " ideal model delta sigma weight residual 1.454 1.484 -0.029 1.29e-02 6.01e+03 5.20e+00 ... (remaining 9434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 12490 1.79 - 3.58: 238 3.58 - 5.37: 48 5.37 - 7.15: 20 7.15 - 8.94: 3 Bond angle restraints: 12799 Sorted by residual: angle pdb=" N PRO R 137 " pdb=" CA PRO R 137 " pdb=" C PRO R 137 " ideal model delta sigma weight residual 113.75 107.30 6.45 1.49e+00 4.50e-01 1.87e+01 angle pdb=" CB LYS A 305 " pdb=" CG LYS A 305 " pdb=" CD LYS A 305 " ideal model delta sigma weight residual 111.30 119.59 -8.29 2.30e+00 1.89e-01 1.30e+01 angle pdb=" CA GLN A 19 " pdb=" CB GLN A 19 " pdb=" CG GLN A 19 " ideal model delta sigma weight residual 114.10 121.13 -7.03 2.00e+00 2.50e-01 1.24e+01 angle pdb=" O TYR P 1 " pdb=" C TYR P 1 " pdb=" N AIB P 2 " ideal model delta sigma weight residual 123.00 128.37 -5.37 1.60e+00 3.91e-01 1.13e+01 angle pdb=" CA TYR P 1 " pdb=" C TYR P 1 " pdb=" O TYR P 1 " ideal model delta sigma weight residual 120.80 115.13 5.67 1.70e+00 3.46e-01 1.11e+01 ... (remaining 12794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4648 17.57 - 35.14: 674 35.14 - 52.71: 213 52.71 - 70.28: 33 70.28 - 87.84: 10 Dihedral angle restraints: 5578 sinusoidal: 2205 harmonic: 3373 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual 93.00 176.25 -83.25 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS N 101 " pdb=" SG CYS N 101 " pdb=" SG CYS N 109 " pdb=" CB CYS N 109 " ideal model delta sinusoidal sigma weight residual -86.00 -123.82 37.82 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual -86.00 -48.55 -37.45 1 1.00e+01 1.00e-02 1.98e+01 ... (remaining 5575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1143 0.053 - 0.105: 232 0.105 - 0.158: 34 0.158 - 0.210: 1 0.210 - 0.263: 1 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CA 2ML P 13 " pdb=" C 2ML P 13 " pdb=" CB1 2ML P 13 " pdb=" CB2 2ML P 13 " both_signs ideal model delta sigma weight residual False -2.84 -3.10 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA GLN R 140 " pdb=" N GLN R 140 " pdb=" C GLN R 140 " pdb=" CB GLN R 140 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 1408 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR P 1 " -0.014 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C TYR P 1 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR P 1 " -0.020 2.00e-02 2.50e+03 pdb=" N AIB P 2 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 55 " 0.047 5.00e-02 4.00e+02 7.20e-02 8.28e+00 pdb=" N PRO R 56 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO R 56 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 56 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 126 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C CYS R 126 " 0.043 2.00e-02 2.50e+03 pdb=" O CYS R 126 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU R 127 " -0.014 2.00e-02 2.50e+03 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 407 2.71 - 3.26: 9221 3.26 - 3.80: 15551 3.80 - 4.35: 18823 4.35 - 4.90: 32345 Nonbonded interactions: 76347 Sorted by model distance: nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.163 3.040 nonbonded pdb=" O ARG B 27 " pdb=" NE2 GLN B 264 " model vdw 2.170 3.120 nonbonded pdb=" OH TYR R 241 " pdb=" OE2 GLU R 364 " model vdw 2.185 3.040 nonbonded pdb=" OG SER B 166 " pdb=" OD1 ASP B 168 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP R 67 " pdb=" N GLU R 68 " model vdw 2.225 3.120 ... (remaining 76342 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=0.00 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 0.112 9445 Z= 0.196 Angle : 0.656 8.942 12811 Z= 0.355 Chirality : 0.043 0.263 1411 Planarity : 0.004 0.072 1626 Dihedral : 17.968 87.844 3382 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 7.83 % Allowed : 32.83 % Favored : 59.