Starting phenix.real_space_refine on Fri Aug 7 14:25:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q25_72150/08_2026/9q25_72150_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q25_72150/08_2026/9q25_72150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q25_72150/08_2026/9q25_72150_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q25_72150/08_2026/9q25_72150_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q25_72150/08_2026/9q25_72150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q25_72150/08_2026/9q25_72150.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 4 5.21 5 S 67 5.16 5 C 7416 2.51 5 N 2071 2.21 5 O 2243 1.98 5 H 9484 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21300 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 5164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5164 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 312} Chain breaks: 1 Chain: "D" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4704 Classifications: {'peptide': 306} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 297} Chain breaks: 1 Chain: "G" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2335 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 294} Chain breaks: 1 Chain: "H" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "R" Number of atoms: 5044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 5044 Classifications: {'peptide': 321} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 300} Chain breaks: 2 Chain: "X" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3833 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.72, per 1000 atoms: 0.13 Number of scatterers: 21300 At special positions: 0 Unit cell: (93.4, 106.476, 152.242, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 67 16.00 P 15 15.00 Mg 4 11.99 O 2243 8.00 N 2071 7.00 C 7416 6.00 H 9484 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.71 Conformation dependent library (CDL) restraints added in 498.7 milliseconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2782 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 10 sheets defined 53.1% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 35 through 40 removed outlier: 4.530A pdb=" N GLU C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.603A pdb=" N ILE C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 143 through 144 No H-bonds generated for 'chain 'C' and resid 143 through 144' Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 165 through 188 removed outlier: 3.530A pdb=" N LYS C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 199 removed outlier: 3.514A pdb=" N ARG C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix removed outlier: 3.576A pdb=" N GLU C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 277 Processing helix chain 'C' and resid 303 through 308 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 46 through 61 Processing helix chain 'D' and resid 68 through 79 Processing helix chain 'D' and resid 86 through 93 Processing helix chain 'D' and resid 112 through 128 Processing helix chain 'D' and resid 142 through 152 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'D' and resid 174 through 193 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.734A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'D' and resid 220 through 240 removed outlier: 4.160A pdb=" N LEU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 270 removed outlier: 4.137A pdb=" N TRP D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 32 Processing helix chain 'G' and resid 34 through 44 Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 67 through 81 Processing helix chain 'G' and resid 88 through 96 Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 132 through 145 removed outlier: 4.069A pdb=" N GLN G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.573A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 188 Processing helix chain 'G' and resid 196 through 214 Processing helix chain 'G' and resid 223 through 232 removed outlier: 4.386A pdb=" N LEU G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 289 through 294 removed outlier: 3.796A pdb=" N ALA G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 289 through 294' Processing helix chain 'R' and resid 1 through 6 Processing helix chain 'R' and resid 9 through 20 Processing helix chain 'R' and resid 23 through 30 removed outlier: 3.595A pdb=" N PHE R 30 " --> pdb=" O GLU R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 40 Processing helix chain 'R' and resid 42 through 59 Processing helix chain 'R' and resid 64 through 71 Processing helix chain 'R' and resid 75 through 80 removed outlier: 3.751A pdb=" N HIS R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 94 Processing helix chain 'R' and resid 112 through 124 Processing helix chain 'R' and resid 125 through 126 No H-bonds generated for 'chain 'R' and resid 125 through 126' Processing helix chain 'R' and resid 127 through 131 Processing helix chain 'R' and resid 147 through 162 Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 