Starting phenix.real_space_refine on Sat Aug 23 00:37:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j18_35913/08_2025/8j18_35913.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j18_35913/08_2025/8j18_35913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j18_35913/08_2025/8j18_35913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j18_35913/08_2025/8j18_35913.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j18_35913/08_2025/8j18_35913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j18_35913/08_2025/8j18_35913.map" } resolution = 2.89 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= 0.006 sd= 0.062 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 59 5.16 5 C 5652 2.51 5 N 1528 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8860 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1759 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 12, 'TRANS': 278} Chain breaks: 1 Chain: "S" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'HXD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.23 Number of scatterers: 8860 At special positions: 0 Unit cell: (109.5, 109.5, 121.91, 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 59 16.00 O 1621 8.00 N 1528 7.00 C 5652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 166 " distance=2.03 Simple disulfide: pdb=" SG CYS R 93 " - pdb=" SG CYS R 168 " 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: 0.70 Conformation dependent library (CDL) restraints added in 255.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 37.6% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 4.055A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.536A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.415A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.827A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 328 through 351 removed outlier: 4.101A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.771A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.511A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 19 through 48 Processing helix chain 'R' and resid 49 through 52 Processing helix chain 'R' and resid 55 through 72 removed outlier: 3.839A pdb=" N ILE R 59 " --> pdb=" O PHE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 79 Processing helix chain 'R' and resid 90 through 124 removed outlier: 4.160A pdb=" N ARG R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 133 through 153 removed outlier: 3.756A pdb=" N VAL R 138 " --> pdb=" O ALA R 134 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 157 No H-bonds generated for 'chain 'R' and resid 155 through 157' Processing helix chain 'R' and resid 175 through 213 Processing helix chain 'R' and resid 214 through 216 No H-bonds generated for 'chain 'R' and resid 214 through 216' Processing helix chain 'R' and resid 316 through 342 Proline residue: R 334 - end of helix Processing helix chain 'R' and resid 350 through 370 removed outlier: 3.616A pdb=" N TRP R 360 " --> pdb=" O ALA R 356 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU R 361 " --> pdb=" O ASN R 357 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY R 363 " --> pdb=" O THR R 359 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS R 364 " --> pdb=" O TRP R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 388 Processing helix chain 'R' and resid 389 through 394 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.827A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.577A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.113A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.508A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.983A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.189A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.542A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.618A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.716A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 159 through 161 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.562A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.297A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1266 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: 1.08 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1412 1.29 - 1.42: 2409 1.42 - 1.55: 5131 1.55 - 1.68: 9 1.68 - 1.81: 82 Bond restraints: 9043 Sorted by residual: bond pdb=" C THR R 35 " pdb=" O THR R 35 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.16e-02 7.43e+03 4.11e+01 bond pdb=" C ASN B 313 " pdb=" O ASN B 313 " ideal model delta sigma weight residual 1.234 1.159 0.075 1.28e-02 6.10e+03 3.44e+01 bond pdb=" C ASP