Starting phenix.real_space_refine on Tue Mar 11 16:55:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwh_27754/03_2025/8dwh_27754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwh_27754/03_2025/8dwh_27754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwh_27754/03_2025/8dwh_27754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwh_27754/03_2025/8dwh_27754.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwh_27754/03_2025/8dwh_27754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwh_27754/03_2025/8dwh_27754.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 44 5.16 5 C 4136 2.51 5 N 1103 2.21 5 O 1161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6444 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1704 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2480 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1879 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 241} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'U2U': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.62, per 1000 atoms: 0.72 Number of scatterers: 6444 At special positions: 0 Unit cell: (90.64, 101.2, 121.44, 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 44 16.00 O 1161 8.00 N 1103 7.00 C 4136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " 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: 1.82 Conformation dependent library (CDL) restraints added in 923.1 milliseconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 46.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.597A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.627A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP B 102 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 132 through 135 removed outlier: 3.663A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.517A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.756A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.710A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'C' and resid 4 through 23 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'R' and resid 26 through 55 removed outlier: 4.027A pdb=" N GLY R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS R 54 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 88 removed outlier: 3.546A pdb=" N ILE R 63 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE R 87 " --> pdb=" O SER R 83 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE R 88 " --> pdb=" O LEU R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 126 removed outlier: 3.865A pdb=" N TYR R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) Proline residue: R 100 - end of helix removed outlier: 4.927A pdb=" N PHE R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 132 Processing helix chain 'R' and resid 137 through 161 Processing helix chain 'R' and resid 172 through 204 removed outlier: 3.985A pdb=" N SER R 176 " --> pdb=" O TRP R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 229 removed outlier: 3.873A pdb=" N PHE R 225 " --> pdb=" O THR R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 235 removed outlier: 3.661A pdb=" N ILE R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 242 Processing helix chain 'R' and resid 245 through 252 removed outlier: 4.125A pdb=" N PHE R 250 " --> pdb=" O ARG R 246 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N CYS R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 273 removed outlier: 3.524A pdb=" N SER R 265 " --> pdb=" O SER R 261 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER R 266 " --> pdb=" O ALA R 262 " (cutoff:3.500A) Proline residue: R 269 - end of helix Processing helix chain 'R' and resid 274 through 278 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.341A pdb=" N LEU B 34 " --> pdb=" O HIS B 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.214A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.891A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.769A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.965A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.595A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.762A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.603A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.950A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 