Starting phenix.real_space_refine on Thu Mar 13 09:55:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j18_35913/03_2025/8j18_35913.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j18_35913/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j18_35913/03_2025/8j18_35913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j18_35913/03_2025/8j18_35913.map" model { file = "/net/cci-nas-00/data/ceres_data/8j18_35913/03_2025/8j18_35913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j18_35913/03_2025/8j18_35913.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.51, per 1000 atoms: 0.62 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.13 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: 2.52 Time building geometry restraints manager: 2.86 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.750 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- 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 9043 Z= 0.274 Angle : 0.707 6.765 12250 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 : 6.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 83 PHE 0.009 0.001 PHE R 152 TYR 0.041 0.002 TYR S 59 ARG 0.007 0.001 ARG B 22 *********************** 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 : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8275 (mt) cc_final: 0.7683 (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: 0.8331 (mmm) REVERT: B 189 SER cc_start: 0.8703 (t) cc_final: 0.8260 (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: 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: 0.7856 (m-80) REVERT: R 170 PHE cc_start: 0.8046 (p90) cc_final: 0.7081 (p90) REVERT: R 171 ASP cc_start: 0.8440 (t0) cc_final: 0.7953 (t0) REVERT: S 3 GLN cc_start: 0.7756 (tt0) cc_final: 0.7260 (pt0) REVERT: S 218 ARG cc_start: 0.6257 (ptp-170) cc_final: 0.6011 (ptp90) outliers start: 12 outliers final: 2 residues processed: 182 average time/residue: 1.3496 time to fit residues: 260.7938 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 : 0.998 ------------------------------------------------------------------------------- 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 93 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** S 171 ASN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.163197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.115887 restraints weight = 12095.441| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.85 r_work: 0.3301 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9043 Z= 0.253 Angle : 0.615 8.236 12250 Z= 0.324 Chirality : 0.045 0.210 1400 Planarity : 0.004 0.035 1544 Dihedral : 5.925 55.375 1252 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 3.57 % Allowed : 19.73 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1119 helix: 1.37 (0.27), residues: 379 sheet: -0.26 (0.29), residues: 286 loop : -0.57 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.005 0.001 HIS R 393 PHE 0.020 0.002 PHE B 253 TYR 0.016 0.002 TYR B 59 ARG 0.007 0.001 ARG R 94 *********************** 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 198 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8328 (mt) cc_final: 0.7793 (tp) REVERT: B 188 MET cc_start: 0.8673 (mmm) cc_final: 0.8304 (mmm) REVERT: B 189 SER cc_start: 0.8671 (t) cc_final: 0.8160 (t) REVERT: B 217 MET cc_start: 0.8286 (tpp) cc_final: 0.8005 (tpt) REVERT: B 259 GLN cc_start: 0.7539 (pt0) cc_final: 0.6975 (pt0) REVERT: B 270 ILE cc_start: 0.9149 (tt) cc_final: 0.8908 (pp) REVERT: G 36 ASP cc_start: 0.8271 (m-30) cc_final: 0.8038 (m-30) REVERT: G 52 THR cc_start: 0.7476 (t) cc_final: 0.7133 (p) REVERT: G 58 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8020 (mp0) REVERT: G 62 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6944 (ttm110) REVERT: R 9 PHE cc_start: 0.7364 (m-80) cc_final: 0.7144 (m-10) REVERT: R 74 GLN cc_start: 0.8799 (tp-100) cc_final: 0.8473 (tp-100) REVERT: R 170 PHE cc_start: 0.7918 (p90) cc_final: 0.7024 (p90) REVERT: R 171 ASP cc_start: 0.8355 (t0) cc_final: 0.7832 (t0) REVERT: R 327 CYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7813 (t) REVERT: S 3 GLN cc_start: 0.7522 (tt0) cc_final: 0.7133 (pt0) REVERT: S 20 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8272 (mt) REVERT: S 39 GLN cc_start: 0.8087 (tt0) cc_final: 0.7498 (tp40) REVERT: S 233 LEU cc_start: 0.8091 (tp) cc_final: 0.7720 (mt) REVERT: S 234 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7866 (mt-10) outliers start: 34 outliers final: 12 residues processed: 190 average time/residue: 1.1479 time to fit residues: 233.3646 Evaluate side-chains 159 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 262 MET 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 68 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 365 ILE Chi-restraints excluded: chain R residue 390 ARG 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 104 optimal weight: 0.0170 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 101 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 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 = 0.4028 r_free = 0.4028 target = 0.167176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120378 restraints weight = 12055.767| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.93 r_work: 0.3374 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9043 Z= 0.155 Angle : 0.560 7.629 12250 Z= 0.290 Chirality : 0.042 0.205 1400 Planarity : 0.003 0.030 1544 Dihedral : 5.289 47.371 1252 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 3.78 % Allowed : 20.15 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1119 helix: 1.50 (0.27), residues: 381 sheet: -0.15 (0.29), residues: 284 loop : -0.47 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS R 393 PHE 0.016 0.001 PHE B 253 TYR 0.017 0.001 TYR B 59 ARG 0.005 0.000 ARG A 32 *********************** 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 210 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8359 (mt) cc_final: 0.7838 (tp) REVERT: A 312 LYS cc_start: 0.8323 (mmtm) cc_final: 0.7983 (mmmt) REVERT: A 318 GLU cc_start: 0.7905 (tt0) cc_final: 0.7311 (pm20) REVERT: B 42 ARG cc_start: 0.7459 (tpp-160) cc_final: 0.7227 (tpp-160) REVERT: B 188 MET cc_start: 0.8614 (mmm) cc_final: 0.8260 (mmm) REVERT: B 189 SER cc_start: 0.8465 (t) cc_final: 0.7958 (t) REVERT: B 217 MET cc_start: 0.8221 (tpp) cc_final: 0.7939 (tpt) REVERT: B 259 GLN cc_start: 0.7500 (pt0) cc_final: 0.6851 (pt0) REVERT: G 36 ASP cc_start: 0.8313 (m-30) cc_final: 0.8054 (m-30) REVERT: G 44 HIS cc_start: 0.7172 (m90) cc_final: 0.6935 (m90) REVERT: G 52 THR cc_start: 0.7425 (t) cc_final: 0.7201 (p) REVERT: R 9 PHE cc_start: 0.7318 (m-80) cc_final: 0.7034 (m-10) REVERT: R 74 GLN cc_start: 0.8728 (tp-100) cc_final: 0.8418 (tp-100) REVERT: R 170 PHE cc_start: 0.7775 (p90) cc_final: 0.6996 (p90) REVERT: R 171 ASP cc_start: 0.8209 (t0) cc_final: 0.7706 (t0) REVERT: R 357 ASN cc_start: 0.9078 (m-40) cc_final: 0.8855 (m110) REVERT: S 3 GLN cc_start: 0.7441 (tt0) cc_final: 0.7039 (pt0) REVERT: S 39 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7388 (tp40) REVERT: S 59 TYR cc_start: 0.6834 (m-10) cc_final: 0.6448 (m-80) REVERT: S 83 MET cc_start: 0.7782 (mtm) cc_final: 0.7511 (mpp) REVERT: S 179 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7179 (mm-40) REVERT: S 233 LEU cc_start: 0.7993 (tp) cc_final: 0.7622 (mt) outliers start: 36 outliers final: 11 residues processed: 195 average time/residue: 1.1216 time to fit residues: 234.3313 Evaluate side-chains 157 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET 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 365 ILE Chi-restraints excluded: chain R residue 390 ARG 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 83 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.162458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114880 restraints weight = 12087.169| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.92 r_work: 0.3306 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9043 Z= 0.281 Angle : 0.587 7.732 12250 Z= 0.307 Chirality : 0.044 0.240 1400 Planarity : 0.004 0.030 1544 Dihedral : 5.441 53.739 1252 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 3.36 % Allowed : 23.08 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1119 