B 228 " pdb=" O ASP B 228 " ideal model delta sigma weight residual 1.234 1.177 0.057 1.21e-02 6.83e+03 2.25e+01 bond pdb=" C ARG R 176 " pdb=" O ARG R 176 " ideal model delta sigma weight residual 1.238 1.196 0.042 9.50e-03 1.11e+04 1.98e+01 bond pdb=" C ILE S 157 " pdb=" O ILE S 157 " ideal model delta sigma weight residual 1.236 1.193 0.044 9.90e-03 1.02e+04 1.93e+01 ... (remaining 9038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 11595 1.35 - 2.71: 490 2.71 - 4.06: 124 4.06 - 5.41: 27 5.41 - 6.76: 14 Bond angle restraints: 12250 Sorted by residual: angle pdb=" CA THR R 35 " pdb=" C THR R 35 " pdb=" O THR R 35 " ideal model delta sigma weight residual 120.90 114.94 5.96 1.03e+00 9.43e-01 3.35e+01 angle pdb=" N VAL R 78 " pdb=" CA VAL R 78 " pdb=" C VAL R 78 " ideal model delta sigma weight residual 110.72 105.40 5.32 1.01e+00 9.80e-01 2.78e+01 angle pdb=" CA THR R 35 " pdb=" C THR R 35 " pdb=" N VAL R 36 " ideal model delta sigma weight residual 117.02 123.00 -5.98 1.17e+00 7.31e-01 2.62e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 111.56 105.01 6.55 1.38e+00 5.25e-01 2.25e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" C ASP B 228 " ideal model delta sigma weight residual 110.24 116.34 -6.10 1.30e+00 5.92e-01 2.20e+01 ... (remaining 12245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4718 17.35 - 34.70: 468 34.70 - 52.05: 128 52.05 - 69.39: 33 69.39 - 86.74: 13 Dihedral angle restraints: 5360 sinusoidal: 2070 harmonic: 3290 Sorted by residual: dihedral pdb=" CA VAL R 78 " pdb=" C VAL R 78 " pdb=" N ASP R 79 " pdb=" CA ASP R 79 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1235 0.065 - 0.130: 145 0.130 - 0.195: 15 0.195 - 0.260: 4 0.260 - 0.325: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA THR R 35 " pdb=" N THR R 35 " pdb=" C THR R 35 " pdb=" CB THR R 35 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA ARG R 176 " pdb=" N ARG R 176 " pdb=" C ARG R 176 " pdb=" CB ARG R 176 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA TYR R 332 " pdb=" N TYR R 332 " pdb=" C TYR R 332 " pdb=" CB TYR R 332 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1397 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 312 " -0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ASP B 312 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP B 312 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN B 313 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 175 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C GLY R 175 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY R 175 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG R 176 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 247 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C ASP B 247 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP B 247 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA B 248 " -0.016 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 478 2.72 - 3.27: 9376 3.27 - 3.81: 14676 3.81 - 4.36: 18450 4.36 - 4.90: 32221 Nonbonded interactions: 75201 Sorted by model distance: nonbonded pdb=" O ASP R 79 " pdb=" OG1 THR R 80 " model vdw 2.181 3.040 nonbonded pdb=" O ASP B 163 " pdb=" CG2 THR B 164 " model vdw 2.269 3.460 nonbonded pdb=" OG1 THR B 164 " pdb=" O HIS B 183 " model vdw 2.280 3.040 nonbonded pdb=" O LYS G 32 " pdb=" OD1 ASP G 36 " model vdw 2.301 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.303 3.040 ... (remaining 75196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.670 Find NCS groups from input model: 0.030 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.260 ------------------------------------------------------------------------------- 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 0.075 9045 Z= 0.265 Angle : 0.707 6.765 12254 Z= 0.430 Chirality : 0.045 0.325 1400 Planarity : 0.004 0.052 1544 Dihedral : 15.965 86.742 3234 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.26 % Allowed : 20.15 % Favored : 78.59 % 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: -0.18 (0.25), residues: 1119 helix: 0.95 (0.29), residues: 370 sheet: -0.45 (0.29), residues: 290 loop : -0.67 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 22 TYR 0.041 0.002 TYR S 59 PHE 0.009 0.001 PHE R 152 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 83 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9043) covalent geometry : angle 0.70717 (12250) SS BOND : bond 0.00425 ( 2) SS BOND : angle 0.29384 ( 4) hydrogen bonds : bond 0.16498 ( 448) hydrogen bonds : angle 7.30456 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8275 (mt) cc_final: 0.7690 (tp) REVERT: B 124 TYR cc_start: 0.9060 (m-80) cc_final: 0.8703 (m-80) REVERT: B 188 MET cc_start: 0.8746 (mmm) cc_final: 0.8333 (mmm) REVERT: B 189 SER cc_start: 0.8703 (t) cc_final: 0.8263 (t) REVERT: B 217 MET cc_start: 0.8116 (tpp) cc_final: 0.7897 (tpt) REVERT: B 237 ASN cc_start: 0.8259 (t0) cc_final: 0.7993 (t0) REVERT: B 259 GLN cc_start: 0.7583 (pt0) cc_final: 0.7085 (pt0) REVERT: B 262 MET cc_start: 0.7694 (mtp) cc_final: 0.7410 (ttp) REVERT: G 62 ARG cc_start: 0.7203 (ttm110) cc_final: 0.6820 (ttm110) REVERT: R 81 TYR cc_start: 0.8313 (m-80) cc_final: 0.7855 (m-80) REVERT: R 170 PHE cc_start: 0.8046 (p90) cc_final: 0.7080 (p90) REVERT: R 171 ASP cc_start: 0.8440 (t0) cc_final: 0.7954 (t0) REVERT: S 3 GLN cc_start: 0.7756 (tt0) cc_final: 0.7261 (pt0) outliers start: 12 outliers final: 2 residues processed: 182 average time/residue: 0.6046 time to fit residues: 116.3281 Evaluate side-chains 149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 390 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 333 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS R 202 HIS ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 339 ASN S 171 ASN S 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.164868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117638 restraints weight = 12146.574| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.86 r_work: 0.3321 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9045 Z= 0.141 Angle : 0.594 7.966 12254 Z= 0.313 Chirality : 0.044 0.207 1400 Planarity : 0.004 0.037 1544 Dihedral : 5.764 49.899 1252 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 3.46 % Allowed : 19.41 % Favored : 77.12 % 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: 0.29 (0.25), residues: 1119 helix: 1.43 (0.27), residues: 379 sheet: -0.19 (0.29), residues: 284 loop : -0.51 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 94 TYR 0.014 0.001 TYR B 59 PHE 0.019 0.001 PHE B 253 TRP 0.013 0.001 TRP B 339 HIS 0.005 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9043) covalent geometry : angle 0.59434 (12250) SS BOND : bond 0.00351 ( 2) SS BOND : angle 0.55492 ( 4) hydrogen bonds : bond 0.04412 ( 448) hydrogen bonds : angle 4.99684 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8243 (m-30) cc_final: 0.8000 (m-30) REVERT: A 232 LEU cc_start: 0.8333 (mt) cc_final: 0.7801 (tp) REVERT: B 124 TYR cc_start: 0.8961 (m-80) cc_final: 0.8654 (m-80) REVERT: B 188 MET cc_start: 0.8674 (mmm) cc_final: 0.8334 (mmm) REVERT: B 189 SER cc_start: 0.8638 (t) cc_final: 0.8135 (t) REVERT: B 217 MET cc_start: 0.8301 (tpp) cc_final: 0.8019 (tpt) REVERT: B 259 GLN cc_start: 0.7592 (pt0) cc_final: 0.7003 (pt0) REVERT: B 270 ILE cc_start: 0.9131 (tt) cc_final: 0.8912 (pp) REVERT: G 36 ASP cc_start: 0.8268 (m-30) cc_final: 0.8043 (m-30) REVERT: G 52 THR cc_start: 0.7443 (t) cc_final: 0.7118 (p) REVERT: G 58 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8038 (mp0) REVERT: R 74 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8412 (tp-100) REVERT: R 170 PHE cc_start: 0.7882 (p90) cc_final: 0.7003 (p90) REVERT: R 171 ASP cc_start: 0.8335 (t0) cc_final: 0.7822 (t0) REVERT: S 3 GLN cc_start: 0.7499 (tt0) cc_final: 0.7136 (pt0) REVERT: S 20 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8250 (mt) REVERT: S 39 GLN cc_start: 0.8058 (tt0) cc_final: 0.7488 (tp40) REVERT: S 233 LEU cc_start: 0.8088 (tp) cc_final: 0.7728 (mt) REVERT: S 234 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7845 (mt-10) outliers start: 33 outliers final: 11 residues processed: 193 average time/residue: 0.5775 time to fit residues: 119.0970 Evaluate side-chains 159 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 154 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 0.1980 chunk 89 optimal weight: 0.0060 chunk 81 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN R 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.166395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119508 restraints weight = 12030.086| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.89 r_work: 0.3359 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9045 Z= 0.128 Angle : 0.574 8.369 12254 Z= 0.296 Chirality : 0.043 0.209 1400 Planarity : 0.003 0.030 1544 Dihedral : 5.441 47.081 1252 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 3.78 % Allowed : 20.57 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.36 (0.25), residues: 1119 helix: 1.46 (0.27), residues: 380 sheet: -0.11 (0.29), residues: 282 loop : -0.48 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.022 0.001 TYR B 59 PHE 0.016 0.001 PHE B 253 TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9043) covalent geometry : angle 0.57351 (12250) SS BOND : bond 0.00304 ( 2) SS BOND : angle 0.57892 ( 4) hydrogen bonds : bond 0.03961 ( 448) hydrogen bonds : angle 4.76617 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8197 (m-30) cc_final: 0.7945 (m-30) REVERT: A 232 LEU cc_start: 0.8367 (mt) cc_final: 0.7846 (tp) REVERT: A 312 LYS cc_start: 0.8310 (mmtm) cc_final: 0.7977 (mmmt) REVERT: A 318 GLU cc_start: 0.7974 (tt0) cc_final: 0.7380 (pm20) REVERT: B 124 TYR cc_start: 0.8926 (m-80) cc_final: 0.8565 (m-80) REVERT: B 188 MET cc_start: 0.8671 (mmm) cc_final: 0.8290 (mmm) REVERT: B 189 SER cc_start: 0.8572 (t) cc_final: 0.8074 (t) REVERT: B 217 MET cc_start: 0.8249 (tpp) cc_final: 0.7972 (ppp) REVERT: B 259 GLN cc_start: 0.7571 (pt0) cc_final: 0.6801 (pt0) REVERT: G 36 ASP cc_start: 0.8323 (m-30) cc_final: 0.8060 (m-30) REVERT: G 44 HIS cc_start: 0.7299 (m90) cc_final: 0.7078 (m90) REVERT: G 52 THR cc_start: 0.7507 (t) cc_final: 0.7279 (p) REVERT: G 58 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8001 (mp0) REVERT: R 74 GLN cc_start: 0.8710 (tp-100) cc_final: 0.8369 (tp-100) REVERT: R 81 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: R 170 PHE cc_start: 0.7826 (p90) cc_final: 0.6917 (p90) REVERT: R 171 ASP cc_start: 0.8280 (t0) cc_final: 0.7755 (t0) REVERT: R 357 ASN cc_start: 0.9115 (m-40) cc_final: 0.8888 (m110) REVERT: S 3 GLN cc_start: 0.7483 (tt0) cc_final: 0.7065 (pt0) REVERT: S 39 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7359 (tp40) REVERT: S 83 MET cc_start: 0.7846 (mtm) cc_final: 0.7548 (mpp) REVERT: S 179 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7184 (mm-40) REVERT: S 233 LEU cc_start: 0.8087 (tp) cc_final: 0.7723 (mt) outliers start: 36 outliers final: 10 residues processed: 188 average time/residue: 0.5582 time to fit residues: 112.4714 Evaluate side-chains 158 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 179 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 239 ASN ** R 210 GLN ** 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 = 0.3965 r_free = 0.3965 target = 0.161208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113054 restraints weight = 12232.896| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.94 r_work: 0.3279 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9045 Z= 0.216 Angle : 0.612 7.619 12254 Z= 0.321 Chirality : 0.045 0.251 1400 Planarity : 0.004 0.031 1544 Dihedral : 5.787 54.895 1252 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 3.88 % Allowed : 22.04 % Favored : 74.08 % 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: 0.21 (0.25), residues: 1119 helix: 1.36 (0.27), residues: 381 sheet: -0.24 (0.28), residues: 296 loop : -0.57 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 32 TYR 0.025 0.002 TYR B 59 PHE 0.017 0.002 PHE B 253 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 9043) covalent geometry : angle 0.61174 (12250) SS BOND : bond 0.00424 ( 2) SS BOND : angle 0.71956 ( 4) hydrogen bonds : bond 0.04320 ( 448) hydrogen bonds : angle 4.89963 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8249 (m-30) cc_final: 0.7974 (m-30) REVERT: A 232 LEU cc_start: 0.8440 (mt) cc_final: 0.7915 (tp) REVERT: B 188 MET cc_start: 0.8678 (mmm) cc_final: 0.8378 (mmm) REVERT: B 189 SER cc_start: 0.8561 (t) cc_final: 0.8003 (t) REVERT: B 259 GLN cc_start: 0.7508 (pt0) cc_final: 0.6798 (pt0) REVERT: G 36 ASP cc_start: 0.8278 (m-30) cc_final: 0.7957 (m-30) REVERT: G 58 GLU cc_start: 0.8969 (mm-30) cc_final: 0.7992 (mp0) REVERT: R 74 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8426 (tp-100) REVERT: R 87 ARG cc_start: 0.6206 (OUTLIER) cc_final: 0.5254 (ttt-90) REVERT: R 170 PHE cc_start: 0.7949 (p90) cc_final: 0.6986 (p90) REVERT: R 171 ASP cc_start: 0.8325 (t0) cc_final: 0.7779 (t0) REVERT: R 206 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7018 (ttmt) REVERT: R 357 ASN cc_start: 0.9215 (m-40) cc_final: 0.8958 (m110) REVERT: S 39 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7413 (tp40) REVERT: S 179 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7323 (mm-40) REVERT: S 233 LEU cc_start: 0.8045 (tp) cc_final: 0.7677 (mt) outliers start: 37 outliers final: 17 residues processed: 170 average time/residue: 0.6010 time to fit residues: 109.0137 Evaluate side-chains 164 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 204 GLN ** R 210 GLN ** 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 = 0.3967 r_free = 0.3967 target = 0.161498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113251 restraints weight = 12235.047| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.95 