166 through 172 Processing helix chain 'R' and resid 174 through 178 removed outlier: 3.576A pdb=" N GLN R 178 " --> pdb=" O ARG R 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 174 through 178' Processing helix chain 'R' and resid 186 through 204 removed outlier: 4.564A pdb=" N VAL R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Proline residue: R 199 - end of helix Processing helix chain 'R' and resid 215 through 221 removed outlier: 3.991A pdb=" N PHE R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 250 removed outlier: 3.768A pdb=" N ALA R 232 " --> pdb=" O SER R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 290 removed outlier: 3.730A pdb=" N TRP R 288 " --> pdb=" O LEU R 284 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 67 Processing helix chain 'X' and resid 68 through 72 Processing helix chain 'X' and resid 88 through 99 Processing helix chain 'X' and resid 104 through 113 Processing helix chain 'X' and resid 122 through 140 removed outlier: 4.025A pdb=" N GLU X 134 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 153 No H-bonds generated for 'chain 'X' and resid 151 through 153' Processing helix chain 'X' and resid 154 through 162 Processing helix chain 'X' and resid 165 through 188 removed outlier: 4.971A pdb=" N THR X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU X 173 " --> pdb=" O GLN X 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 235 removed outlier: 3.761A pdb=" N LEU X 234 " --> pdb=" O ALA X 230 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.210A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN D 131 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D 202 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG D 275 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AA3, first strand: chain 'C' and resid 208 through 212 removed outlier: 5.752A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 238 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 279 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 208 through 212 removed outlier: 5.752A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 238 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 279 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR C 121 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASN C 284 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE C 123 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N MET C 286 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY C 125 " --> pdb=" O MET C 286 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N THR C 288 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR C 120 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 313 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU C 122 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE C 315 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N CYS C 124 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N TRP C 317 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG C 322 " --> pdb=" O PHE C 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.505A pdb=" N VAL X 78 " --> pdb=" O PHE X 116 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL X 118 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE X 80 " --> pdb=" O VAL X 118 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU X 77 " --> pdb=" O LEU X 143 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU X 145 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE X 43 " --> pdb=" O HIS X 237 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N MET X 239 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU X 45 " --> pdb=" O MET X 239 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE X 241 " --> pdb=" O GLU X 45 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N HIS X 47 " --> pdb=" O PHE X 241 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N LYS X 243 " --> pdb=" O HIS X 47 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLN X 252 " --> pdb=" O GLN X 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'D' and resid 251 through 253 Processing sheet with id=AA8, first strand: chain 'G' and resid 189 through 193 removed outlier: 6.430A pdb=" N LYS G 156 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE G 220 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N MET G 158 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP G 222 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE G 160 " --> pdb=" O ASP G 222 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA G 217 " --> pdb=" O ALA G 262 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL G 264 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU G 219 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR G 266 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL G 221 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE G 122 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU G 300 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N LYS G 304 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 81 through 82 