helix: 1.47 (0.27), residues: 381 sheet: -0.25 (0.28), residues: 298 loop : -0.51 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 PHE 0.017 0.002 PHE B 253 TYR 0.021 0.002 TYR B 59 ARG 0.007 0.001 ARG A 32 *********************** 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 187 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.019 Fit side-chains REVERT: A 205 ARG cc_start: 0.7801 (mmt-90) cc_final: 0.7597 (mmt-90) REVERT: A 232 LEU cc_start: 0.8422 (mt) cc_final: 0.7902 (tp) REVERT: A 312 LYS cc_start: 0.8353 (mmtm) cc_final: 0.8016 (mmmt) REVERT: B 42 ARG cc_start: 0.7524 (tpp-160) cc_final: 0.7248 (tpp-160) REVERT: B 188 MET cc_start: 0.8661 (mmm) cc_final: 0.8335 (mmm) REVERT: B 189 SER cc_start: 0.8614 (t) cc_final: 0.8055 (t) REVERT: B 259 GLN cc_start: 0.7561 (pt0) cc_final: 0.7128 (pt0) REVERT: G 36 ASP cc_start: 0.8302 (m-30) cc_final: 0.8002 (m-30) REVERT: G 44 HIS cc_start: 0.7438 (m90) cc_final: 0.7108 (m-70) REVERT: G 58 GLU cc_start: 0.8942 (mm-30) cc_final: 0.7974 (mp0) REVERT: R 9 PHE cc_start: 0.7335 (m-80) cc_final: 0.7078 (m-10) REVERT: R 74 GLN cc_start: 0.8783 (tp-100) cc_final: 0.8516 (tp-100) REVERT: R 170 PHE cc_start: 0.7883 (p90) cc_final: 0.6932 (p90) REVERT: R 171 ASP cc_start: 0.8296 (t0) cc_final: 0.7763 (t0) REVERT: R 357 ASN cc_start: 0.9192 (m-40) cc_final: 0.8965 (m110) REVERT: S 39 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7411 (tp40) REVERT: S 179 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7255 (mm-40) REVERT: S 233 LEU cc_start: 0.8026 (tp) cc_final: 0.7679 (mt) outliers start: 32 outliers final: 14 residues processed: 173 average time/residue: 1.1354 time to fit residues: 210.1109 Evaluate side-chains 161 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET 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 A residue 332 VAL 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 138 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 179 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN 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 = 0.4006 r_free = 0.4006 target = 0.165262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118121 restraints weight = 12045.451| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.91 r_work: 0.3357 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9043 Z= 0.168 Angle : 0.538 7.045 12250 Z= 0.282 Chirality : 0.042 0.223 1400 Planarity : 0.003 0.031 1544 Dihedral : 4.867 59.017 1248 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 3.25 % Allowed : 23.50 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1119 helix: 1.56 (0.27), residues: 383 sheet: -0.19 (0.28), residues: 297 loop : -0.50 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 PHE 0.014 0.001 PHE B 253 TYR 0.018 0.001 TYR B 59 ARG 0.010 0.000 ARG A 32 *********************** 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: 31 poor density : 159 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8501 (mt) cc_final: 0.7999 (tp) REVERT: A 312 LYS cc_start: 0.8353 (mmtm) cc_final: 0.8028 (mmmt) REVERT: A 318 GLU cc_start: 0.7903 (tt0) cc_final: 0.7315 (pm20) REVERT: A 330 LYS cc_start: 0.8187 (mmtp) cc_final: 0.7653 (mppt) REVERT: B 44 GLN cc_start: 0.9020 (tt0) cc_final: 0.8755 (tp40) REVERT: B 188 MET cc_start: 0.8604 (mmm) cc_final: 0.8237 (mmm) REVERT: B 189 SER cc_start: 0.8489 (t) cc_final: 0.7955 (t) REVERT: B 217 MET cc_start: 0.8185 (tpp) cc_final: 0.7608 (tpt) REVERT: B 228 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6420 (p0) REVERT: B 249 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7297 (t) REVERT: B 259 GLN cc_start: 0.7608 (pt0) cc_final: 0.7009 (pt0) REVERT: B 292 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7694 (m-80) REVERT: G 36 ASP cc_start: 0.8307 (m-30) cc_final: 0.7989 (m-30) REVERT: G 44 HIS cc_start: 0.7345 (m90) cc_final: 0.6978 (m-70) REVERT: G 62 ARG cc_start: 0.7196 (ttm110) cc_final: 0.6815 (tpp-160) REVERT: R 74 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8540 (tp-100) REVERT: R 87 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5212 (ttt-90) REVERT: R 106 VAL cc_start: 