r_work: 0.3286 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9045 Z= 0.187 Angle : 0.585 7.106 12254 Z= 0.307 Chirality : 0.044 0.242 1400 Planarity : 0.004 0.031 1544 Dihedral : 5.621 58.222 1252 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 3.88 % Allowed : 22.77 % Favored : 73.35 % 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: 0.23 (0.25), residues: 1119 helix: 1.44 (0.27), residues: 382 sheet: -0.28 (0.28), residues: 296 loop : -0.59 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 32 TYR 0.021 0.002 TYR B 59 PHE 0.016 0.002 PHE B 253 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9043) covalent geometry : angle 0.58529 (12250) SS BOND : bond 0.00387 ( 2) SS BOND : angle 0.66947 ( 4) hydrogen bonds : bond 0.04078 ( 448) hydrogen bonds : angle 4.83426 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8251 (m-30) cc_final: 0.7952 (m-30) REVERT: A 232 LEU cc_start: 0.8509 (mt) cc_final: 0.8024 (tp) REVERT: A 330 LYS cc_start: 0.8251 (mmtp) cc_final: 0.7703 (mppt) REVERT: B 44 GLN cc_start: 0.9004 (tt0) cc_final: 0.8753 (tp40) REVERT: B 188 MET cc_start: 0.8645 (mmm) cc_final: 0.8327 (mmm) REVERT: B 189 SER cc_start: 0.8632 (t) cc_final: 0.8087 (t) REVERT: B 228 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6524 (p0) REVERT: B 259 GLN cc_start: 0.7541 (pt0) cc_final: 0.6865 (pt0) REVERT: G 36 ASP cc_start: 0.8273 (m-30) cc_final: 0.7941 (m-30) REVERT: G 58 GLU cc_start: 0.8921 (mm-30) cc_final: 0.7962 (mp0) REVERT: R 74 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8401 (tp-100) REVERT: R 151 SER cc_start: 0.9233 (m) cc_final: 0.8821 (p) REVERT: R 170 PHE cc_start: 0.7921 (p90) cc_final: 0.6986 (p90) REVERT: R 171 ASP cc_start: 0.8312 (t0) cc_final: 0.7730 (t0) REVERT: R 357 ASN cc_start: 0.9206 (m-40) cc_final: 0.8992 (m110) REVERT: S 39 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7373 (tp40) REVERT: S 87 ARG cc_start: 0.5446 (OUTLIER) cc_final: 0.5008 (ptt90) REVERT: S 179 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7260 (mm-40) REVERT: S 233 LEU cc_start: 0.8069 (tp) cc_final: 0.7738 (mt) outliers start: 37 outliers final: 21 residues processed: 180 average time/residue: 0.5737 time to fit residues: 109.9931 Evaluate side-chains 167 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 390 ARG Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 230 ASN ** R 210 GLN ** 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 = 0.3972 r_free = 0.3972 target = 0.162011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113813 restraints weight = 12107.531| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.94 r_work: 0.3290 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9045 Z= 0.163 Angle : 0.577 7.693 12254 Z= 0.302 Chirality : 0.043 0.244 1400 Planarity : 0.003 0.037 1544 Dihedral : 5.412 54.713 1252 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 3.99 % Allowed : 23.71 % Favored : 72.30 % 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: 0.28 (0.25), residues: 1119 helix: 1.50 (0.27), residues: 383 sheet: -0.22 (0.28), residues: 294 loop : -0.61 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 32 TYR 0.016 0.002 TYR B 59 PHE 0.016 0.001 PHE B 253 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9043) covalent geometry : angle 0.57733 (12250) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.64491 ( 4) hydrogen bonds : bond 0.03943 ( 448) hydrogen bonds : angle 4.80403 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8235 (m-30) cc_final: 0.7923 (m-30) REVERT: A 232 LEU cc_start: 0.8544 (mt) cc_final: 0.8080 (tp) REVERT: A 312 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8021 (mmmt) REVERT: A 330 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7658 (mppt) REVERT: B 44 GLN cc_start: 0.9011 (tt0) cc_final: 0.8763 (tp40) REVERT: B 175 GLN cc_start: 0.8193 (pt0) cc_final: 0.7475 (pp30) REVERT: B 188 MET cc_start: 0.8631 (mmm) cc_final: 0.8324 (mmm) REVERT: B 189 SER cc_start: 0.8612 (t) cc_final: 0.8076 (t) REVERT: B 228 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6432 (p0) REVERT: B 259 GLN cc_start: 0.7475 (pt0) cc_final: 0.6806 (pt0) REVERT: G 36 ASP cc_start: 0.8302 (m-30) cc_final: 0.7972 (m-30) REVERT: G 58 GLU cc_start: 0.8916 (mm-30) cc_final: 0.7977 (mp0) REVERT: G 62 ARG cc_start: 0.7128 (ttm110) cc_final: 0.6898 (mtm-85) REVERT: R 74 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8465 (tp-100) REVERT: R 151 SER cc_start: 0.9183 (m) cc_final: 0.8805 (p) REVERT: R 170 PHE cc_start: 0.7891 (p90) cc_final: 0.6968 (p90) REVERT: R 206 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6984 (ttmt) REVERT: R 357 ASN cc_start: 0.9214 (m-40) cc_final: 0.8983 (m110) REVERT: S 39 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7302 (tp40) REVERT: S 87 ARG cc_start: 0.5382 (OUTLIER) cc_final: 0.4949 (ptt90) REVERT: S 179 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7303 (mm-40) REVERT: S 223 ASP cc_start: 0.5999 (m-30) cc_final: 0.5766 (m-30) REVERT: S 227 TYR cc_start: 0.7457 (m-10) cc_final: 0.6692 (m-10) REVERT: S 233 LEU cc_start: 0.8075 (tp) cc_final: 0.7758 (mt) outliers start: 38 outliers final: 20 residues processed: 177 average time/residue: 0.5824 time to fit residues: 110.0042 Evaluate side-chains 167 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.164547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117205 restraints weight = 12205.039| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.93 r_work: 0.3337 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9045 Z= 0.115 Angle : 0.550 6.614 12254 Z= 0.287 Chirality : 0.042 0.217 1400 Planarity : 0.003 0.045 1544 Dihedral : 4.837 51.756 1248 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 3.67 % Allowed : 24.55 % Favored : 71.77 % 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: 0.37 (0.25), residues: 1119 helix: 1.63 (0.27), residues: 383 sheet: -0.25 (0.28), residues: 292 loop : -0.54 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 32 TYR 0.017 0.001 TYR B 124 PHE 0.014 0.001 PHE B 253 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9043) covalent geometry : angle 0.54970 (12250) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.56059 ( 4) hydrogen bonds : bond 0.03608 ( 448) hydrogen bonds : angle 4.67114 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8171 (m-30) cc_final: 0.7865 (m-30) REVERT: A 232 LEU cc_start: 0.8529 (mt) cc_final: 0.8095 (tp) REVERT: A 249 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8216 (tt) REVERT: A 312 LYS cc_start: 0.8295 (mmtm) cc_final: 0.8009 (mmmt) REVERT: A 330 LYS cc_start: 0.8162 (mmtp) cc_final: 0.7646 (mppt) REVERT: B 44 GLN cc_start: 0.8992 (tt0) cc_final: 0.8728 (tp40) REVERT: B 175 GLN cc_start: 0.8183 (pt0) cc_final: 0.7477 (pp30) REVERT: B 188 MET cc_start: 0.8586 (mmm) cc_final: 0.8230 (mmm) REVERT: B 189 SER cc_start: 0.8517 (t) cc_final: 0.7981 (t) REVERT: B 228 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6308 (p0) REVERT: B 259 GLN cc_start: 0.7474 (pt0) cc_final: 0.6778 (pt0) REVERT: B 292 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: G 36 ASP cc_start: 0.8292 (m-30) cc_final: 0.7962 (m-30) REVERT: G 58 GLU cc_start: 0.8901 (mm-30) cc_final: 0.7930 (mp0) REVERT: G 62 ARG cc_start: 0.7176 (ttm110) cc_final: 0.6953 (mtm-85) REVERT: R 52 ARG cc_start: 0.8481 (mtp180) cc_final: 0.8208 (mtp180) REVERT: R 74 GLN cc_start: 0.8830 (tp-100) cc_final: 0.7971 (tp-100) REVERT: R 151 SER cc_start: 0.9165 (m) cc_final: 0.8661 (p) REVERT: R 170 PHE cc_start: 0.7780 (p90) cc_final: 0.6945 (p90) REVERT: R 178 TYR cc_start: 0.7514 (t80) cc_final: 0.7144 (t80) REVERT: R 206 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6370 (ttmt) REVERT: R 210 GLN cc_start: 0.7686 (mt0) cc_final: 0.7032 (mp10) REVERT: R 373 MET cc_start: 0.7958 (mmm) cc_final: 0.7708 (mtt) REVERT: S 39 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7080 (tp-100) REVERT: S 87 ARG cc_start: 0.5389 (OUTLIER) cc_final: 0.4956 (ptt90) REVERT: S 179 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7258 (mm-40) REVERT: S 223 ASP cc_start: 0.5919 (m-30) cc_final: 0.5585 (m-30) REVERT: S 227 TYR cc_start: 0.7464 (m-10) cc_final: 0.6754 (m-10) outliers start: 35 outliers final: 18 residues processed: 194 average time/residue: 0.5096 time to fit residues: 105.9145 Evaluate side-chains 166 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 232 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 101 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.166229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119041 restraints weight = 12071.439| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.88 r_work: 0.3368 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9045 Z= 0.113 Angle : 0.561 8.999 12254 Z= 0.290 Chirality : 0.042 0.223 1400 Planarity : 0.003 0.061 1544 Dihedral : 4.596 48.557 1248 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 3.36 % Allowed : 26.34 % Favored : 70.30 % 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: 0.37 (0.25), residues: 1119 helix: 1.64 (0.27), residues: 382 sheet: -0.23 (0.29), residues: 291 loop : -0.56 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 32 TYR 0.017 0.001 TYR R 119 PHE 0.014 