978 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: 1.90 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2079 1.34 - 1.46: 1452 1.46 - 1.58: 2990 1.58 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 6578 Sorted by residual: bond pdb=" C22 U2U R 401 " pdb=" N3 U2U R 401 " ideal model delta sigma weight residual 1.370 1.341 0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" CB PRO D 60 " pdb=" CG PRO D 60 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.51e+00 bond pdb=" CG LEU R 191 " pdb=" CD2 LEU R 191 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" C21 U2U R 401 " pdb=" N2 U2U R 401 " ideal model delta sigma weight residual 1.359 1.339 0.020 2.00e-02 2.50e+03 9.93e-01 bond pdb=" CA ASP B 85 " pdb=" CB ASP B 85 " ideal model delta sigma weight residual 1.536 1.560 -0.024 2.53e-02 1.56e+03 8.92e-01 ... (remaining 6573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 8780 1.58 - 3.17: 148 3.17 - 4.75: 24 4.75 - 6.33: 10 6.33 - 7.91: 2 Bond angle restraints: 8964 Sorted by residual: angle pdb=" N ASP C 153 " pdb=" CA ASP C 153 " pdb=" C ASP C 153 " ideal model delta sigma weight residual 108.24 104.62 3.62 1.32e+00 5.74e-01 7.53e+00 angle pdb=" N GLY C 319 " pdb=" CA GLY C 319 " pdb=" C GLY C 319 " ideal model delta sigma weight residual 110.87 114.62 -3.75 1.54e+00 4.22e-01 5.91e+00 angle pdb=" CB ARG C 304 " pdb=" CG ARG C 304 " pdb=" CD ARG C 304 " ideal model delta sigma weight residual 111.30 106.02 5.28 2.30e+00 1.89e-01 5.27e+00 angle pdb=" CA LEU C 190 " pdb=" CB LEU C 190 " pdb=" CG LEU C 190 " ideal model delta sigma weight residual 116.30 124.21 -7.91 3.50e+00 8.16e-02 5.11e+00 angle pdb=" C ASP C 195 " pdb=" N THR C 196 " pdb=" CA THR C 196 " ideal model delta sigma weight residual 122.46 125.59 -3.13 1.41e+00 5.03e-01 4.94e+00 ... (remaining 8959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.96: 3374 13.96 - 27.92: 333 27.92 - 41.88: 103 41.88 - 55.83: 23 55.83 - 69.79: 2 Dihedral angle restraints: 3835 sinusoidal: 1340 harmonic: 2495 Sorted by residual: dihedral pdb=" CA PRO R 100 " pdb=" C PRO R 100 " pdb=" N VAL R 101 " pdb=" CA VAL R 101 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ASN B 223 " pdb=" CB ASN B 223 " pdb=" CG ASN B 223 " pdb=" OD1 ASN B 223 " ideal model delta sinusoidal sigma weight residual 120.00 -175.31 -64.69 2 2.00e+01 2.50e-03 9.81e+00 dihedral pdb=" CG ARG C 68 " pdb=" CD ARG C 68 " pdb=" NE ARG C 68 " pdb=" CZ ARG C 68 " ideal model delta sinusoidal sigma weight residual -90.00 -131.73 41.73 2 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 619 0.030 - 0.060: 296 0.060 - 0.090: 90 0.090 - 0.120: 46 0.120 - 0.150: 10 Chirality restraints: 1061 Sorted by residual: chirality pdb=" CA PRO R 231 " pdb=" N PRO R 231 " pdb=" C PRO R 231 " pdb=" CB PRO R 231 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CG LEU R 191 " pdb=" CB LEU R 191 " pdb=" CD1 LEU R 191 " pdb=" CD2 LEU R 191 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ASN B 43 " pdb=" N ASN B 43 " pdb=" C ASN B 43 " pdb=" CB ASN B 43 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1058 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 230 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO R 231 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 231 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 231 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO C 236 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO D 49 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " 0.020 5.00e-02 4.00e+02 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 117 2.68 - 3.24: 6284 3.24 - 3.79: 9795 3.79 - 4.35: 13265 4.35 - 4.90: 22169 Nonbonded interactions: 51630 Sorted by model distance: nonbonded pdb=" OH TYR R 64 " pdb=" OE2 GLU R 119 " model vdw 2.129 3.040 nonbonded pdb=" OD1 ASP C 153 " pdb=" N ASP C 154 " model vdw 2.133 3.120 nonbonded pdb=" OH TYR B 243 " pdb=" OH TYR R 130 " model vdw 2.159 3.040 nonbonded pdb=" OE1 GLU B 182 " pdb=" OG1 THR B 187 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR R 106 " pdb=" O PHE R 232 " model vdw 2.216 3.040 ... (remaining 51625 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 0.061 6578 Z= 0.260 Angle : 0.567 7.913 8964 Z= 0.309 Chirality : 0.042 0.150 1061 Planarity : 0.003 0.052 1122 Dihedral : 12.917 69.793 2210 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.94 (0.29), residues: 844 helix: 0.07 (0.28), residues: 356 sheet: -0.32 (0.45), residues: 145 loop : -1.41 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE C 199 TYR 0.009 0.001 TYR C 105 ARG 0.011 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.669 Fit side-chains REVERT: B 122 LEU cc_start: 0.7986 (mp) cc_final: 0.7733 (mp) REVERT: B 128 ILE cc_start: 0.8048 (mm) cc_final: 0.7847 (mt) REVERT: B 145 LYS cc_start: 0.8297 (mtpp) cc_final: 0.8001 (mtpt) REVERT: B 210 ILE cc_start: 0.8138 (mt) cc_final: 0.7906 (mt) REVERT: C 68 ARG cc_start: 0.8105 (ttt180) cc_final: 0.7497 (ttt-90) REVERT: C 134 ARG cc_start: 0.6814 (pmt-80) cc_final: 0.6428 (pmt-80) REVERT: C 258 ASP cc_start: 0.7135 (t70) cc_final: 0.6340 (t0) REVERT: C 285 LEU cc_start: 0.8462 (tt) cc_final: 0.8258 (tt) REVERT: R 65 ILE cc_start: 0.7733 (mm) cc_final: 0.7487 (mt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2351 time to fit residues: 48.0554 Evaluate side-chains 145 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** R 264 ASN ** 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 = 0.3452 r_free = 0.3452 target = 0.116211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099975 restraints weight = 9385.063| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.17 r_work: 0.3094 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6578 Z= 0.282 Angle : 0.604 7.115 8964 Z= 0.313 Chirality : 0.044 0.137 1061 Planarity : 0.004 0.036 1122 Dihedral : 4.458 25.568 927 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.09 % Allowed : 8.40 % Favored : 90.51 % 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: -0.03 (0.30), residues: 844 helix: 1.31 (0.29), residues: 360 sheet: -0.28 (0.41), residues: 163 loop : -1.39 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.012 0.001 PHE R 225 TYR 0.014 0.002 TYR C 59 ARG 0.007 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.902 Fit side-chains REVERT: B 8 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6661 (tm-30) REVERT: B 122 LEU cc_start: 0.7990 (mp) cc_final: 0.7688 (mp) REVERT: C 68 ARG cc_start: 0.8373 (ttt180) cc_final: 0.7713 (ttt-90) REVERT: C 76 ASP cc_start: 0.7489 (p0) cc_final: 0.7244 (p0) REVERT: C 102 THR cc_start: 0.8246 (m) cc_final: 0.7950 (p) REVERT: C 134 ARG cc_start: 0.7173 (pmt-80) cc_final: 0.6755 (pmt-80) REVERT: C 219 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7691 (mtt180) REVERT: C 258 ASP cc_start: 0.7643 (t70) cc_final: 0.6766 (t0) REVERT: C 285 LEU cc_start: 0.8615 (tt) cc_final: 0.8385 (tt) REVERT: R 51 LEU cc_start: 0.8072 (mt) cc_final: 0.7744 (mp) REVERT: R 158 TRP cc_start: 0.8096 (t60) cc_final: 0.7684 (t60) REVERT: R 172 TRP cc_start: 0.6680 (m100) cc_final: 0.6471 (m100) outliers start: 7 outliers final: 4 residues processed: 159 average time/residue: 0.2976 time to fit residues: 58.6060 Evaluate side-chains 151 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 147 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** R 264 ASN ** 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 = 0.3508 r_free = 0.3508 target = 0.120284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104669 restraints weight = 9109.318| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.01 r_work: 0.3115 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6578 Z= 0.267 Angle : 0.564 5.836 8964 Z= 0.293 Chirality : 0.043 0.134 1061 Planarity : 0.003 0.036 1122 Dihedral : 4.319 23.446 927 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.33 % Allowed : 10.42 % Favored : 87.25 % 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: 0.35 (0.30), residues: 844 helix: 1.74 (0.28), residues: 359 sheet: -0.17 (0.40), residues: 173 loop : -1.32 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.011 0.001 PHE R 178 TYR 0.013 0.001 TYR C 59 ARG 0.005 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.695 Fit side-chains REVERT: B 8 