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.26), residues: 1130 helix: 1.90 (0.25), residues: 437 sheet: -0.19 (0.32), residues: 251 loop : -0.66 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG R 44 TYR 0.017 0.001 TYR R 148 PHE 0.014 0.001 PHE R 230 TRP 0.035 0.001 TRP N 49 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9439) covalent geometry : angle 0.65574 (12799) SS BOND : bond 0.00192 ( 6) SS BOND : angle 0.86778 ( 12) hydrogen bonds : bond 0.13440 ( 471) hydrogen bonds : angle 5.43644 ( 1329) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 134 time to evaluate : 0.293 Fit side-chains revert: symmetry clash outliers start: 77 outliers final: 70 residues processed: 206 average time/residue: 0.4313 time to fit residues: 96.8323 Evaluate side-chains 202 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 132 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 37 ASN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain P residue 5 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 33 ASN N 76 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.088750 restraints weight = 14805.625| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.91 r_work: 0.3058 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9445 Z= 0.125 Angle : 0.555 7.718 12811 Z= 0.290 Chirality : 0.041 0.140 1411 Planarity : 0.004 0.060 1626 Dihedral : 8.852 87.662 1369 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 6.20 % Allowed : 30.49 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1130 helix: 2.18 (0.25), residues: 432 sheet: -0.08 (0.32), residues: 249 loop : -0.63 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 317 TYR 0.018 0.001 TYR R 148 PHE 0.012 0.001 PHE R 230 TRP 0.021 0.001 TRP N 49 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9439) covalent geometry : angle 0.55270 (12799) SS BOND : bond 0.00166 ( 6) SS BOND : angle 1.56895 ( 12) hydrogen bonds : bond 0.03800 ( 471) hydrogen bonds : angle 4.49768 ( 1329) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 137 time to evaluate : 0.358 Fit side-chains REVERT: N 33 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6835 (t160) REVERT: B 193 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8764 (mmp) REVERT: B 222 MET cc_start: 0.8388 (pmm) cc_final: 0.8173 (pmm) REVERT: B 306 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7599 (tptt) REVERT: A 356 ARG cc_start: 0.8040 (mpp-170) cc_final: 0.7752 (mtp180) REVERT: R 215 ASP cc_start: 0.8733 (m-30) cc_final: 0.8472 (m-30) outliers start: 61 outliers final: 34 residues processed: 189 average time/residue: 0.5274 time to fit residues: 107.2495 Evaluate side-chains 170 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.0270 chunk 87 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 67 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 33 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 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 = 0.3751 r_free = 0.3751 target = 0.129501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.090414 restraints weight = 14710.416| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.92 r_work: 0.3072 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9445 Z= 0.110 Angle : 0.528 7.632 12811 Z= 0.275 Chirality : 0.040 0.143 1411 Planarity : 0.004 0.059 1626 Dihedral : 6.982 59.521 1309 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.88 % Allowed : 32.93 % Favored : 62.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.26), residues: 1130 helix: 2.32 (0.25), residues: 433 sheet: -0.03 (0.32), residues: 249 loop : -0.68 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 44 TYR 0.018 0.001 TYR R 148 PHE 0.011 0.001 PHE N 105 TRP 0.022 0.001 TRP N 49 HIS 0.002 0.000 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9439) covalent geometry : angle 0.52659 (12799) SS BOND : bond 0.00168 ( 6) SS BOND : angle 1.33660 ( 12) hydrogen bonds : bond 0.03558 ( 471) hydrogen bonds : angle 4.29423 ( 1329) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.372 Fit side-chains REVERT: B 222 MET cc_start: 0.8309 (pmm) cc_final: 0.7941 (pmm) REVERT: B 263 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.6808 (t0) REVERT: A 13 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7680 (pmt170) REVERT: A 23 ASN cc_start: 0.7870 (t0) cc_final: 0.7616 (t0) REVERT: A 265 ARG cc_start: 0.6398 (OUTLIER) cc_final: 0.5619 (pmt-80) REVERT: A 392 GLU cc_start: 0.8344 (mp0) cc_final: 0.7926 (mp0) REVERT: R 215 ASP cc_start: 0.8693 (m-30) cc_final: 0.8396 (m-30) REVERT: R 372 ASP cc_start: 0.6062 (p0) cc_final: 0.5833 (p0) REVERT: R 397 MET cc_start: 0.8223 (mtp) cc_final: 0.7895 (mmt) outliers start: 48 outliers final: 26 residues processed: 188 average time/residue: 0.5174 time to fit residues: 105.0617 Evaluate side-chains 164 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.129236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.090115 restraints weight = 14856.906| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.91 r_work: 0.3066 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9445 Z= 0.119 Angle : 0.524 6.833 12811 Z= 0.272 Chirality : 0.040 0.155 1411 Planarity : 0.004 0.058 1626 Dihedral : 6.413 59.226 1299 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.59 % Allowed : 33.84 % Favored : 60.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1130 helix: 2.26 (0.25), residues: 439 sheet: -0.06 (0.32), residues: 249 loop : -0.80 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 44 TYR 0.018 0.001 TYR R 148 PHE 0.012 0.001 PHE R 230 TRP 0.024 0.001 TRP N 49 HIS 0.002 0.000 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9439) covalent geometry : angle 0.52277 (12799) SS BOND : bond 0.00190 ( 6) SS BOND : angle 1.18555 ( 12) hydrogen bonds : bond 0.03521 ( 471) hydrogen bonds : angle 4.25568 ( 1329) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: N 33 ASN cc_start: 0.6745 (OUTLIER) cc_final: 0.6526 (t160) REVERT: B 222 MET cc_start: 0.8287 (pmm) cc_final: 0.7861 (pmm) REVERT: B 263 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.6795 (t0) REVERT: A 13 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7687 (pmt170) REVERT: A 23 ASN cc_start: 0.7964 (t0) cc_final: 0.7694 (t0) REVERT: A 265 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5590 (pmt-80) REVERT: A 347 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7878 (ttp-110) REVERT: A 392 GLU cc_start: 0.8306 (mp0) cc_final: 0.7929 (mp0) REVERT: R 215 ASP cc_start: 0.8651 (m-30) cc_final: 0.8345 (m-30) REVERT: R 294 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7785 (pp20) REVERT: R 372 ASP cc_start: 0.6095 (p0) cc_final: 0.5827 (p0) REVERT: R 397 MET cc_start: 0.8242 (mtp) cc_final: 0.7905 (mmt) outliers start: 55 outliers final: 30 residues processed: 186 average time/residue: 0.5828 time to fit residues: 116.1425 Evaluate side-chains 170 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain P residue 11 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 273 ASN A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN G 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.089200 restraints weight = 14864.760| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.92 r_work: 0.3049 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9445 Z= 0.143 Angle : 0.543 7.201 12811 Z= 0.281 Chirality : 0.041 0.138 1411 Planarity : 0.004 0.058 1626 Dihedral : 6.247 58.753 1297 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.88 % Allowed : 34.96 % Favored : 60.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.26), residues: 1130 helix: 2.22 (0.25), residues: 439 sheet: -0.09 (0.32), residues: 249 loop : -0.80 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 44 TYR 0.020 0.001 TYR N 82 PHE 0.012 0.001 PHE R 230 TRP 0.026 0.001 TRP N 49 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9439) covalent geometry : angle 0.54168 (12799) SS BOND : bond 0.00239 ( 6) SS BOND : angle 1.12072 ( 12) hydrogen bonds : bond 0.03650 ( 471) hydrogen bonds : angle 4.24899 ( 1329) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 0.371 Fit side-chains REVERT: B 49 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8225 (mm-40) REVERT: B 222 MET cc_start: 0.8260 (pmm) cc_final: 0.7705 (pmm) REVERT: B 306 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7550 (tptt) REVERT: A 13 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7795 (pmt170) REVERT: A 17 LYS cc_start: 0.8803 (pmtt) cc_final: 0.8583 (pmtt) REVERT: A 23 ASN cc_start: 0.7972 (t0) cc_final: 0.7732 (t0) REVERT: A 392 GLU cc_start: 0.8299 (mp0) cc_final: 0.7861 (mp0) REVERT: R 215 ASP cc_start: 0.8669 (m-30) cc_final: 0.8355 (m-30) REVERT: R 294 