0.8184 (t) cc_final: 0.7909 (m) REVERT: R 151 SER cc_start: 0.9223 (m) cc_final: 0.8841 (p) REVERT: R 170 PHE cc_start: 0.7822 (p90) cc_final: 0.6943 (p90) REVERT: R 373 MET cc_start: 0.7914 (mmm) cc_final: 0.7696 (mtt) REVERT: S 39 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7105 (tp-100) REVERT: S 179 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7222 (mm-40) REVERT: S 233 LEU cc_start: 0.7984 (tp) cc_final: 0.7680 (mt) outliers start: 31 outliers final: 9 residues processed: 180 average time/residue: 1.2113 time to fit residues: 233.2665 Evaluate side-chains 161 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR 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 72 LEU Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 179 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.165536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118680 restraints weight = 12002.101| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.86 r_work: 0.3359 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9043 Z= 0.171 Angle : 0.549 8.248 12250 Z= 0.285 Chirality : 0.042 0.226 1400 Planarity : 0.003 0.040 1544 Dihedral : 4.692 56.514 1248 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 3.25 % Allowed : 24.66 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1119 helix: 1.58 (0.27), residues: 383 sheet: -0.23 (0.28), residues: 297 loop : -0.47 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 PHE 0.014 0.001 PHE B 253 TYR 0.014 0.001 TYR B 124 ARG 0.012 0.000 ARG A 32 *********************** 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 195 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8507 (mt) cc_final: 0.8045 (tp) REVERT: A 312 LYS cc_start: 0.8388 (mmtm) cc_final: 0.8043 (mmmt) REVERT: A 318 GLU cc_start: 0.7911 (tt0) cc_final: 0.7389 (pm20) REVERT: A 330 LYS cc_start: 0.8166 (mmtp) cc_final: 0.7631 (mppt) REVERT: B 44 GLN cc_start: 0.9009 (tt0) cc_final: 0.8747 (tp40) REVERT: B 188 MET cc_start: 0.8604 (mmm) cc_final: 0.8296 (mmm) REVERT: B 189 SER cc_start: 0.8504 (t) cc_final: 0.7979 (t) REVERT: B 215 GLU cc_start: 0.7706 (tt0) cc_final: 0.7478 (mm-30) REVERT: B 228 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6430 (p0) REVERT: B 249 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7357 (t) REVERT: B 259 GLN cc_start: 0.7659 (pt0) cc_final: 0.7056 (pt0) REVERT: B 292 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: G 36 ASP cc_start: 0.8292 (m-30) cc_final: 0.7968 (m-30) REVERT: G 44 HIS cc_start: 0.7398 (m90) cc_final: 0.7002 (m-70) REVERT: G 62 ARG cc_start: 0.7265 (ttm110) cc_final: 0.6907 (tpp-160) REVERT: R 52 ARG cc_start: 0.8416 (mtp180) cc_final: 0.7946 (mpp80) REVERT: R 74 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8578 (tp-100) REVERT: R 151 SER cc_start: 0.9182 (m) cc_final: 0.8816 (p) REVERT: R 170 PHE cc_start: 0.7842 (p90) cc_final: 0.6966 (p90) REVERT: R 373 MET cc_start: 0.7953 (mmm) cc_final: 0.7749 (mtm) REVERT: S 39 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7128 (tp-100) REVERT: S 179 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7270 (mm-40) REVERT: S 233 LEU cc_start: 0.8066 (tp) cc_final: 0.7834 (mt) outliers start: 31 outliers final: 12 residues processed: 185 average time/residue: 1.1059 time to fit residues: 219.0012 Evaluate side-chains 167 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR 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 332 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR 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 72 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** R 339 ASN R 357 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.163060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115416 restraints weight = 12173.908| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.92 r_work: 0.3315 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9043 Z= 0.246 Angle : 0.589 10.126 12250 Z= 0.303 Chirality : 0.043 0.238 1400 Planarity : 0.003 0.034 1544 Dihedral : 4.868 53.384 1248 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 3.04 % Allowed : 25.60 