Processing sheet with id=AB1, first strand: chain 'R' and resid 179 through 183 removed outlier: 6.494A pdb=" N ALA R 137 " --> pdb=" O PHE R 180 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLU R 182 " --> pdb=" O ALA R 137 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR R 139 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLY R 136 " --> pdb=" O ALA R 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU R 209 " --> pdb=" O GLY R 136 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE R 102 " --> pdb=" O VAL R 294 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LEU R 296 " --> pdb=" O ILE R 102 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLU R 104 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA R 298 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA R 106 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG R 295 " --> pdb=" O LEU R 318 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG R 313 " --> pdb=" O TYR R 330 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1779 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: 4.15 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9453 1.03 - 1.23: 38 1.23 - 1.42: 4809 1.42 - 1.61: 7096 1.61 - 1.81: 98 Bond restraints: 21494 Sorted by residual: bond pdb=" N MET R 1 " pdb=" H2 MET R 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N MET D 1 " pdb=" H3 MET D 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N MET D 1 " pdb=" H2 MET D 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N MET R 1 " pdb=" H3 MET R 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1' DT H 8 " pdb=" N1 DT H 8 " ideal model delta sigma weight residual 1.468 1.494 -0.026 1.40e-02 5.10e+03 3.46e+00 ... (remaining 21489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.71: 37792 20.71 - 41.42: 0 41.42 - 62.14: 0 62.14 - 82.85: 0 82.85 - 103.56: 1 Bond angle restraints: 37793 Sorted by residual: angle pdb=" H1 MET R 1 " pdb=" N MET R 1 " pdb=" H2 MET R 1 " ideal model delta sigma weight residual 109.47 5.91 103.56 3.00e+00 1.11e-01 1.19e+03 angle pdb=" C ASP X 149 " pdb=" N SER X 150 " pdb=" CA SER X 150 " ideal model delta sigma weight residual 121.70 130.37 -8.67 1.80e+00 3.09e-01 2.32e+01 angle pdb=" C2' ADP R 401 " pdb=" C1' ADP R 401 " pdb=" N9 ADP R 401 " ideal model delta sigma weight residual 109.47 123.50 -14.03 3.00e+00 1.11e-01 2.19e+01 angle pdb=" H1 MET D 1 " pdb=" N MET D 1 " pdb=" H3 MET D 1 " ideal model delta sigma weight residual 109.47 96.67 12.80 3.00e+00 1.11e-01 1.82e+01 angle pdb=" N3 DT H 11 " pdb=" C4 DT H 11 " pdb=" O4 DT H 11 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 37788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9858 17.93 - 35.85: 299 35.85 - 53.78: 146 53.78 - 71.71: 49 71.71 - 89.63: 15 Dihedral angle restraints: 10367 sinusoidal: 5618 harmonic: 4749 Sorted by residual: dihedral pdb=" CA PRO G 83 " pdb=" C PRO G 83 " pdb=" N MET G 84 " pdb=" CA MET G 84 " ideal model delta harmonic sigma weight residual 180.00 -162.31 -17.69 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" N MET C 10 " pdb=" CA MET C 10 " pdb=" CB MET C 10 " pdb=" CG MET C 10 " ideal model delta sinusoidal sigma weight residual -60.00 -113.92 53.92 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" CA ARG X 64 " pdb=" CB ARG X 64 " pdb=" CG ARG X 64 " pdb=" CD ARG X 64 " ideal model delta sinusoidal sigma weight residual 60.00 113.07 -53.07 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 10364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 1903 0.349 - 0.698: 0 0.698 - 1.048: 0 1.048 - 1.397: 0 1.397 - 1.746: 1 Chirality restraints: 1904 Sorted by residual: chirality pdb=" C1' ADP R 401 " pdb=" C2' ADP R 401 " pdb=" N9 ADP R 401 " pdb=" O4' ADP R 401 " both_signs ideal model delta sigma weight residual False 2.48 0.74 1.75 2.00e-01 2.50e+01 7.62e+01 chirality pdb=" C2' ATP X 301 " pdb=" C1' ATP X 301 " pdb=" C3' ATP X 301 " pdb=" O2' ATP X 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP D 401 " pdb=" C1' ATP D 401 " pdb=" C3' ATP D 401 " pdb=" O2' ATP D 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1901 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 82 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO G 83 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 83 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 83 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER X 37 " 0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO X 38 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO X 38 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO X 38 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 124 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C VAL D 124 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL D 124 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA D 125 " 0.007 2.00e-02 2.50e+03 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 831 2.19 - 2.79: 40501 2.79 - 3.39: 55054 3.39 - 4.00: 74077 4.00 - 4.60: 117069 Nonbonded interactions: 287532 Sorted by model distance: nonbonded