Starting phenix.real_space_refine on Mon Apr 6 20:47:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q25_72150/04_2026/9q25_72150_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q25_72150/04_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_72150/04_2026/9q25_72150_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q25_72150/04_2026/9q25_72150_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q25_72150/04_2026/9q25_72150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q25_72150/04_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-2.1rc1-6017/lib/python3.9/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: 3.70, per 1000 atoms: 0.17 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: 1.95 Conformation dependent library (CDL) restraints added in 602.0 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: 0.59 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: 4.79 Time building geometry restraints manager: 2.59 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=" N MET R 1 " pdb=" CA MET R 1 " ideal model delta sigma weight residual 1.491 1.457 0.034 2.10e-02 2.27e+03 2.61e+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=" N9 ADP R 401 " pdb=" C1' ADP R 401 " pdb=" O4' ADP R 401 " ideal model delta sigma weight residual 109.47 121.37 -11.90 3.00e+00 1.11e-01 1.57e+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: 4.880 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: 0.120 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.480 Find NCS groups from input model: 0.100 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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= 0.099 Angle : 0.486 14.029 16272 Z= 0.237 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 covalent geometry : bond 0.00208 (12010) covalent geometry : angle 0.48610 (16272) hydrogen bonds : bond 0.16217 ( 616) hydrogen bonds : angle 6.64468 ( 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 : 0.625 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: 0.3681 time to fit residues: 112.8917 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 : 0.595 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 233 HIS C 294 GLN D 301 GLN G 62 ASN G 294 HIS G 330 ASN 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 = 0.3467 r_free = 0.3467 target = 0.093134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.063966 restraints weight = 64235.591| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.53 r_work: 0.2742 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12010 Z= 0.147 Angle : 0.522 6.117 16272 Z= 0.266 Chirality : 0.040 0.149 1904 Planarity : 0.003 0.036 2049 Dihedral : 9.532 87.121 1750 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 0.87 % Allowed : 5.83 % Favored : 93.31 % 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: 1.84 (0.23), residues: 1470 helix: 2.56 (0.21), residues: 681 sheet: -0.07 (0.33), residues: 253 loop : 0.19 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 128 TYR 0.006 0.001 TYR C 209 PHE 0.018 0.001 PHE G 129 TRP 0.006 0.001 TRP R 47 HIS 0.004 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00324 (12010) covalent geometry : angle 0.52191 (16272) hydrogen bonds : bond 0.03672 ( 616) hydrogen bonds : angle 5.11872 ( 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 149 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.663 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: 0.8588 (m-30) cc_final: 0.8173 (m-30) REVERT: C 277 ARG cc_start: 0.8605 (mtt180) cc_final: 0.7990 (mmt180) REVERT: C 303 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8533 (pt0) REVERT: C 320 LYS cc_start: 0.9300 (mttt) cc_final: 0.8963 (mmmt) REVERT: C 327 TYR cc_start: 0.9137 (t80) cc_final: 0.8668 (t80) REVERT: D 1 MET cc_start: 0.6292 (mtt) cc_final: 0.5769 (mtm) REVERT: D 201 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8456 (tppt) REVERT: G 34 ASN cc_start: 0.8929 (m-40) cc_final: 0.8685 (t0) REVERT: G 158 MET cc_start: 0.6759 (ttm) cc_final: 0.6541 (mtp) REVERT: G 211 MET cc_start: 0.8967 (mtp) cc_final: 0.8706 (mtp) REVERT: G 228 TYR cc_start: 0.5306 (m-80) cc_final: 0.5074 (m-80) REVERT: G 243 MET cc_start: 0.7925 (ttm) cc_final: 0.7365 (tpp) REVERT: G 250 ARG cc_start: 0.8657 (ttt180) cc_final: 0.8356 (ttm-80) REVERT: G 259 PHE cc_start: 0.7291 (m-80) cc_final: 0.6787 (m-80) REVERT: G 326 MET cc_start: 0.8182 (mtt) cc_final: 0.7890 (tpp) REVERT: R 244 GLU cc_start: 0.8857 (tt0) cc_final: 0.8410 (tp30) REVERT: X 24 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7278 (mt) REVERT: X 28 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7495 (tm-30) REVERT: X 131 TYR cc_start: 0.9112 (m-80) cc_final: 0.8861 (m-10) REVERT: X 185 ASN cc_start: 0.8849 (m-40) cc_final: 0.8579 (m110) REVERT: X 224 ARG cc_start: 0.7965 (ttt90) cc_final: 0.7677 (tmt170) outliers start: 11 outliers final: 7 residues processed: 147 average time/residue: 0.3414 time to fit residues: 65.1116 Evaluate side-chains 130 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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: 0.9980 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.062423 restraints weight = 64302.732| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.50 r_work: 0.2709 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12010 Z= 0.195 Angle : 0.513 5.908 16272 Z= 0.261 Chirality : 0.040 0.139 1904 Planarity : 0.004 0.042 2049 Dihedral : 8.948 79.520 1750 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.28 % Rotamer: Outliers : 0.71 % Allowed : 6.54 % Favored : 92.76 % 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: 2.53 (0.20), residues: 680 sheet: -0.40 (0.32), residues: 255 loop : 0.12 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 65 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 C 316 Details of bonding type rmsd covalent geometry : bond 0.00431 (12010) covalent geometry : angle 0.51341 (16272) hydrogen bonds : bond 0.03355 ( 616) hydrogen bonds : angle 4.81547 ( 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 131 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.623 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 165 MET cc_start: 0.8927 (mmp) cc_final: 0.8673 (mmt) REVERT: C 277 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8026 (mmt180) REVERT: C 303 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8459 (pt0) REVERT: C 320 LYS cc_start: 0.9303 (mttt) cc_final: 0.8980 (mmmt) REVERT: C 327 TYR cc_start: 0.9132 (t80) cc_final: 0.8732 (t80) REVERT: D 201 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8535 (tppt) REVERT: G 34 ASN cc_start: 0.8846 (m-40) cc_final: 0.8616 (t0) REVERT: G 158 MET cc_start: 0.6762 (ttm) cc_final: 0.6438 (mtp) REVERT: G 210 MET cc_start: 0.9109 (mtt) cc_final: 0.8855 (mpp) REVERT: G 211 MET cc_start: 0.8887 (mtp) cc_final: 0.8658 (mmm) REVERT: G 228 TYR cc_start: 0.5426 (m-80) cc_final: 0.5149 (m-80) REVERT: G 250 ARG cc_start: 0.8827 (ttt180) cc_final: 0.8565 (ttm-80) REVERT: G 326 MET cc_start: 0.8221 (mtt) cc_final: 0.7736 (mmt) REVERT: R 244 GLU cc_start: 0.8899 (tt0) cc_final: 0.8491 (tp30) REVERT: X 24 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7295 (mt) REVERT: X 131 TYR cc_start: 0.9136 (m-80) cc_final: 0.8876 (m-10) REVERT: X 185 ASN cc_start: 0.8883 (m-40) cc_final: 0.8608 (m110) REVERT: X 224 ARG cc_start: 0.8009 (ttt90) cc_final: 0.7715 (tmt170) outliers start: 9 outliers final: 7 residues processed: 129 average time/residue: 0.3174 time to fit residues: 53.9827 Evaluate side-chains 124 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 109 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=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: 0.3980 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 125 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3523 r_free = 0.3523 target = 0.094697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.066841 restraints weight = 64251.958| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.34 r_work: 0.2827 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12010 Z= 0.121 Angle : 0.473 5.704 16272 Z= 0.238 Chirality : 0.039 0.140 1904 Planarity : 0.003 0.044 2049 Dihedral : 8.588 77.140 1750 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 0.79 % Allowed : 6.85 % Favored : 92.36 % 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: 1.76 (0.23), residues: 1470 helix: 2.68 (0.20), residues: 679 sheet: -0.47 (0.32), residues: 254 loop : 0.11 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 65 TYR 0.005 0.001 TYR C 209 PHE 0.011 0.001 PHE G 92 TRP 0.003 0.001 TRP D 268 HIS 0.002 0.001 HIS R 29 Details of bonding type rmsd covalent geometry : bond 0.00265 (12010) covalent geometry : angle 0.47330 (16272) hydrogen bonds : bond 0.02847 ( 