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6766 (tm-30) REVERT: B 28 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6959 (mm-30) REVERT: C 68 ARG cc_start: 0.8357 (ttt180) cc_final: 0.7669 (ttt-90) REVERT: C 76 ASP cc_start: 0.7506 (p0) cc_final: 0.7231 (p0) REVERT: C 134 ARG cc_start: 0.7175 (pmt-80) cc_final: 0.6679 (pmt-80) REVERT: C 219 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7613 (mtt180) REVERT: C 258 ASP cc_start: 0.7628 (t70) cc_final: 0.6744 (t0) REVERT: C 277 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8158 (t) REVERT: C 285 LEU cc_start: 0.8457 (tt) cc_final: 0.8216 (tt) REVERT: C 318 LEU cc_start: 0.8113 (tt) cc_final: 0.7863 (tp) REVERT: C 336 LEU cc_start: 0.8218 (mp) cc_final: 0.7982 (mp) REVERT: R 51 LEU cc_start: 0.8044 (mt) cc_final: 0.7714 (mp) REVERT: R 158 TRP cc_start: 0.8115 (t60) cc_final: 0.7720 (t60) outliers start: 15 outliers final: 8 residues processed: 163 average time/residue: 0.2750 time to fit residues: 54.9203 Evaluate side-chains 161 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS C 239 ASN ** R 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100329 restraints weight = 9529.290| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.23 r_work: 0.3095 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6578 Z= 0.238 Angle : 0.535 5.328 8964 Z= 0.280 Chirality : 0.042 0.132 1061 Planarity : 0.003 0.036 1122 Dihedral : 4.225 24.064 927 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.95 % Allowed : 12.60 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.30), residues: 844 helix: 2.00 (0.28), residues: 359 sheet: -0.14 (0.40), residues: 175 loop : -1.26 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE C 278 TYR 0.011 0.001 TYR C 59 ARG 0.006 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.691 Fit side-chains REVERT: B 8 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6760 (tm-30) REVERT: B 28 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6964 (mm-30) REVERT: B 31 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7939 (ttp80) REVERT: B 32 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7370 (mtm-85) REVERT: C 68 ARG cc_start: 0.8373 (ttt180) cc_final: 0.7691 (ttt-90) REVERT: C 76 ASP cc_start: 0.7592 (p0) cc_final: 0.7283 (p0) REVERT: C 134 ARG cc_start: 0.7205 (pmt-80) cc_final: 0.6678 (pmt-80) REVERT: C 188 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7864 (mtp) REVERT: C 258 ASP cc_start: 0.7699 (t70) cc_final: 0.6812 (t0) REVERT: C 285 LEU cc_start: 0.8450 (tt) cc_final: 0.8204 (tt) REVERT: C 318 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7958 (tp) REVERT: C 336 LEU cc_start: 0.8234 (mp) cc_final: 0.8012 (mp) REVERT: R 30 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6719 (mm) REVERT: R 49 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8415 (mp) REVERT: R 51 LEU cc_start: 0.8058 (mt) cc_final: 0.7722 (mp) outliers start: 19 outliers final: 10 residues processed: 157 average time/residue: 0.2728 time to fit residues: 52.3912 Evaluate side-chains 159 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 72 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN C 239 ASN R 264 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099745 restraints weight = 9448.676| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.21 r_work: 0.3087 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6578 Z= 0.260 Angle : 0.544 5.360 8964 Z= 0.284 Chirality : 0.042 0.136 1061 Planarity : 0.003 0.039 1122 Dihedral : 4.256 24.018 927 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.80 % Allowed : 14.93 % Favored : 82.27 % 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: 0.60 (0.30), residues: 844 helix: 2.09 (0.28), residues: 359 sheet: -0.09 (0.42), residues: 164 loop : -1.34 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE R 178 TYR 0.011 0.001 TYR B 243 ARG 0.009 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.687 Fit side-chains REVERT: B 8 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6791 (tm-30) REVERT: B 28 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6917 (mm-30) REVERT: B 32 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7399 (mtm-85) REVERT: C 68 ARG cc_start: 0.8367 (ttt180) cc_final: 0.7678 (ttt-90) REVERT: C 76 ASP cc_start: 0.7564 (p0) cc_final: 0.7269 (p0) REVERT: C 134 ARG cc_start: 0.7219 (pmt-80) cc_final: 0.6685 (pmt-80) REVERT: C 188 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7903 (mtp) REVERT: C 258 ASP cc_start: 0.7704 (t70) cc_final: 0.6828 (t0) REVERT: C 283 ARG cc_start: 0.8254 (tpp80) cc_final: 0.7983 (tpt-90) REVERT: C 285 LEU cc_start: 0.8442 (tt) cc_final: 0.8192 (tt) REVERT: C 336 LEU cc_start: 0.8235 (mp) cc_final: 0.7999 (mp) REVERT: C 338 ILE cc_start: 0.8612 (mm) cc_final: 0.8258 (mm) REVERT: R 30 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6694 (mm) REVERT: R 49 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8399 (mp) REVERT: R 51 LEU cc_start: 0.8040 (mt) cc_final: 0.7713 (mp) outliers start: 18 outliers final: 10 residues processed: 158 average time/residue: 0.2829 time to fit residues: 54.4622 Evaluate side-chains 161 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.0270 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101016 restraints weight = 9448.725| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.21 r_work: 0.3106 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6578 Z= 0.198 Angle : 0.512 5.360 8964 Z= 0.268 Chirality : 0.042 0.234 1061 Planarity : 0.003 0.034 1122 Dihedral : 4.119 24.934 927 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.49 % Allowed : 15.55 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.30), residues: 844 helix: 2.40 (0.28), residues: 355 sheet: -0.10 (0.42), residues: 164 loop : -1.21 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE R 178 TYR 0.009 0.001 TYR C 59 ARG 0.008 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.758 Fit side-chains REVERT: B 8 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6772 (tm-30) REVERT: B 28 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7007 (mm-30) REVERT: B 31 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7894 (ttp80) REVERT: B 32 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7318 (mtm-85) REVERT: C 68 ARG cc_start: 0.8352 (ttt180) cc_final: 0.7635 (ttt-90) REVERT: C 76 ASP cc_start: 0.7573 (p0) cc_final: 0.7301 (p0) REVERT: C 134 ARG cc_start: 0.7230 (pmt-80) cc_final: 0.6708 (pmt-80) REVERT: C 153 ASP cc_start: 0.7749 (t0) cc_final: 0.7531 (t0) REVERT: C 188 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7901 (mtp) REVERT: C 258 ASP cc_start: 0.7701 (t70) cc_final: 0.6830 (t0) REVERT: C 268 ASN cc_start: 0.7796 (m-40) cc_final: 0.7513 (m-40) REVERT: C 283 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7971 (tpt-90) REVERT: C 285 LEU cc_start: 0.8399 (tt) cc_final: 0.8155 (tt) REVERT: C 289 TYR cc_start: 0.8406 (m-80) cc_final: 0.8161 (m-80) REVERT: C 304 ARG cc_start: 0.7979 (ttt-90) cc_final: 0.7621 (ttt-90) REVERT: C 336 LEU cc_start: 0.8198 (mp) cc_final: 0.7975 (mp) REVERT: C 338 ILE cc_start: 0.8597 (mm) cc_final: 0.8221 (mm) REVERT: R 30 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6549 (mm) REVERT: R 49 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8350 (mp) REVERT: R 51 LEU cc_start: 0.8025 (mt) cc_final: 0.7679 (mp) outliers start: 16 outliers final: 7 residues processed: 163 average time/residue: 0.2640 time to fit residues: 52.8246 Evaluate side-chains 158 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 83 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102404 restraints weight = 9096.150| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.02 r_work: 0.3097 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6578 Z= 0.280 Angle : 0.551 8.887 8964 Z= 0.287 Chirality : 0.043 0.214 1061 Planarity : 0.003 0.040 1122 Dihedral : 4.245 23.429 927 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.80 % Allowed : 16.49 % Favored : 80.72 % 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: 0.77 (0.30), residues: 844 helix: 2.34 (0.28), residues: 354 sheet: -0.21 (0.41), residues: 165 loop : -1.21 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.013 0.001 PHE C 278 TYR 0.012 0.001 TYR C 59 ARG 0.010 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.745 Fit side-chains REVERT: B 8 