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7800 (pp20) REVERT: R 372 ASP cc_start: 0.6120 (p0) cc_final: 0.5867 (p0) REVERT: R 397 MET cc_start: 0.8280 (mtp) cc_final: 0.7929 (mmt) outliers start: 48 outliers final: 29 residues processed: 179 average time/residue: 0.5571 time to fit residues: 107.2017 Evaluate side-chains 164 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 292 ASN G 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.127844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088538 restraints weight = 14900.805| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.91 r_work: 0.3039 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9445 Z= 0.164 Angle : 0.563 10.073 12811 Z= 0.290 Chirality : 0.041 0.138 1411 Planarity : 0.004 0.057 1626 Dihedral : 6.150 58.353 1295 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.59 % Allowed : 35.06 % Favored : 59.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.25), residues: 1130 helix: 2.17 (0.25), residues: 438 sheet: -0.14 (0.32), residues: 249 loop : -0.81 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 61 TYR 0.019 0.001 TYR R 148 PHE 0.018 0.001 PHE N 105 TRP 0.027 0.001 TRP N 49 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9439) covalent geometry : angle 0.56194 (12799) SS BOND : bond 0.00278 ( 6) SS BOND : angle 1.09616 ( 12) hydrogen bonds : bond 0.03792 ( 471) hydrogen bonds : angle 4.27447 ( 1329) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 135 time to evaluate : 0.387 Fit side-chains REVERT: B 222 MET cc_start: 0.8216 (pmm) cc_final: 0.7626 (pmm) REVERT: B 263 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.6835 (t0) REVERT: B 306 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7551 (tptt) REVERT: A 13 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7859 (pmt170) REVERT: A 392 GLU cc_start: 0.8304 (mp0) cc_final: 0.7791 (mp0) REVERT: R 215 ASP cc_start: 0.8705 (m-30) cc_final: 0.8405 (m-30) REVERT: R 294 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7741 (pp20) REVERT: R 372 ASP cc_start: 0.6188 (p0) cc_final: 0.5918 (p0) outliers start: 55 outliers final: 33 residues processed: 180 average time/residue: 0.5386 time to fit residues: 104.2297 Evaluate side-chains 168 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain P residue 11 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 0.0770 chunk 100 optimal weight: 0.0970 chunk 76 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 239 ASN A 292 ASN G 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.129705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.090564 restraints weight = 14857.819| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.91 r_work: 0.3072 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 9445 Z= 0.108 Angle : 0.537 9.698 12811 Z= 0.275 Chirality : 0.040 0.136 1411 Planarity : 0.004 0.057 1626 Dihedral : 6.066 58.730 1295 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.78 % Allowed : 35.26 % Favored : 59.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1130 helix: 2.27 (0.25), residues: 439 sheet: -0.09 (0.32), residues: 249 loop : -0.77 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 44 TYR 0.020 0.001 TYR N 82 PHE 0.017 0.001 PHE N 105 TRP 0.029 0.001 TRP N 49 HIS 0.002 0.000 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9439) covalent geometry : angle 0.53656 (12799) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.94441 ( 12) hydrogen bonds : bond 0.03418 ( 471) hydrogen bonds : angle 4.17318 ( 1329) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.399 Fit side-chains REVERT: B 222 MET cc_start: 0.8235 (pmm) cc_final: 0.7678 (pmm) REVERT: B 263 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.6779 (t0) REVERT: A 23 ASN cc_start: 0.7835 (t0) cc_final: 0.7465 (t0) REVERT: A 347 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8236 (ttp-110) REVERT: A 392 GLU cc_start: 0.8300 (mp0) cc_final: 0.7809 (mp0) REVERT: R 215 ASP cc_start: 0.8667 (m-30) cc_final: 0.8348 (m-30) REVERT: R 221 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7488 (mm-40) REVERT: R 294 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7813 (pp20) REVERT: R 372 ASP cc_start: 