616) hydrogen bonds : angle 4.52189 ( 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 128 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.628 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: C 277 ARG cc_start: 0.8781 (mtt180) cc_final: 0.8459 (mmt180) REVERT: C 327 TYR cc_start: 0.9009 (t80) cc_final: 0.8721 (t80) REVERT: D 201 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8800 (tppt) REVERT: G 34 ASN cc_start: 0.8924 (m-40) cc_final: 0.8693 (t0) REVERT: G 158 MET cc_start: 0.7316 (ttm) cc_final: 0.6920 (mtp) REVERT: G 210 MET cc_start: 0.9002 (mtt) cc_final: 0.8701 (mpp) REVERT: G 228 TYR cc_start: 0.5888 (m-80) cc_final: 0.5589 (m-80) REVERT: G 326 MET cc_start: 0.8197 (mtt) cc_final: 0.7959 (mmt) REVERT: R 54 SER cc_start: 0.9495 (m) cc_final: 0.9213 (p) REVERT: R 244 GLU cc_start: 0.8792 (tt0) cc_final: 0.8558 (tp30) REVERT: X 24 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7210 (mt) REVERT: X 131 TYR cc_start: 0.9391 (m-80) cc_final: 0.9163 (m-10) REVERT: X 136 MET cc_start: 0.9094 (ttm) cc_final: 0.8868 (ttt) REVERT: X 185 ASN cc_start: 0.8940 (m-40) cc_final: 0.8645 (m110) outliers start: 10 outliers final: 6 residues processed: 124 average time/residue: 0.2951 time to fit residues: 49.5196 Evaluate side-chains 117 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 0.0030 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3523 r_free = 0.3523 target = 0.094737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.067046 restraints weight = 64275.799| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.31 r_work: 0.2827 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3128 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= 0.124 Angle : 0.471 5.562 16272 Z= 0.236 Chirality : 0.039 0.136 1904 Planarity : 0.003 0.037 2049 Dihedral : 8.359 77.130 1750 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.21 % Rotamer: Outliers : 1.02 % Allowed : 7.01 % Favored : 91.97 % 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: 1.83 (0.23), residues: 1470 helix: 2.82 (0.21), residues: 673 sheet: -0.54 (0.33), residues: 244 loop : 0.09 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 254 TYR 0.006 0.001 TYR C 209 PHE 0.011 0.001 PHE G 92 TRP 0.003 0.001 TRP C 317 HIS 0.002 0.001 HIS X 60 Details of bonding type rmsd covalent geometry : bond 0.00273 (12010) covalent geometry : angle 0.47134 (16272) hydrogen bonds : bond 0.02731 ( 616) hydrogen bonds : angle 4.38562 ( 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 128 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.528 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: 0.8522 (m-30) cc_final: 0.8204 (m-30) REVERT: C 193 ARG cc_start: 0.8856 (mtt180) cc_final: 0.8527 (mpp80) REVERT: C 277 ARG cc_start: 0.8764 (mtt180) cc_final: 0.8442 (mmt180) REVERT: C 327 TYR cc_start: 0.9026 (t80) cc_final: 0.8745 (t80) REVERT: D 201 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8800 (tppt) REVERT: G 34 ASN cc_start: 0.8925 (m-40) cc_final: 0.8690 (t0) REVERT: G 158 MET cc_start: 0.7418 (ttm) cc_final: 0.6881 (mtp) REVERT: G 210 MET cc_start: 0.8944 (mtt) cc_final: 0.8428 (mtt) REVERT: G 211 MET cc_start: 0.8358 (mmm) cc_final: 0.8075 (mmm) REVERT: G 228 TYR cc_start: 0.5868 (m-80) cc_final: 0.5594 (m-80) REVERT: G 254 ARG cc_start: 0.8544 (ptt-90) cc_final: 0.8338 (ptt90) REVERT: G 326 MET cc_start: 0.8204 (mtt) cc_final: 0.7964 (mmt) REVERT: R 54 SER cc_start: 0.9500 (m) cc_final: 0.9246 (p) REVERT: R 244 GLU cc_start: 0.8795 (tt0) cc_final: 0.8567 (tp30) REVERT: X 24 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7115 (mt) REVERT: X 131 TYR cc_start: 0.9391 (m-80) cc_final: 0.9156 (m-10) REVERT: X 185 ASN cc_start: 0.8953 (m-40) cc_final: 0.8650 (m110) REVERT: X 239 MET cc_start: 0.8898 (mtt) cc_final: 0.8503 (mtt) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.3084 time to fit residues: 51.4451 Evaluate side-chains 121 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 52 VAL Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 221 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 108 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.093668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.065911 restraints weight = 64476.494| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.32 r_work: 0.2808 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12010 Z= 0.169 Angle : 0.487 