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6789 (tm-30) REVERT: B 28 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6967 (mm-30) REVERT: B 32 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7378 (mtm-85) REVERT: C 68 ARG cc_start: 0.8295 (ttt180) cc_final: 0.7586 (ttt-90) REVERT: C 76 ASP cc_start: 0.7515 (p0) cc_final: 0.7201 (p0) REVERT: C 88 ASN cc_start: 0.7975 (m110) cc_final: 0.7755 (m110) REVERT: C 134 ARG cc_start: 0.7166 (pmt-80) cc_final: 0.6561 (pmt-80) REVERT: C 188 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7888 (mtp) REVERT: C 258 ASP cc_start: 0.7651 (t70) cc_final: 0.6778 (t0) REVERT: C 285 LEU cc_start: 0.8394 (tt) cc_final: 0.8142 (tt) REVERT: C 289 TYR cc_start: 0.8397 (m-80) cc_final: 0.8105 (m-80) REVERT: C 304 ARG cc_start: 0.7993 (ttt-90) cc_final: 0.7738 (ttt-90) REVERT: C 336 LEU cc_start: 0.8187 (mp) cc_final: 0.7977 (mp) REVERT: C 338 ILE cc_start: 0.8572 (mm) cc_final: 0.8186 (mt) REVERT: R 30 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6632 (mm) REVERT: R 51 LEU cc_start: 0.7984 (mt) cc_final: 0.7645 (mp) REVERT: R 172 TRP cc_start: 0.5922 (OUTLIER) cc_final: 0.5045 (m100) outliers start: 18 outliers final: 12 residues processed: 155 average time/residue: 0.2675 time to fit residues: 50.7693 Evaluate side-chains 164 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101776 restraints weight = 9285.689| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.09 r_work: 0.3094 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6578 Z= 0.284 Angle : 0.552 7.954 8964 Z= 0.287 Chirality : 0.043 0.132 1061 Planarity : 0.003 0.042 1122 Dihedral : 4.310 23.619 927 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.80 % Allowed : 17.11 % Favored : 80.09 % 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: 0.71 (0.30), residues: 844 helix: 2.26 (0.29), residues: 360 sheet: -0.23 (0.41), residues: 167 loop : -1.28 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.013 0.002 PHE C 278 TYR 0.011 0.001 TYR C 59 ARG 0.010 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.668 Fit side-chains REVERT: B 8 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6811 (tm-30) REVERT: B 28 GLU cc_start: 0.7237 (mm-30) cc_final: 0.7021 (mm-30) REVERT: B 32 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7425 (mtm-85) REVERT: C 68 ARG cc_start: 0.8329 (ttt180) cc_final: 0.7692 (ttt-90) REVERT: C 76 ASP cc_start: 0.7534 (p0) cc_final: 0.7230 (p0) REVERT: C 134 ARG cc_start: 0.7200 (pmt-80) cc_final: 0.6608 (pmt-80) REVERT: C 258 ASP cc_start: 0.7665 (t70) cc_final: 0.6804 (t0) REVERT: C 283 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7969 (tpt-90) REVERT: C 285 LEU cc_start: 0.8465 (tt) cc_final: 0.8212 (tt) REVERT: C 289 TYR cc_start: 0.8431 (m-80) cc_final: 0.8121 (m-80) REVERT: C 304 ARG cc_start: 0.7998 (ttt-90) cc_final: 0.7786 (ttt-90) REVERT: C 318 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8122 (mp) REVERT: C 336 LEU cc_start: 0.8196 (mp) cc_final: 0.7990 (mp) REVERT: C 338 ILE cc_start: 0.8594 (mm) cc_final: 0.8210 (mt) REVERT: R 30 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6691 (mm) REVERT: R 51 LEU cc_start: 0.8029 (mt) cc_final: 0.7693 (mp) REVERT: R 172 TRP cc_start: 0.5995 (OUTLIER) cc_final: 0.4789 (m100) outliers start: 18 outliers final: 10 residues processed: 149 average time/residue: 0.2889 time to fit residues: 52.4280 Evaluate side-chains 154 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100132 restraints weight = 9515.545| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.32 r_work: 0.3092 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6578 Z= 0.227 Angle : 0.533 7.488 8964 Z= 0.278 Chirality : 0.042 0.130 1061 Planarity : 0.003 0.041 1122 Dihedral : 4.207 24.178 927 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.02 % Allowed : 18.20 % Favored : 79.78 % 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: 0.85 (0.30), residues: 844 helix: 2.49 (0.29), residues: 354 sheet: -0.26 (0.41), residues: 165 loop : -1.22 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.011 0.001 PHE R 178 TYR 0.011 0.001 TYR C 59 ARG 0.010 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.747 