0.001 PHE B 253 TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9043) covalent geometry : angle 0.56101 (12250) SS BOND : bond 0.00253 ( 2) SS BOND : angle 0.56751 ( 4) hydrogen bonds : bond 0.03549 ( 448) hydrogen bonds : angle 4.64568 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8275 (m-30) cc_final: 0.7947 (m-30) REVERT: A 232 LEU cc_start: 0.8545 (mt) cc_final: 0.8121 (tp) REVERT: A 249 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8304 (tt) REVERT: A 312 LYS cc_start: 0.8328 (mmtm) cc_final: 0.8052 (mmmt) REVERT: A 318 GLU cc_start: 0.7932 (tt0) cc_final: 0.7448 (pm20) REVERT: A 330 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7640 (mppt) REVERT: B 44 GLN cc_start: 0.8970 (tt0) cc_final: 0.8727 (tp40) REVERT: B 175 GLN cc_start: 0.8241 (pt0) cc_final: 0.7557 (pp30) REVERT: B 188 MET cc_start: 0.8626 (mmm) cc_final: 0.8327 (mmm) REVERT: B 228 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6449 (p0) REVERT: B 259 GLN cc_start: 0.7586 (pt0) cc_final: 0.6963 (pt0) REVERT: B 292 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: G 36 ASP cc_start: 0.8309 (m-30) cc_final: 0.7991 (m-30) REVERT: G 44 HIS cc_start: 0.7503 (m90) cc_final: 0.7167 (m-70) REVERT: G 58 GLU cc_start: 0.8876 (mm-30) cc_final: 0.7990 (mp0) REVERT: G 62 ARG cc_start: 0.7322 (ttm110) cc_final: 0.6812 (tpp-160) REVERT: R 74 GLN cc_start: 0.8739 (tp-100) cc_final: 0.7951 (tp-100) REVERT: R 106 VAL cc_start: 0.8303 (t) cc_final: 0.8058 (m) REVERT: R 151 SER cc_start: 0.9116 (m) cc_final: 0.8634 (p) REVERT: R 170 PHE cc_start: 0.7841 (p90) cc_final: 0.6988 (p90) REVERT: R 178 TYR cc_start: 0.7586 (t80) cc_final: 0.7184 (t80) REVERT: R 326 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7444 (tm) REVERT: S 39 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7201 (tp-100) REVERT: S 87 ARG cc_start: 0.5471 (OUTLIER) cc_final: 0.5045 (ptt90) REVERT: S 179 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7380 (mm-40) REVERT: S 223 ASP cc_start: 0.5764 (m-30) cc_final: 0.5549 (m-30) REVERT: S 227 TYR cc_start: 0.7462 (m-10) cc_final: 0.6751 (m-10) outliers start: 32 outliers final: 16 residues processed: 188 average time/residue: 0.5658 time to fit residues: 113.6108 Evaluate side-chains 169 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 101 optimal weight: 30.0000 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.162240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114429 restraints weight = 12102.380| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.92 r_work: 0.3308 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9045 Z= 0.186 Angle : 0.619 8.299 12254 Z= 0.320 Chirality : 0.044 0.253 1400 Planarity : 0.004 0.070 1544 Dihedral : 5.022 46.666 1248 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 3.25 % Allowed : 26.55 % Favored : 70.20 % 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: 0.26 (0.25), residues: 1119 helix: 1.46 (0.27), residues: 384 sheet: -0.31 (0.28), residues: 290 loop : -0.52 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 32 TYR 0.033 0.002 TYR B 59 PHE 0.017 0.002 PHE B 253 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9043) covalent geometry : angle 0.61899 (12250) SS BOND : bond 0.00377 ( 2) SS BOND : angle 0.70437 ( 4) hydrogen bonds : bond 0.03931 ( 448) hydrogen bonds : angle 4.77701 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8588 (mt) cc_final: 0.8143 (tp) REVERT: A 312 LYS cc_start: 0.8345 (mmtm) cc_final: 0.8057 (mmmt) REVERT: A 330 LYS cc_start: 0.8180 (mmtp) cc_final: 0.7581 (mppt) REVERT: B 44 GLN cc_start: 0.8968 (tt0) cc_final: 0.8724 (tp40) REVERT: B 175 GLN cc_start: 0.8237 (pt0) cc_final: 0.7533 (pp30) REVERT: B 188 MET cc_start: 0.8622 (mmm) cc_final: 0.8347 (mmm) REVERT: B 189 SER cc_start: 0.8603 (t) cc_final: 0.8019 (t) REVERT: B 228 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6382 (p0) REVERT: B 259 GLN cc_start: 0.7522 (pt0) cc_final: 0.6883 (pt0) REVERT: B 292 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: G 36 ASP cc_start: 0.8237 (m-30) cc_final: 0.7910 (m-30) REVERT: G 58 GLU cc_start: 0.8896 (mm-30) cc_final: 0.7949 (mp0) REVERT: G 62 ARG cc_start: 0.7292 (ttm110) cc_final: 0.7070 (mtm-85) REVERT: R 52 ARG cc_start: 0.8430 (mtp180) cc_final: 0.7965 (mpp80) REVERT: R 74 GLN cc_start: 0.8787 (tp-100) cc_final: 0.7912 (tp-100) REVERT: R 151 SER cc_start: 0.9162 (m) cc_final: 0.8816 (p) REVERT: R 170 PHE cc_start: 0.7908 (p90) cc_final: 0.6920 (p90) REVERT: R 210 GLN cc_start: 0.7739 (mt0) cc_final: 0.7116 (mp10) REVERT: S 39 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7170 (tp-100) REVERT: S 