5.524 16272 Z= 0.245 Chirality : 0.039 0.135 1904 Planarity : 0.003 0.035 2049 Dihedral : 8.307 77.112 1750 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 12.29 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: 1.74 (0.23), residues: 1470 helix: 2.72 (0.20), residues: 680 sheet: -0.64 (0.33), residues: 244 loop : 0.07 (0.28), residues: 546 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 0.004 0.001 TRP D 314 HIS 0.003 0.001 HIS R 29 Details of bonding type rmsd covalent geometry : bond 0.00373 (12010) covalent geometry : angle 0.48707 (16272) hydrogen bonds : bond 0.02769 ( 616) hydrogen bonds : angle 4.41348 ( 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 124 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.723 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: 0.8886 (mtt180) cc_final: 0.8543 (mpp80) REVERT: C 277 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8461 (mmt180) REVERT: C 327 TYR cc_start: 0.9036 (t80) cc_final: 0.8757 (t80) REVERT: D 201 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8826 (tppt) REVERT: D 314 TRP cc_start: 0.6931 (OUTLIER) cc_final: 0.5323 (m-90) REVERT: G 34 ASN cc_start: 0.8914 (m-40) cc_final: 0.8678 (t0) REVERT: G 210 MET cc_start: 0.8878 (mtt) cc_final: 0.8596 (mtt) REVERT: G 228 TYR cc_start: 0.5934 (m-80) cc_final: 0.5650 (m-80) REVERT: G 326 MET cc_start: 0.8230 (mtt) cc_final: 0.7973 (mmt) REVERT: R 54 SER cc_start: 0.9496 (m) cc_final: 0.9244 (p) REVERT: R 244 GLU cc_start: 0.8807 (tt0) cc_final: 0.8579 (tp30) REVERT: X 24 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7195 (mt) REVERT: X 50 GLU cc_start: 0.8669 (pp20) cc_final: 0.8338 (pp20) REVERT: X 131 TYR cc_start: 0.9404 (m-80) cc_final: 0.9170 (m-10) REVERT: X 185 ASN cc_start: 0.8963 (m-40) cc_final: 0.8658 (m110) REVERT: X 239 MET cc_start: 0.8938 (mtt) cc_final: 0.8557 (mtt) outliers start: 15 outliers final: 12 residues processed: 121 average time/residue: 0.2984 time to fit residues: 48.7786 Evaluate side-chains 121 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 204 LEU Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 221 CYS 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: 0.0470 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.093886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.066251 restraints weight = 64121.281| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.31 r_work: 0.2816 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3330 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= 0.131 Angle : 0.475 5.575 16272 Z= 0.237 Chirality : 0.039 0.135 1904 Planarity : 0.003 0.035 2049 Dihedral : 8.155 77.189 1750 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.41 % Rotamer: Outliers : 0.79 % Allowed : 7.80 % 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: 1.78 (0.23), residues: 1470 helix: 2.75 (0.20), residues: 681 sheet: -0.63 (0.33), residues: 244 loop : 0.09 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 65 TYR 0.007 0.001 TYR G 216 PHE 0.011 0.001 PHE G 92 TRP 0.003 0.001 TRP C 317 HIS 0.003 0.001 HIS X 60 Details of bonding type rmsd covalent geometry : bond 0.00290 (12010) covalent geometry : angle 0.47524 (16272) hydrogen bonds : bond 0.02627 ( 616) hydrogen bonds : angle 4.30342 ( 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 121 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.647 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 193 ARG cc_start: 0.8881 (mtt180) cc_final: 0.8535 (mpp80) REVERT: C 277 ARG cc_start: 0.8785 (mtt180) cc_final: 0.8463 (mmt180) REVERT: C 327 TYR cc_start: 0.9030 (t80) cc_final: 0.8765 (t80) REVERT: D 201 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8815 (tppt) REVERT: D 314 TRP cc_start: 0.6942 (OUTLIER) cc_final: 0.5380 (m-90) REVERT: G 30 GLN cc_start: 0.8842 (mp10) cc_final: 0.8527 (pp30) REVERT: G 34 ASN cc_start: 0.8902 (m-40) cc_final: 0.8667 (t0) REVERT: G 228 TYR cc_start: 0.5946 (m-80) cc_final: 0.5672 (m-80) REVERT: R 244 GLU cc_start: 0.8807 (tt0) cc_final: 0.8576 (tp30) REVERT: X 24 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7135 (mt) REVERT: X 131 TYR cc_start: 0.9404 (m-80) cc_final: 0.9158 (m-10) REVERT: X 185 ASN cc_start: 0.8958 (m-40) cc_final: 0.8647 (m110) REVERT: X 239 MET cc_start: 0.8942 (mtt) cc_final: 0.8579 (mtt) outliers start: 10 outliers final: 8 residues processed: 119 average time/residue: 