pdb=" OE1 GLU D 104 " pdb=" HE ARG D 275 " model vdw 1.586 2.450 nonbonded pdb=" HG SER C 47 " pdb=" O ILE C 52 " model vdw 1.607 2.450 nonbonded pdb=" OE1 GLU X 28 " pdb=" H LEU X 31 " model vdw 1.635 2.450 nonbonded pdb=" HG1 THR D 84 " pdb=" OD1 ASP D 90 " model vdw 1.639 2.450 nonbonded pdb=" OD1 ASP C 254 " pdb=" HG SER C 256 " model vdw 1.646 2.450 ... (remaining 287527 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: 3.860 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: 0.090 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.780 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 : 0.002 0.034 12010 Z= 0.114 Angle : 0.494 14.029 16272 Z= 0.261 Chirality : 0.057 1.746 1904 Planarity : 0.002 0.030 2049 Dihedral : 9.723 87.668 4536 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 0.71 % Allowed : 1.81 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.24), residues: 1470 helix: 2.96 (0.21), residues: 650 sheet: 0.07 (0.34), residues: 253 loop : 0.24 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.005 0.001 TYR D 72 PHE 0.005 0.001 PHE G 248 TRP 0.005 0.001 TRP D 314 HIS 0.002 0.000 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (12010) covalent geometry : angle 0.49362 / 0.26 (16272) hydrogen bonds : bond 0.16217 / 10.74 ( 616) hydrogen bonds : angle 6.64468 / 4.84 ( 1779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 236 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ASP cc_start: 0.7817 (m-30) cc_final: 0.7601 (m-30) REVERT: C 263 ASN cc_start: 0.9040 (m-40) cc_final: 0.8759 (m-40) REVERT: C 277 ARG cc_start: 0.8217 (mtt180) cc_final: 0.7607 (mmt180) REVERT: C 303 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8519 (pt0) REVERT: C 320 LYS cc_start: 0.9270 (mttt) cc_final: 0.8868 (mmmt) REVERT: C 327 TYR cc_start: 0.9027 (t80) cc_final: 0.8461 (t80) REVERT: D 201 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8157 (tppt) REVERT: G 34 ASN cc_start: 0.9036 (m-40) cc_final: 0.8786 (t0) REVERT: G 47 HIS cc_start: 0.7841 (m-70) cc_final: 0.7530 (m-70) REVERT: G 158 MET cc_start: 0.6637 (ttm) cc_final: 0.6278 (mtp) REVERT: G 250 ARG cc_start: 0.8869 (ttt180) cc_final: 0.8599 (ttp80) REVERT: G 326 MET cc_start: 0.7994 (mtt) cc_final: 0.7410 (mmt) REVERT: R 134 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8715 (mm-30) REVERT: R 181 ILE cc_start: 0.9207 (mt) cc_final: 0.8818 (mt) REVERT: R 182 GLU cc_start: 0.8383 (tp30) cc_final: 0.7732 (mm-30) REVERT: R 244 GLU cc_start: 0.8770 (tt0) cc_final: 0.8344 (tp30) REVERT: R 299 ASP cc_start: 0.8386 (t0) cc_final: 0.8130 (t70) REVERT: X 24 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7132 (mt) REVERT: X 131 TYR cc_start: 0.8985 (m-80) cc_final: 0.8758 (m-10) REVERT: X 167 ASN cc_start: 0.8866 (m-40) cc_final: 0.8438 (t0) REVERT: X 185 ASN cc_start: 0.8753 (m-40) cc_final: 0.8492 (m110) REVERT: X 224 ARG cc_start: 0.7714 (ttt90) cc_final: 0.7304 (tmt170) outliers start: 9 outliers final: 2 residues processed: 241 average time/residue: 0.3103 time to fit residues: 96.6666 Evaluate side-chains 140 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.0030 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 294 GLN D 123 ASN D 301 GLN G 62 ASN G 294 HIS X 233 GLN X 251 ASN X 252 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.093017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.064107 restraints weight = 64232.198| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.45 r_work: 0.2748 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12010 Z= 0.151 Angle : 0.521 6.332 16272 Z= 0.267 Chirality : 0.040 0.160 1904 Planarity : 0.003 0.035 2049 Dihedral : 9.692 87.919 1750 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 0.87 % Allowed : 5.59 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.23), residues: 1470 helix: 2.52 (0.21), residues: 680 sheet: -0.05 (0.33), residues: 253 loop : 0.16 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 128 TYR 0.007 0.001 TYR G 54 PHE 0.018 0.001 PHE G 129 TRP 0.004 0.001 TRP R 47 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (12010) covalent geometry : angle 0.52119 / 0.27 (16272) hydrogen bonds : bond 0.04209 / 2.86 ( 616) hydrogen bonds : angle 5.28860 / 3.84 ( 1779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASP cc_start: 0.8633 (m-30) cc_final: 0.8212 (m-30) REVERT: C 277 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8007 (mmt180) REVERT: C 303 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8552 (pt0) REVERT: C 320 LYS cc_start: 0.9301 (mttt) cc_final: 0.8981 (mmmt) REVERT: C 327 TYR cc_start: 0.9144 (t80) cc_final: 0.8602 (t80) REVERT: C 342 LYS cc_start: 0.8723 (mttt) cc_final: 0.8523 (mttm) REVERT: D 201 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8440 (tppt) REVERT: G 34 ASN cc_start: 0.9038 (m-40) cc_final: 0.8778 (t0) REVERT: G 158 MET cc_start: 0.6801 (ttm) cc_final: 0.6538 (mtp) REVERT: G 211 MET cc_start: 0.8995 (mtp) cc_final: 0.8718 (mtp) REVERT: G 250 ARG cc_start: 0.8635 (ttt180) cc_final: 0.8354 (ttm-80) REVERT: G 259 PHE cc_start: 0.7300 (m-80) cc_final: 0.6802 (m-80) REVERT: G 326 MET cc_start: 0.8198 (mtt) cc_final: 0.7875 (tpp) REVERT: R 244 GLU cc_start: 0.8868 (tt0) cc_final: 0.8426 (tp30) REVERT: X 24 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7320 (mt) REVERT: X 28 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7550 (tm-30) REVERT: X 131 TYR cc_start: 0.9156 (m-80) cc_final: 0.8911 (m-10) REVERT: X 185 ASN cc_start: 0.8879 (m-40) cc_final: 0.8610 (m110) REVERT: X 224 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7580 (tmt170) outliers start: 11 outliers final: 7 residues processed: 146 average time/residue: 0.2806 time to fit residues: 54.6348 Evaluate side-chains 127 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 174 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 263 ASN G 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.092668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.063967 restraints weight = 63671.710| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.43 r_work: 0.2744 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12010 Z= 0.132 Angle : 0.488 5.874 16272 Z= 0.247 Chirality : 0.039 0.141 1904 Planarity : 0.004 0.056 2049 Dihedral : 9.165 82.044 1750 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 0.79 % Allowed : 6.54 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.23), residues: 1470 helix: 2.59 (0.20), residues: 680 sheet: -0.24 (0.33), residues: 249 loop : 0.16 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 65 TYR 0.006 0.001 TYR C 209 PHE 0.011 0.001 PHE X 270 TRP 0.002 0.001 TRP D 314 HIS 0.003 0.001 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (12010) covalent geometry : angle 0.48846 / 0.25 (16272) hydrogen bonds : bond 0.03240 / 2.22 ( 616) hydrogen bonds : angle 4.83200 / 3.51 ( 1779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASP cc_start: 0.8602 (m-30) cc_final: 0.8169 (m-30) REVERT: C 165 MET cc_start: 0.8925 (mmp) cc_final: 0.8582 (mmt) REVERT: C 274 ASN cc_start: 0.9117 (t0) cc_final: 0.8914 (t0) REVERT: C 277 ARG cc_start: 0.8684 (mtt180) cc_final: 0.8080 (mmt180) REVERT: C 303 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8523 (pt0) REVERT: C 320 LYS cc_start: 0.9299 (mttt) cc_final: 0.8988 (mmmt) REVERT: C 327 TYR cc_start: 0.9147 (t80) cc_final: 0.8712 (t80) REVERT: C 342 LYS cc_start: 0.8715 (mttt) cc_final: 0.8511 (mttm) REVERT: D 1 MET cc_start: 0.6331 (mtt) cc_final: 0.5812 (mtm) REVERT: D 201 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8530 (tppt) REVERT: G 34 ASN cc_start: 0.8952 (m-40) cc_final: 0.8699 (t0) REVERT: G 158 MET cc_start: 0.6904 (ttm) cc_final: 0.6656 (mtp) REVERT: G 210 MET cc_start: 0.9127 (mtt) cc_final: 0.8862 (mpp) REVERT: G 211 MET cc_start: 0.8865 (mtp) cc_final: 0.8656 (mtp) REVERT: G 250 ARG cc_start: 0.8765 (ttt180) cc_final: 0.8368 (ttm-80) REVERT: G 259 PHE cc_start: 0.7202 (m-80) cc_final: 0.6736 (m-80) REVERT: G 326 MET cc_start: 0.8221 (mtt) cc_final: 0.7791 (mmt) REVERT: R 244 GLU cc_start: 0.8871 (tt0) cc_final: 0.8437 (tp30) REVERT: X 24 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7231 (mt) REVERT: X 131 TYR cc_start: 0.9172 (m-80) cc_final: 0.8899 (m-10) REVERT: X 185 ASN cc_start: 0.8891 (m-40) cc_final: 0.8615 (m110) REVERT: X 224 ARG cc_start: 0.7996 (ttt90) cc_final: 0.7660 (ttt-90) outliers start: 10 outliers final: 7 residues processed: 131 average time/residue: 0.2570 time to fit residues: 45.5514 Evaluate side-chains 122 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 174 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065815 restraints weight = 64535.230| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.34 r_work: 0.2805 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12010 Z= 0.188 Angle : 0.501 5.860 16272 Z= 0.254 Chirality : 0.039 0.139 1904 Planarity : 0.003 0.037 2049 Dihedral : 8.735 79.208 1750 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 0.87 % Allowed : 6.61 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.23), residues: 1470 helix: 2.57 (0.20), residues: 679 sheet: -0.51 (0.32), residues: 254 loop : 0.12 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 21 TYR 0.008 0.001 TYR C 209 PHE 0.012 0.001 PHE G 92 TRP 0.004 0.001 TRP D 314 HIS 0.003 0.001 HIS R 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (12010) covalent geometry : angle 0.50069 / 0.25 (16272) hydrogen bonds : bond 0.03108 / 2.10 ( 616) hydrogen bonds : angle 4.66534 / 3.39 ( 1779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASP cc_start: 0.8499 (m-30) cc_final: 0.8185 (m-30) REVERT: C 277 ARG cc_start: 0.8808 (mtt180) cc_final: 0.8475 (mmt180) REVERT: C 327 TYR cc_start: 0.9019 (t80) cc_final: 0.8711 (t80) REVERT: D 201 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8807 (tppt) REVERT: G 34 ASN cc_start: 0.8944 (m-40) cc_final: 0.8716 (t0) REVERT: G 158 MET cc_start: 0.7312 (ttm) cc_final: 0.6858 (mtp) REVERT: G 210 MET cc_start: 0.9008 (mtt) cc_final: 0.8697 (mpp) REVERT: G 326 MET cc_start: 0.8190 (mtt) cc_final: 0.7937 (mmt) REVERT: R 244 GLU cc_start: 0.8796 (tt0) cc_final: 0.8568 (tp30) REVERT: X 24 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7192 (mt) REVERT: X 131 TYR cc_start: 0.9403 (m-80) cc_final: 0.9183 (m-10) REVERT: X 136 MET cc_start: 0.9108 (ttm) cc_final: 0.8856 (ttt) REVERT: X 185 ASN cc_start: 0.8962 (m-40) cc_final: 0.8671 (m110) outliers start: 11 outliers final: 7 residues processed: 124 average time/residue: 0.2546 time to fit residues: 43.2883 Evaluate side-chains 117 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 174 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.094075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.066187 restraints weight = 64229.974| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.33 r_work: 0.2815 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12010 Z= 0.154 Angle : 0.485 5.633 16272 Z= 0.245 Chirality : 0.039 0.136 1904 Planarity : 0.003 0.048 2049 Dihedral : 8.548 77.942 1750 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 0.87 % Allowed : 6.85 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.23), residues: 1470 helix: 2.62 (0.20), residues: 679 sheet: -0.61 (0.32), residues: 254 loop : 0.11 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 65 TYR 0.007 0.001 TYR D 72 PHE 0.011 0.001 PHE G 92 TRP 0.003 0.001 TRP C 317 HIS 0.004 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (12010) covalent geometry : angle 0.48494 / 0.24 (16272) hydrogen bonds : bond 0.02905 / 1.98 ( 616) hydrogen bonds : angle 4.53246 / 3.29 ( 1779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 ARG cc_start: 0.8780 (mtt180) cc_final: 0.8449 (mmt180) REVERT: C 327 TYR cc_start: 0.9022 (t80) cc_final: 0.8733 (t80) REVERT: D 201 LYS cc_start: 0.9086 (mmtt) cc_final: 0.8811 (tppt) REVERT: G 34 ASN cc_start: 0.8923 (m-40) cc_final: 0.8691 (t0) REVERT: G 158 MET cc_start: 0.7474 (ttm) cc_final: 0.6778 (mtp) REVERT: G 210 MET cc_start: 0.8964 (mtt) cc_final: 0.8414 (mtt) REVERT: G 211 MET cc_start: 0.8388 (mmm) cc_final: 0.8094 (mmm) REVERT: G 326 MET cc_start: 0.8224 (mtt) cc_final: 0.7953 (mmt) REVERT: R 54 SER cc_start: 0.9502 (m) cc_final: 0.9218 (p) REVERT: R 244 GLU cc_start: 0.8795 (tt0) cc_final: 0.8564 (tp30) REVERT: X 24 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7200 (mt) REVERT: X 131 TYR cc_start: 0.9403 (m-80) cc_final: 0.9174 (m-10) REVERT: X 136 MET cc_start: 0.9102 (ttm) cc_final: 0.8846 (ttt) REVERT: X 185 ASN cc_start: 0.8955 (m-40) cc_final: 0.8657 (m110) outliers start: 11 outliers final: 9 residues processed: 119 average time/residue: 0.2406 time to fit residues: 40.3092 Evaluate side-chains 116 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 108 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.094040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.066491 restraints weight = 64414.735| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.30 r_work: 0.2812 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12010 Z= 0.154 Angle : 0.483 5.536 16272 Z= 0.243 Chirality : 0.039 0.136 1904 Planarity : 0.003 0.040 2049 Dihedral : 8.413 78.228 1750 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 1.10 % Allowed : 7.09 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.23), residues: 1470 helix: 2.69 (0.20), residues: 672 sheet: -0.65 (0.32), residues: 254 loop : 0.07 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 65 TYR 0.007 0.001 TYR C 209 PHE 0.012 0.001 PHE G 92 TRP 0.003 0.001 TRP C 317 HIS 0.003 0.001 HIS R 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (12010) covalent geometry : angle 0.48276 / 0.24 (16272) hydrogen bonds : bond 0.02823 / 1.92 ( 616) hydrogen bonds : angle 4.45354 / 3.23 ( 1779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 193 ARG cc_start: 0.8868 (mtt180) cc_final: 0.8584 (mpp80) REVERT: C 277 ARG cc_start: 0.8777 (mtt180) cc_final: 0.8443 (mmt180) REVERT: C 327 TYR cc_start: 0.9021 (t80) cc_final: 0.8743 (t80) REVERT: D 201 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8814 (tppt) REVERT: G 34 ASN cc_start: 0.8911 (m-40) cc_final: 0.8680 (t0) REVERT: G 210 MET cc_start: 0.8888 (mtt) cc_final: 0.8644 (mtt) REVERT: G 326 MET cc_start: 0.8234 (mtt) cc_final: 0.7956 (mmt) REVERT: R 54 SER cc_start: 0.9497 (m) cc_final: 0.9242 (p) REVERT: R 244 GLU cc_start: 0.8804 (tt0) cc_final: 0.8581 (tp30) REVERT: X 24 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7177 (mt) REVERT: X 131 TYR cc_start: 0.9396 (m-80) cc_final: 0.9164 (m-10) REVERT: X 136 MET cc_start: 0.9111 (ttm) cc_final: 0.8902 (ttt) REVERT: X 185 ASN cc_start: 0.8953 (m-40) cc_final: 0.8649 (m110) outliers start: 14 outliers final: 10 residues processed: 119 average time/residue: 0.2585 time to fit residues: 42.9810 Evaluate side-chains 117 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 174 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 32 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066423 restraints weight = 64304.115| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.30 r_work: 0.2811 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12010 Z= 0.147 Angle : 0.481 5.513 16272 Z= 0.241 Chirality : 