0.6077 (p0) cc_final: 0.5834 (p0) REVERT: R 397 MET cc_start: 0.8237 (mtp) cc_final: 0.7895 (mmt) outliers start: 47 outliers final: 25 residues processed: 184 average time/residue: 0.5467 time to fit residues: 108.1774 Evaluate side-chains 169 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 221 GLN Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 92 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 292 ASN P 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.090218 restraints weight = 14719.188| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.89 r_work: 0.3067 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9445 Z= 0.132 Angle : 0.568 10.020 12811 Z= 0.290 Chirality : 0.040 0.163 1411 Planarity : 0.004 0.057 1626 Dihedral : 5.912 59.083 1291 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.47 % Allowed : 36.28 % Favored : 59.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1130 helix: 2.25 (0.25), residues: 439 sheet: -0.11 (0.32), residues: 249 loop : -0.75 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 44 TYR 0.017 0.001 TYR R 148 PHE 0.017 0.001 PHE N 105 TRP 0.031 0.001 TRP N 49 HIS 0.002 0.000 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9439) covalent geometry : angle 0.56788 (12799) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.95480 ( 12) hydrogen bonds : bond 0.03514 ( 471) hydrogen bonds : angle 4.16843 ( 1329) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.370 Fit side-chains REVERT: B 222 MET cc_start: 0.8207 (pmm) cc_final: 0.7654 (pmm) REVERT: B 263 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.6794 (t0) REVERT: B 306 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7527 (tptt) REVERT: A 17 LYS cc_start: 0.8738 (pmtt) cc_final: 0.8536 (pmtt) REVERT: A 23 ASN cc_start: 0.7918 (t0) cc_final: 0.7567 (t0) REVERT: A 317 ARG cc_start: 0.8715 (mmp80) cc_final: 0.8506 (mmp80) REVERT: A 392 GLU cc_start: 0.8312 (mp0) cc_final: 0.7771 (mp0) REVERT: R 44 ARG cc_start: 0.9027 (ttp80) cc_final: 0.8799 (ttp80) REVERT: R 215 ASP cc_start: 0.8646 (m-30) cc_final: 0.8297 (m-30) REVERT: R 221 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7490 (mm-40) REVERT: R 294 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7705 (pp20) REVERT: R 372 ASP cc_start: 0.6106 (p0) cc_final: 0.5826 (p0) REVERT: R 397 MET cc_start: 0.8268 (mtp) cc_final: 0.7919 (mmt) REVERT: R 418 GLU cc_start: 0.8362 (tp30) cc_final: 0.8128 (tp30) outliers start: 44 outliers final: 25 residues processed: 181 average time/residue: 0.5333 time to fit residues: 103.6935 Evaluate side-chains 167 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 221 GLN Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 106 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 239 ASN A 292 ASN P 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.129993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.090917 restraints weight = 14709.284| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.89 r_work: 0.3081 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9445 Z= 0.118 Angle : 0.569 10.047 12811 Z= 0.288 Chirality : 0.040 0.162 1411 Planarity : 0.004 0.061 1626 Dihedral : 5.907 59.495 1291 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.35 % Allowed : 37.20 % Favored : 59.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.26), residues: 1130 helix: 2.30 (0.25), residues: 439 sheet: -0.09 (0.32), residues: 249 loop : -0.76 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 61 TYR 0.021 0.001 TYR N 82 PHE 0.017 0.001 PHE N 105 TRP 0.033 0.001 TRP N 49 HIS 0.002 0.000 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9439) covalent geometry : angle 0.56865 (12799) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.90313 ( 12) hydrogen bonds : bond 0.03381 ( 471) hydrogen bonds : angle 4.11917 ( 1329) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.362 Fit side-chains REVERT: B 222 MET cc_start: 0.8208 (pmm) cc_final: 0.7648 (pmm) REVERT: B 263 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.6768 (t0) REVERT: A 23 ASN cc_start: 0.7811 (t0) cc_final: 0.7454 (t0) REVERT: A 392 GLU cc_start: 0.8298 (mp0) cc_final: 0.7764 (mp0) REVERT: R 44 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8719 (ttp80) REVERT: R 215 ASP cc_start: 0.8618 (m-30) cc_final: 0.8252 (m-30) REVERT: R 221 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7481 (mm-40) REVERT: R 294 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7427 (pp20) REVERT: R 372 ASP cc_start: 0.6107 (p0) cc_final: 0.5854 (p0) REVERT: R 397 MET cc_start: 0.8241 (mtp) cc_final: 0.7895 (mmt) outliers start: 33 outliers final: 24 residues processed: 166 average time/residue: 0.5326 time to fit residues: 95.0950 Evaluate side-chains 165 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 221 GLN Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 72 optimal weight: 0.0020 chunk 92 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 292 ASN P 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.129895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.090876 restraints weight = 14769.188| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.90 r_work: 0.3077 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9445 Z= 0.122 Angle : 0.582 10.117 12811 Z= 0.295 Chirality : 0.040 0.161 1411 Planarity : 0.004 0.064 1626 Dihedral : 5.899 60.000 1290 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.66 % Allowed : 36.99 % Favored : 59.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.26), residues: 1130 helix: 2.34 (0.25), residues: 438 sheet: -0.09 (0.32), residues: 249 loop : -0.76 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 61 TYR 0.016 0.001 TYR R 148 PHE 0.016 0.001 PHE N 105 TRP 0.035 0.001 TRP N 49 HIS 0.002 0.000 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9439) covalent geometry : angle 0.58176 (12799) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.87902 ( 12) hydrogen bonds : bond 0.03393 ( 471) hydrogen bonds : angle 4.10843 ( 1329) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: B 222 MET cc_start: 0.8190 (pmm) cc_final: 0.7680 (pmm) REVERT: B 263 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.6765 (t0) REVERT: B 306 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7489 (tptt) REVERT: A 23 ASN cc_start: 0.7820 (t0) cc_final: 0.7434 (t0) REVERT: A 347 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7999 (ttp-110) REVERT: A 392 GLU cc_start: 0.8298 (mp0) cc_final: 0.7780 (mp0) REVERT: R 44 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8676 (ttp80) REVERT: R 215 ASP cc_start: 0.8590 (m-30) cc_final: 0.8207 (m-30) REVERT: R 221 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7464 (mm-40) REVERT: R 294 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7389 (pp20) REVERT: R 372 ASP cc_start: 0.6108 (p0) cc_final: 0.5822 (p0) outliers start: 36 outliers final: 23 residues processed: 172 average time/residue: 0.5373 time to fit residues: 99.2679 Evaluate side-chains 168 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 48 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 80 PHE Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 221 GLN Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.128996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089862 restraints weight = 14622.370| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.88 r_work: 0.3062 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9445 Z= 0.152 Angle : 0.593 10.225 12811 Z= 0.303 Chirality : 0.041 0.160 1411 Planarity : 0.004 0.057 1626 Dihedral : 5.983 59.797 1290 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.15 % Allowed : 37.30 % Favored : 59.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.26), residues: 1130 helix: 2.28 (0.25), residues: 438 sheet: -0.09 (0.32), residues: 244 loop : -0.84 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 61 TYR 0.022 0.001 TYR N 82 PHE 0.016 0.001 PHE N 105 TRP 0.036 0.001 TRP N 49 HIS 0.003 0.000 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9439) covalent geometry : angle 0.59279 (12799) SS BOND : bond 0.00200 ( 6) SS BOND : angle 0.93356 ( 12) hydrogen bonds : bond 0.03601 ( 471) hydrogen bonds : angle 4.21512 ( 1329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3815.01 seconds wall clock time: 65 minutes 49.91 seconds (3949.91 seconds total)