0.3074 time to fit residues: 49.0991 Evaluate side-chains 117 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 136 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3490 r_free = 0.3490 target = 0.092898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.065321 restraints weight = 64384.692| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.28 r_work: 0.2794 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12010 Z= 0.186 Angle : 0.500 5.976 16272 Z= 0.251 Chirality : 0.039 0.140 1904 Planarity : 0.003 0.049 2049 Dihedral : 8.229 79.956 1750 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 1.26 % Allowed : 7.80 % 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: 1.68 (0.23), residues: 1470 helix: 2.69 (0.20), residues: 681 sheet: -0.74 (0.33), residues: 244 loop : 0.04 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 237 TYR 0.009 0.001 TYR D 72 PHE 0.012 0.001 PHE G 92 TRP 0.005 0.001 TRP D 314 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00415 (12010) covalent geometry : angle 0.49954 (16272) hydrogen bonds : bond 0.02797 ( 616) hydrogen bonds : angle 4.37782 ( 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 121 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.612 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: C 193 ARG cc_start: 0.8883 (mtt180) cc_final: 0.8525 (mpp80) REVERT: C 277 ARG cc_start: 0.8793 (mtt180) cc_final: 0.8466 (mmt180) REVERT: C 327 TYR cc_start: 0.9056 (t80) cc_final: 0.8796 (t80) REVERT: D 201 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8811 (tppt) REVERT: D 314 TRP cc_start: 0.6877 (OUTLIER) cc_final: 0.5574 (m-90) REVERT: G 30 GLN cc_start: 0.8842 (mp10) cc_final: 0.8507 (pp30) REVERT: G 34 ASN cc_start: 0.8890 (m-40) cc_final: 0.8641 (t0) REVERT: G 210 MET cc_start: 0.8737 (mtt) cc_final: 0.8474 (mpp) REVERT: G 228 TYR cc_start: 0.6059 (m-80) cc_final: 0.5767 (m-80) REVERT: R 244 GLU cc_start: 0.8810 (tt0) cc_final: 0.8586 (tp30) REVERT: X 24 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7261 (mt) REVERT: X 131 TYR cc_start: 0.9413 (m-80) cc_final: 0.9192 (m-10) REVERT: X 239 MET cc_start: 0.8966 (mtt) cc_final: 0.8590 (mtt) outliers start: 16 outliers final: 13 residues processed: 116 average time/residue: 0.3045 time to fit residues: 47.3780 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 : 0.591 ------------------------------------------------------------------------------- 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 221 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 80 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 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: 1.9990 chunk 64 optimal weight: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3473 r_free = 0.3473 target = 0.091914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.063968 restraints weight = 65105.054| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.32 r_work: 0.2766 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12010 Z= 0.266 Angle : 0.542 6.482 16272 Z= 0.275 Chirality : 0.041 0.159 1904 Planarity : 0.004 0.048 2049 Dihedral : 8.427 89.795 1750 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 1.18 % Allowed : 8.19 % Favored : 90.63 % 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: 1.46 (0.23), residues: 1470 helix: 2.53 (0.20), residues: 678 sheet: -0.97 (0.32), residues: 244 loop : -0.02 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 65 TYR 0.011 0.001 TYR D 72 PHE 0.013 0.001 PHE G 92 TRP 0.006 0.001 TRP D 314 HIS 0.004 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00596 (12010) covalent geometry : angle 0.54198 (16272) hydrogen bonds : bond 0.03016 ( 616) hydrogen bonds : angle 4.53940 ( 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 121 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.624 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: C 193 ARG cc_start: 0.8907 (mtt180) cc_final: 0.8540 (mpp80) REVERT: C 277 ARG cc_start: 0.8801 (mtt180) cc_final: 0.8549 (mtt-85) REVERT: C 327 TYR cc_start: 0.9079 (t80) cc_final: 0.8828 (t80) REVERT: D 45 LEU cc_start: 0.8599 (mm) cc_final: 0.8376 (mm) REVERT: D 201 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8833 (tppt) REVERT: D 314 TRP cc_start: 0.6987 (OUTLIER) cc_final: 0.6222 (m-90) REVERT: G 30 GLN cc_start: 0.8893 (mp10) cc_final: 0.8551 (pp30) REVERT: G 34 ASN cc_start: 0.8880 (m-40) cc_final: 