0.039 0.138 1904 Planarity : 0.003 0.036 2049 Dihedral : 8.283 78.479 1750 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.94 % Rotamer: Outliers : 1.18 % Allowed : 7.17 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.23), residues: 1470 helix: 2.71 (0.20), residues: 673 sheet: -0.71 (0.33), residues: 244 loop : 0.09 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 65 TYR 0.008 0.001 TYR G 216 PHE 0.011 0.001 PHE G 92 TRP 0.004 0.001 TRP C 317 HIS 0.003 0.001 HIS X 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (12010) covalent geometry : angle 0.48052 / 0.24 (16272) hydrogen bonds : bond 0.02726 / 1.85 ( 616) hydrogen bonds : angle 4.38806 / 3.18 ( 1779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 193 ARG cc_start: 0.8874 (mtt180) cc_final: 0.8558 (mpp80) REVERT: C 277 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8458 (mmt180) REVERT: C 327 TYR cc_start: 0.9029 (t80) cc_final: 0.8757 (t80) REVERT: D 201 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8819 (tppt) REVERT: D 314 TRP cc_start: 0.6955 (OUTLIER) cc_final: 0.5391 (m-90) REVERT: G 34 ASN cc_start: 0.8918 (m-40) cc_final: 0.8686 (t0) REVERT: G 326 MET cc_start: 0.8226 (mtt) cc_final: 0.7952 (mmt) REVERT: R 54 SER cc_start: 0.9492 (m) cc_final: 0.9242 (p) REVERT: R 244 GLU cc_start: 0.8810 (tt0) cc_final: 0.8581 (tp30) REVERT: X 24 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7110 (mt) REVERT: X 131 TYR cc_start: 0.9397 (m-80) cc_final: 0.9163 (m-10) REVERT: X 136 MET cc_start: 0.9111 (ttm) cc_final: 0.8898 (ttt) REVERT: X 185 ASN cc_start: 0.8958 (m-40) cc_final: 0.8653 (m110) REVERT: X 239 MET cc_start: 0.8937 (mtt) cc_final: 0.8539 (mtt) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 0.2713 time to fit residues: 44.0087 Evaluate side-chains 120 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 28 GLU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 174 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 136 optimal weight: 1.9990 chunk 128 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.093793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.066296 restraints weight = 64142.678| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.31 r_work: 0.2813 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12010 Z= 0.142 Angle : 0.481 5.506 16272 Z= 0.240 Chirality : 0.039 0.136 1904 Planarity : 0.003 0.035 2049 Dihedral : 8.193 78.575 1750 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Rotamer: Outliers : 1.02 % Allowed : 7.32 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.23), residues: 1470 helix: 2.65 (0.20), residues: 680 sheet: -0.70 (0.33), residues: 244 loop : 0.04 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 254 TYR 0.007 0.001 TYR D 72 PHE 0.011 0.001 PHE G 92 TRP 0.004 0.001 TRP C 317 HIS 0.003 0.001 HIS X 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (12010) covalent geometry : angle 0.48137 / 0.24 (16272) hydrogen bonds : bond 0.02671 / 1.81 ( 616) hydrogen bonds : angle 4.32708 / 3.13 ( 1779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 193 ARG cc_start: 0.8880 (mtt180) cc_final: 0.8559 (mpp80) REVERT: C 277 ARG cc_start: 0.8782 (mtt180) cc_final: 0.8453 (mmt180) REVERT: C 327 TYR cc_start: 0.9028 (t80) cc_final: 0.8763 (t80) REVERT: D 201 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8813 (tppt) REVERT: D 314 TRP cc_start: 0.6962 (OUTLIER) cc_final: 0.5481 (m-90) REVERT: G 33 ILE cc_start: 0.9049 (mm) cc_final: 0.8824 (mm) REVERT: G 34 ASN cc_start: 0.8936 (m-40) cc_final: 0.8697 (t0) REVERT: G 158 MET cc_start: 0.7455 (ttm) cc_final: 0.6958 (mtp) REVERT: G 211 MET cc_start: 0.8274 (mmt) cc_final: 0.7919 (mmm) REVERT: G 326 MET cc_start: 0.8229 (mtt) cc_final: 0.7972 (mmt) REVERT: R 54 SER cc_start: 0.9487 (m) cc_final: 0.9238 (p) REVERT: R 244 GLU cc_start: 0.8811 (tt0) cc_final: 0.8583 (tp30) REVERT: X 24 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7190 (mt) REVERT: X 131 TYR cc_start: 0.9404 (m-80) cc_final: 0.9163 (m-10) REVERT: X 136 MET cc_start: 0.9116 (ttm) cc_final: 0.8900 (ttt) REVERT: X 185 ASN cc_start: 0.8961 (m-40) cc_final: 0.8658 (m110) REVERT: X 239 MET cc_start: 0.8949 (mtt) cc_final: 0.8557 (mtt) outliers start: 13 outliers final: 11 residues processed: 115 average time/residue: 0.2369 time to fit residues: 37.9825 Evaluate side-chains 118 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 174 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 80 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.092401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.064664 restraints weight = 65006.430| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.31 r_work: 0.2777 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12010 Z= 0.271 Angle : 0.546 8.775 16272 Z= 0.277 Chirality : 0.041 0.150 1904 Planarity : 0.003 0.036 2049 Dihedral : 8.358 78.626 1750 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 1.18 % Allowed : 7.40 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.23), residues: 1470 helix: 2.47 (0.20), residues: 680 sheet: -0.92 (0.33), residues: 