Fit side-chains REVERT: B 8 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6822 (tm-30) REVERT: B 28 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7059 (mm-30) REVERT: B 32 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7443 (mtm-85) REVERT: B 145 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8109 (mtpt) REVERT: C 68 ARG cc_start: 0.8364 (ttt180) cc_final: 0.7673 (ttt-90) REVERT: C 76 ASP cc_start: 0.7566 (p0) cc_final: 0.7259 (p0) REVERT: C 134 ARG cc_start: 0.7245 (pmt-80) cc_final: 0.6689 (pmt-80) REVERT: C 189 SER cc_start: 0.8247 (p) cc_final: 0.7915 (t) REVERT: C 258 ASP cc_start: 0.7719 (t70) cc_final: 0.6870 (t0) REVERT: C 283 ARG cc_start: 0.8303 (tpp80) cc_final: 0.8020 (tpt-90) REVERT: C 285 LEU cc_start: 0.8467 (tt) cc_final: 0.8216 (tt) REVERT: C 289 TYR cc_start: 0.8441 (m-80) cc_final: 0.8006 (m-80) REVERT: C 318 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8099 (mp) REVERT: R 30 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6697 (mm) REVERT: R 51 LEU cc_start: 0.8019 (mt) cc_final: 0.7673 (mp) outliers start: 13 outliers final: 10 residues processed: 157 average time/residue: 0.2778 time to fit residues: 53.2275 Evaluate side-chains 160 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099341 restraints weight = 9605.443| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.33 r_work: 0.3075 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6578 Z= 0.316 Angle : 0.583 7.636 8964 Z= 0.302 Chirality : 0.044 0.135 1061 Planarity : 0.004 0.045 1122 Dihedral : 4.427 23.234 927 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.49 % Allowed : 17.57 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.30), residues: 844 helix: 2.29 (0.29), residues: 362 sheet: -0.29 (0.40), residues: 169 loop : -1.32 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.014 0.002 PHE C 278 TYR 0.013 0.002 TYR C 59 ARG 0.011 0.001 ARG B 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.666 Fit side-chains REVERT: B 8 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6873 (tm-30) REVERT: B 28 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7122 (mm-30) REVERT: B 32 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7457 (mtm-85) REVERT: C 68 ARG cc_start: 0.8369 (ttt180) cc_final: 0.7742 (ttt-90) REVERT: C 76 ASP cc_start: 0.7543 (p0) cc_final: 0.7233 (p0) REVERT: C 134 ARG cc_start: 0.7266 (pmt-80) cc_final: 0.6678 (pmt-80) REVERT: C 258 ASP cc_start: 0.7709 (t70) cc_final: 0.6862 (t0) REVERT: C 283 ARG cc_start: 0.8313 (tpp80) cc_final: 0.7971 (tpt-90) REVERT: C 285 LEU cc_start: 0.8503 (tt) cc_final: 0.8256 (tt) REVERT: C 289 TYR cc_start: 0.8439 (m-80) cc_final: 0.8157 (m-80) REVERT: C 318 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8146 (mp) REVERT: C 338 ILE cc_start: 0.8642 (mm) cc_final: 0.8265 (mt) REVERT: R 30 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6799 (mm) REVERT: R 51 LEU cc_start: 0.8018 (mt) cc_final: 0.7692 (mp) REVERT: R 172 TRP cc_start: 0.6055 (OUTLIER) cc_final: 0.4814 (m100) outliers start: 16 outliers final: 11 residues processed: 151 average time/residue: 0.2711 time to fit residues: 49.9488 Evaluate side-chains 161 residues out of total 742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 234 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 83 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.100154 restraints weight = 9690.368| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.24 r_work: 0.3143 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6578 Z= 0.205 Angle : 0.537 8.050 8964 Z= 0.280 Chirality : 0.042 0.131 1061 Planarity : 0.003 0.040 1122 Dihedral : 4.235 24.457 927 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.33 % Allowed : 18.20 % Favored : 79.47 % 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: 0.93 (0.30), residues: 844 helix: 2.58 (0.29), residues: 354 sheet: -0.20 (0.41), residues: 165 loop : -1.21 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.013 0.001 PHE R 178 TYR 0.009 0.001 TYR C 59 ARG 0.010 0.000 ARG B 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4282.18 seconds wall clock time: 73 minutes 56.71 seconds (4436.71 seconds total)