0.8638 (t0) REVERT: G 210 MET cc_start: 0.8756 (mtt) cc_final: 0.8473 (mpp) REVERT: G 228 TYR cc_start: 0.6144 (m-80) cc_final: 0.5861 (m-80) REVERT: R 244 GLU cc_start: 0.8816 (tt0) cc_final: 0.8604 (tp30) REVERT: X 24 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7279 (mt) REVERT: X 131 TYR cc_start: 0.9431 (m-80) cc_final: 0.9219 (m-10) REVERT: X 239 MET cc_start: 0.9009 (mtt) cc_final: 0.8650 (mtt) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 0.2935 time to fit residues: 46.3370 Evaluate side-chains 121 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 221 CYS 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: 2.9990 chunk 115 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 ASN X 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.093029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.065270 restraints weight = 64795.401| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.31 r_work: 0.2796 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3578 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= 0.139 Angle : 0.487 5.817 16272 Z= 0.244 Chirality : 0.039 0.136 1904 Planarity : 0.003 0.046 2049 Dihedral : 8.239 88.652 1750 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 0.94 % Allowed : 8.35 % Favored : 90.71 % 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: 1.55 (0.23), residues: 1470 helix: 2.60 (0.20), residues: 680 sheet: -0.92 (0.33), residues: 244 loop : 0.00 (0.27), residues: 546 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 D 314 HIS 0.003 0.001 HIS X 60 Details of bonding type rmsd covalent geometry : bond 0.00303 (12010) covalent geometry : angle 0.48666 (16272) hydrogen bonds : bond 0.02711 ( 616) hydrogen bonds : angle 4.36836 ( 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 118 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.558 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: C 277 ARG cc_start: 0.8772 (mtt180) cc_final: 0.8531 (mtt-85) REVERT: C 327 TYR cc_start: 0.9062 (t80) cc_final: 0.8822 (t80) REVERT: D 201 LYS cc_start: 0.9103 (mmtt) cc_final: 0.8812 (tppt) REVERT: D 314 TRP cc_start: 0.7007 (OUTLIER) cc_final: 0.6193 (m-90) REVERT: G 30 GLN cc_start: 0.8877 (mp10) cc_final: 0.8530 (pp30) REVERT: G 34 ASN cc_start: 0.8921 (m-40) cc_final: 0.8684 (t0) REVERT: G 210 MET cc_start: 0.8816 (mtt) cc_final: 0.8516 (mpp) REVERT: G 228 TYR cc_start: 0.6092 (m-80) cc_final: 0.5794 (m-80) REVERT: R 244 GLU cc_start: 0.8804 (tt0) cc_final: 0.8592 (tp30) REVERT: X 24 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7235 (mt) REVERT: X 131 TYR cc_start: 0.9426 (m-80) cc_final: 0.9202 (m-10) REVERT: X 239 MET cc_start: 0.8969 (mtt) cc_final: 0.8592 (mtt) REVERT: X 258 ARG cc_start: 0.8341 (ttt180) cc_final: 0.8019 (ttm170) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 0.2922 time to fit residues: 45.0392 Evaluate side-chains 117 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 142 VAL Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 290 ASN Chi-restraints excluded: chain R residue 221 CYS 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: 0.2980 chunk 85 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 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: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.092876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.065192 restraints weight = 64704.603| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.30 r_work: 0.2794 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12010 Z= 0.160 Angle : 0.490 5.885 16272 Z= 0.245 Chirality : 0.039 0.134 1904 Planarity : 0.003 0.046 2049 Dihedral : 8.215 89.106 1750 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 0.94 % Allowed : 8.50 % Favored : 90.55 % 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: 1.58 (0.23), residues: 1470 helix: 2.62 (0.20), residues: 680 sheet: -0.92 (0.33), residues: 242 loop : 0.03 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 65 TYR 0.007 0.001 TYR D 72 PHE 0.011 0.001 PHE G 92 TRP 0.005 0.001 TRP C 317 HIS 0.003 0.001 HIS X 60 Details of bonding type rmsd covalent geometry : bond 0.00356 (12010) covalent geometry : angle 0.48960 (16272) hydrogen bonds : bond 0.02682 ( 616) hydrogen bonds : angle 4.34034 ( 1779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4606.50 seconds wall clock time: 79 minutes 10.12 seconds (4750.12 seconds total)