244 loop : -0.03 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 65 TYR 0.011 0.001 TYR D 72 PHE 0.014 0.001 PHE G 92 TRP 0.006 0.001 TRP C 317 HIS 0.004 0.001 HIS D 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.27 (12010) covalent geometry : angle 0.54592 / 0.28 (16272) hydrogen bonds : bond 0.02987 / 2.02 ( 616) hydrogen bonds : angle 4.56233 / 3.29 ( 1779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 ARG cc_start: 0.8798 (mtt180) cc_final: 0.8507 (mmt180) REVERT: C 327 TYR cc_start: 0.9063 (t80) cc_final: 0.8805 (t80) REVERT: D 45 LEU cc_start: 0.8603 (mm) cc_final: 0.8380 (mm) REVERT: D 201 LYS cc_start: 0.9133 (mmtt) cc_final: 0.8840 (tppt) REVERT: D 314 TRP cc_start: 0.6939 (OUTLIER) cc_final: 0.5744 (m-90) REVERT: G 33 ILE cc_start: 0.9024 (mm) cc_final: 0.8807 (mm) REVERT: G 34 ASN cc_start: 0.8913 (m-40) cc_final: 0.8669 (t0) REVERT: G 326 MET cc_start: 0.8240 (mtt) cc_final: 0.7953 (mmt) REVERT: R 54 SER cc_start: 0.9483 (m) cc_final: 0.9244 (p) REVERT: R 244 GLU cc_start: 0.8828 (tt0) cc_final: 0.8603 (tp30) REVERT: X 24 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7235 (mt) REVERT: X 131 TYR cc_start: 0.9421 (m-80) cc_final: 0.9206 (m-10) REVERT: X 136 MET cc_start: 0.9146 (ttm) cc_final: 0.8931 (ttt) REVERT: X 239 MET cc_start: 0.8989 (mtt) cc_final: 0.8613 (mtt) outliers start: 15 outliers final: 13 residues processed: 116 average time/residue: 0.2512 time to fit residues: 40.5138 Evaluate side-chains 120 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 174 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 66 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 60 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066255 restraints weight = 64547.957| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.33 r_work: 0.2815 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12010 Z= 0.111 Angle : 0.481 7.353 16272 Z= 0.240 Chirality : 0.039 0.149 1904 Planarity : 0.003 0.057 2049 Dihedral : 8.127 78.242 1750 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.21 % Rotamer: Outliers : 1.02 % Allowed : 7.72 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.23), residues: 1470 helix: 2.64 (0.20), residues: 680 sheet: -0.82 (0.33), residues: 244 loop : 0.03 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 65 TYR 0.005 0.001 TYR C 209 PHE 0.010 0.001 PHE G 92 TRP 0.003 0.001 TRP C 317 HIS 0.004 0.001 HIS X 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (12010) covalent geometry : angle 0.48120 / 0.24 (16272) hydrogen bonds : bond 0.02644 / 1.79 ( 616) hydrogen bonds : angle 4.30410 / 3.11 ( 1779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 ARG cc_start: 0.8789 (mtt180) cc_final: 0.8436 (mmt180) REVERT: C 327 TYR cc_start: 0.9052 (t80) cc_final: 0.8794 (t80) REVERT: D 201 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8802 (tppt) REVERT: D 314 TRP cc_start: 0.6919 (OUTLIER) cc_final: 0.5712 (m-90) REVERT: G 33 ILE cc_start: 0.8989 (mm) cc_final: 0.8769 (mm) REVERT: G 34 ASN cc_start: 0.8909 (m-40) cc_final: 0.8668 (t0) REVERT: G 326 MET cc_start: 0.8237 (mtt) cc_final: 0.8031 (ttm) REVERT: R 244 GLU cc_start: 0.8795 (tt0) cc_final: 0.8574 (tp30) REVERT: X 24 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7173 (mt) REVERT: X 131 TYR cc_start: 0.9413 (m-80) cc_final: 0.9172 (m-10) REVERT: X 136 MET cc_start: 0.9112 (ttm) cc_final: 0.8899 (ttt) REVERT: X 239 MET cc_start: 0.8967 (mtt) cc_final: 0.8591 (mtt) outliers start: 13 outliers final: 11 residues processed: 116 average time/residue: 0.2541 time to fit residues: 40.8218 Evaluate side-chains 118 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 224 ASP Chi-restraints excluded: chain X residue 24 LEU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 174 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 104 optimal weight: 0.0870 chunk 85 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 122 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.093563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.065701 restraints weight = 64532.048| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.33 r_work: 0.2804 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12010 Z= 0.142 Angle : 0.486 7.282 16272 Z= 0.242 Chirality : 0.039 0.138 1904 Planarity : 0.003 0.054 2049 Dihedral : 8.091 78.482 1750 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.21 % Rotamer: Outliers : 1.02 % Allowed : 8.03 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.23), residues: 1470 helix: 2.66 (0.20), residues: 679 sheet: -0.79 (0.33), residues: 243 loop : 0.04 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 65 TYR 0.007 0.001 TYR D 72 PHE 0.011 0.001 PHE G 92 TRP 0.004 0.001 TRP C 317 HIS 0.004 0.001 HIS X 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (12010) covalent geometry : angle 0.48636 / 0.24 (16272) hydrogen bonds : bond 0.02667 / 1.80 ( 616) hydrogen bonds : angle 4.30158 / 3.10 ( 1779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4006.96 seconds wall clock time: 68 minutes 55.68 seconds (4135.68 seconds total)