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1119 helix: 1.57 (0.27), residues: 383 sheet: -0.20 (0.28), residues: 295 loop : -0.50 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 PHE 0.015 0.001 PHE B 253 TYR 0.024 0.001 TYR B 59 ARG 0.009 0.001 ARG A 32 *********************** 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 185 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8503 (mt) cc_final: 0.8036 (tp) REVERT: A 312 LYS cc_start: 0.8363 (mmtm) cc_final: 0.8059 (mmmt) REVERT: A 330 LYS cc_start: 0.8179 (mmtp) cc_final: 0.7650 (mppt) REVERT: B 44 GLN cc_start: 0.8994 (tt0) cc_final: 0.8740 (tp40) REVERT: B 188 MET cc_start: 0.8625 (mmm) cc_final: 0.8298 (mmm) REVERT: B 189 SER cc_start: 0.8597 (t) cc_final: 0.8050 (t) REVERT: B 228 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6422 (p0) REVERT: B 259 GLN cc_start: 0.7619 (pt0) cc_final: 0.7057 (pt0) REVERT: B 292 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: G 36 ASP cc_start: 0.8266 (m-30) cc_final: 0.7924 (m-30) REVERT: G 44 HIS cc_start: 0.7475 (m90) cc_final: 0.7153 (m-70) REVERT: G 62 ARG cc_start: 0.7262 (ttm110) cc_final: 0.7031 (mtm-85) REVERT: R 52 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7513 (mtm-85) REVERT: R 74 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8666 (tp-100) REVERT: R 151 SER cc_start: 0.9184 (m) cc_final: 0.8794 (p) REVERT: R 170 PHE cc_start: 0.7889 (p90) cc_final: 0.6967 (p90) REVERT: R 210 GLN cc_start: 0.7717 (mt0) cc_final: 0.7067 (mp10) REVERT: R 373 MET cc_start: 0.7890 (mmm) cc_final: 0.7629 (mtt) REVERT: S 39 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7085 (tp-100) REVERT: S 179 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7182 (mm-40) REVERT: S 233 LEU cc_start: 0.8126 (tp) cc_final: 0.7892 (mt) outliers start: 29 outliers final: 14 residues processed: 178 average time/residue: 1.1942 time to fit residues: 226.7926 Evaluate side-chains 165 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL 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 52 ARG Chi-restraints excluded: chain R residue 81 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 108 optimal weight: 0.0010 chunk 110 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 ** 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 = 0.4013 r_free = 0.4013 target = 0.165882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118650 restraints weight = 12154.543| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.92 r_work: 0.3360 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9043 Z= 0.166 Angle : 0.587 10.056 12250 Z= 0.297 Chirality : 0.043 0.221 1400 Planarity : 0.004 0.070 1544 Dihedral : 4.655 50.605 1248 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 3.04 % Allowed : 25.71 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1119 helix: 1.58 (0.27), residues: 383 sheet: -0.22 (0.29), residues: 292 loop : -0.49 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 PHE 0.014 0.001 PHE B 253 TYR 0.022 0.001 TYR B 59 ARG 0.019 0.001 ARG A 32 *********************** 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 189 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8540 (mt) cc_final: 0.8091 (tp) REVERT: A 312 LYS cc_start: 0.8359 (mmtm) cc_final: 0.8049 (mmmt) REVERT: A 330 LYS cc_start: 0.8146 (mmtp) cc_final: 0.7607 (mppt) REVERT: B 44 GLN cc_start: 0.9000 (tt0) cc_final: 0.8742 (tp40) REVERT: B 175 GLN cc_start: 0.8177 (pt0) cc_final: 0.7470 (pp30) REVERT: B 188 MET cc_start: 0.8598 (mmm) cc_final: 0.8241 (mmm) REVERT: B 189 SER cc_start: 0.8511 (t) cc_final: 0.7973 (t) REVERT: B 228 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6335 (p0) REVERT: B 259 GLN cc_start: 0.7628 (pt0) cc_final: 0.7011 (pt0) REVERT: B 292 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: G 36 ASP cc_start: 0.8260 (m-30) cc_final: 0.7930 (m-30) REVERT: G 44 HIS cc_start: 0.7399 (m90) cc_final: 0.7026 (m-70) REVERT: G 62 ARG cc_start: 0.7268 (ttm110) cc_final: 0.6908 (tpp-160) REVERT: R 52 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7775 (tpp80) REVERT: R 151 SER cc_start: 0.9153 (m) cc_final: 0.8632 (p) REVERT: R 170 PHE cc_start: 