87 ARG cc_start: 0.5277 (OUTLIER) cc_final: 0.4908 (ptt90) REVERT: S 179 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7308 (mm-40) REVERT: S 223 ASP cc_start: 0.5975 (m-30) cc_final: 0.5710 (m-30) REVERT: S 227 TYR cc_start: 0.7479 (m-10) cc_final: 0.6744 (m-10) outliers start: 31 outliers final: 17 residues processed: 176 average time/residue: 0.5629 time to fit residues: 105.8502 Evaluate side-chains 166 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN R 204 GLN ** R 210 GLN ** 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 = 0.3985 r_free = 0.3985 target = 0.163418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.115716 restraints weight = 12065.733| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.92 r_work: 0.3329 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9045 Z= 0.149 Angle : 0.608 11.782 12254 Z= 0.310 Chirality : 0.044 0.235 1400 Planarity : 0.004 0.077 1544 Dihedral : 4.920 44.707 1248 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 2.83 % Allowed : 27.18 % Favored : 69.99 % 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: 0.22 (0.25), residues: 1119 helix: 1.39 (0.27), residues: 384 sheet: -0.33 (0.29), residues: 292 loop : -0.51 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 32 TYR 0.034 0.002 TYR B 59 PHE 0.016 0.001 PHE B 253 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9043) covalent geometry : angle 0.60797 (12250) SS BOND : bond 0.00317 ( 2) SS BOND : angle 0.60852 ( 4) hydrogen bonds : bond 0.03775 ( 448) hydrogen bonds : angle 4.75311 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8581 (mt) cc_final: 0.8145 (tp) REVERT: A 312 LYS cc_start: 0.8342 (mmtm) cc_final: 0.8045 (mmmt) REVERT: A 330 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7615 (mppt) REVERT: B 44 GLN cc_start: 0.8965 (tt0) cc_final: 0.8718 (tp40) REVERT: B 175 GLN cc_start: 0.8224 (pt0) cc_final: 0.7509 (pp30) REVERT: B 188 MET cc_start: 0.8623 (mmm) cc_final: 0.8364 (mmm) REVERT: B 189 SER cc_start: 0.8623 (t) cc_final: 0.8047 (t) REVERT: B 228 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6302 (p0) REVERT: B 259 GLN cc_start: 0.7497 (pt0) cc_final: 0.6814 (pt0) REVERT: B 292 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: G 36 ASP cc_start: 0.8236 (m-30) cc_final: 0.7904 (m-30) REVERT: G 58 GLU cc_start: 0.8878 (mm-30) cc_final: 0.7930 (mp0) REVERT: G 62 ARG cc_start: 0.7277 (ttm110) cc_final: 0.7069 (mtm-85) REVERT: R 52 ARG cc_start: 0.8427 (mtp180) cc_final: 0.7950 (mpp80) REVERT: R 74 GLN cc_start: 0.8773 (tp-100) cc_final: 0.7914 (tp-100) REVERT: R 151 SER cc_start: 0.9137 (m) cc_final: 0.8802 (p) REVERT: R 170 PHE cc_start: 0.7877 (p90) cc_final: 0.6963 (p90) REVERT: R 210 GLN cc_start: 0.7767 (mt0) cc_final: 0.7177 (mp10) REVERT: R 353 MET cc_start: 0.7713 (mmm) cc_final: 0.7493 (mmt) REVERT: S 39 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7196 (tp-100) REVERT: S 87 ARG cc_start: 0.5347 (OUTLIER) cc_final: 0.4992 (ptt90) REVERT: S 179 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7292 (mm-40) REVERT: S 223 ASP cc_start: 0.5932 (m-30) cc_final: 0.5662 (m-30) REVERT: S 227 TYR cc_start: 0.7501 (m-10) cc_final: 0.6771 (m-10) outliers start: 27 outliers final: 16 residues processed: 171 average time/residue: 0.5653 time to fit residues: 103.2834 Evaluate side-chains 168 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 395 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.0570 chunk 73 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.165183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117779 restraints weight = 11954.709| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.88 r_work: 0.3343 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9045 Z= 0.126 Angle : 0.601 11.402 12254 Z= 0.305 Chirality : 0.043 0.210 1400 Planarity : 0.004 0.079 1544 Dihedral : 4.758 43.928 1248 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.51 % Rotamer: Outliers : 2.73 % Allowed : 27.18 % Favored : 70.09 % 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: 0.27 (0.25), residues: 1119 helix: 1.41 (0.27), residues: 383 sheet: -0.23 (0.29), residues: 281 loop : -0.51 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 32 TYR 0.019 0.001 TYR B 59 PHE 0.017 0.001 PHE A 274 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9043) covalent geometry : angle 0.60135 (12250) SS BOND : bond 0.00274 ( 2) SS BOND : angle 0.57148 ( 4) hydrogen bonds : bond 0.03624 ( 448) hydrogen bonds : angle 4.66174 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3700.02 seconds wall clock time: 64 minutes 3.22 seconds (3843.22 seconds total)