0.7798 (p90) cc_final: 0.6930 (p90) REVERT: R 178 TYR cc_start: 0.7524 (t80) cc_final: 0.7126 (t80) REVERT: R 337 LEU cc_start: 0.8162 (mm) cc_final: 0.7934 (mm) REVERT: R 353 MET cc_start: 0.7940 (mmm) cc_final: 0.7695 (mmm) REVERT: R 373 MET cc_start: 0.7926 (mmm) cc_final: 0.7672 (mtm) REVERT: S 39 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7109 (tp-100) REVERT: S 59 TYR cc_start: 0.7496 (m-80) cc_final: 0.7280 (m-10) REVERT: S 179 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7297 (mm-40) outliers start: 29 outliers final: 15 residues processed: 184 average time/residue: 1.1778 time to fit residues: 231.7962 Evaluate side-chains 170 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 A residue 332 VAL 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 327 VAL Chi-restraints excluded: chain R residue 52 ARG Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 179 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS A 333 GLN B 75 GLN B 230 ASN B 340 ASN ** R 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 357 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.168153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121007 restraints weight = 12030.291| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.95 r_work: 0.3368 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9043 Z= 0.156 Angle : 0.576 9.613 12250 Z= 0.292 Chirality : 0.042 0.215 1400 Planarity : 0.004 0.075 1544 Dihedral : 4.493 46.933 1248 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 2.94 % Allowed : 26.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1119 helix: 1.63 (0.27), residues: 382 sheet: -0.21 (0.29), residues: 293 loop : -0.48 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS R 393 PHE 0.014 0.001 PHE B 253 TYR 0.022 0.001 TYR B 59 ARG 0.019 0.001 ARG A 32 *********************** 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 193 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8511 (mt) cc_final: 0.8079 (tp) REVERT: A 257 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8455 (ptmt) REVERT: A 312 LYS cc_start: 0.8391 (mmtm) cc_final: 0.8091 (mmmt) REVERT: A 318 GLU cc_start: 0.7898 (tt0) cc_final: 0.7410 (pm20) REVERT: A 330 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7544 (mppt) REVERT: B 44 GLN cc_start: 0.8985 (tt0) cc_final: 0.8733 (tp40) REVERT: B 129 ARG cc_start: 0.8676 (ptp-110) cc_final: 0.8426 (ptm-80) REVERT: B 175 GLN cc_start: 0.8206 (pt0) cc_final: 0.7511 (pp30) REVERT: B 188 MET cc_start: 0.8618 (mmm) cc_final: 0.8279 (mmm) REVERT: B 189 SER cc_start: 0.8468 (t) cc_final: 0.7932 (t) REVERT: B 228 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6399 (p0) REVERT: B 259 GLN cc_start: 0.7669 (pt0) cc_final: 0.7067 (pt0) REVERT: B 292 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: G 36 ASP cc_start: 0.8252 (m-30) cc_final: 0.7944 (m-30) REVERT: G 44 HIS cc_start: 0.7381 (m90) cc_final: 0.7008 (m-70) REVERT: G 62 ARG cc_start: 0.7300 (ttm110) cc_final: 0.6766 (tpp-160) REVERT: R 52 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7808 (tpp80) REVERT: R 74 GLN cc_start: 0.8738 (tp40) cc_final: 0.8138 (tp-100) REVERT: R 106 VAL cc_start: 0.8214 (t) cc_final: 0.7969 (m) REVERT: R 151 SER cc_start: 0.9117 (m) cc_final: 0.8639 (p) REVERT: R 170 PHE cc_start: 0.7736 (p90) cc_final: 0.6908 (p90) REVERT: R 178 TYR cc_start: 0.7558 (t80) cc_final: 0.7146 (t80) REVERT: R 210 GLN cc_start: 0.7725 (mt0) cc_final: 0.7132 (mp10) REVERT: R 337 LEU cc_start: 0.8178 (mm) cc_final: 0.7911 (mm) REVERT: R 353 MET cc_start: 0.7980 (mmm) cc_final: 0.7754 (mmm) REVERT: R 373 MET cc_start: 0.7970 (mmm) cc_final: 0.7747 (mtm) REVERT: S 39 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7161 (tp-100) REVERT: S 179 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7260 (mm-40) outliers start: 28 outliers final: 15 residues processed: 187 average time/residue: 1.1125 time to fit residues: 222.9818 Evaluate side-chains 180 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 A residue 332 VAL 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 52 ARG Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain S residue 39 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 89 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.7342 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.164388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116771 restraints weight = 12056.942| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.84 r_work: 0.3337 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9043 Z= 0.246 Angle : 0.618 9.232 12250 Z= 0.313 Chirality : 0.044 0.233 1400 Planarity : 0.004 0.076 1544 Dihedral : 4.743 45.941 1248 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 2.41 % Allowed : 27.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1119 helix: 1.58 (0.27), residues: 382 sheet: -0.20 (0.29), residues: 292 loop : -0.49 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 393 PHE 0.016 0.001 PHE B 253 TYR 0.026 0.002 TYR B 59 ARG 0.020 0.001 ARG A 32 ********************** 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 176 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8037 (ttm) cc_final: 0.7581 (mtp) REVERT: A 205 ARG cc_start: 0.8317 (mmm160) cc_final: 0.7784 (mmt-90) REVERT: A 232 LEU cc_start: 0.8536 (mt) cc_final: 0.8119 (tp) REVERT: A 312 LYS cc_start: 0.8441 (mmtm) cc_final: 0.8145 (mmmt) REVERT: A 330 LYS cc_start: 0.8222 (mmtp) cc_final: 0.7605 (mppt) REVERT: B 44 GLN cc_start: 0.8961 (tt0) cc_final: 0.8729 (tp40) REVERT: B 129 ARG cc_start: 0.8716 (ptp-110) cc_final: 0.8464 (ptm-80) REVERT: B 175 GLN cc_start: 0.8307 (pt0) cc_final: 0.7639 (pp30) REVERT: B 188 MET cc_start: 0.8674 (mmm) cc_final: 0.8387 (mmm) REVERT: B 189 SER cc_start: 0.8654 (t) cc_final: 0.8140 (t) REVERT: B 228 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6616 (p0) REVERT: B 259 GLN cc_start: 0.7778 (pt0) cc_final: 0.7245 (pt0) REVERT: B 292 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: G 36 ASP cc_start: 0.8283 (m-30) cc_final: 0.7945 (m-30) REVERT: G 44 HIS cc_start: 0.7550 (m90) cc_final: 0.7235 (m-70) REVERT: R 52 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7874 (tpp80) REVERT: R 74 GLN cc_start: 0.8848 (tp40) cc_final: 0.8174 (tp-100) REVERT: R 81 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8264 (OUTLIER) REVERT: R 151 SER cc_start: 0.9147 (m) cc_final: 0.8811 (p) REVERT: R 170 PHE cc_start: 0.7927 (p90) cc_final: 0.7059 (p90) REVERT: R 210 GLN cc_start: 0.7733 (mt0) cc_final: 0.7166 (mp10) REVERT: R 337 LEU cc_start: 0.8221 (mm) cc_final: 0.7996 (mm) REVERT: R 353 MET cc_start: 0.8027 (mmm) cc_final: 0.7757 (mmm) REVERT: R 373 MET cc_start: 0.8011 (mmm) cc_final: 0.7745 (mtm) REVERT: S 39 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7320 (tp-100) REVERT: S 179 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7437 (mm-40) REVERT: S 227 TYR cc_start: 0.7479 (m-10) cc_final: 0.6741 (m-80) outliers start: 23 outliers final: 17 residues processed: 173 average time/residue: 1.1865 time to fit residues: 219.6897 Evaluate side-chains 169 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 A residue 332 VAL 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 52 ARG Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 179 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 30 optimal weight: 0.0980 chunk 4 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.166964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119582 restraints weight = 11983.972| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.88 r_work: 0.3372 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9043 Z= 0.165 Angle : 0.589 9.353 12250 Z= 0.296 Chirality : 0.042 0.198 1400 Planarity : 0.004 0.080 1544 Dihedral : 4.526 43.938 1248 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 2.62 % Allowed : 27.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1119 helix: 1.59 (0.27), residues: 382 sheet: -0.07 (0.29), residues: 289 loop : -0.51 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 393 PHE 0.014 0.001 PHE B 253 TYR 0.028 0.001 TYR S 59 ARG 0.019 0.001 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7396.37 seconds wall clock time: 127 minutes 19.94 seconds (7639.94 seconds total)