Starting phenix.real_space_refine on Wed Sep 17 14:59:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v7v_64825/09_2025/9v7v_64825.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v7v_64825/09_2025/9v7v_64825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v7v_64825/09_2025/9v7v_64825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v7v_64825/09_2025/9v7v_64825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v7v_64825/09_2025/9v7v_64825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v7v_64825/09_2025/9v7v_64825.map" } resolution = 3.6 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= 0.004 sd= 0.069 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 36 5.16 5 C 5584 2.51 5 N 1520 2.21 5 O 1760 1.98 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8912 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2196 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain: "B" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2196 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain: "C" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2196 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain: "D" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2196 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.95, per 1000 atoms: 0.22 Number of scatterers: 8912 At special positions: 0 Unit cell: (65.27, 54.57, 204.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 12 15.00 O 1760 8.00 N 1520 7.00 C 5584 6.00 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: 0.95 Conformation dependent library (CDL) restraints added in 360.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 48.6% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 67 through 74 removed outlier: 3.572A pdb=" N LEU A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.804A pdb=" N ALA A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.620A pdb=" N ASN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.870A pdb=" N LEU A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 220 removed outlier: 3.706A pdb=" N LEU A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.547A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.739A pdb=" N LYS A 304 " --> pdb=" O CYS A 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 55 Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.593A pdb=" N THR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 106 removed outlier: 3.502A pdb=" N GLY B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.917A pdb=" N GLU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 134 through 144 removed outlier: 3.585A pdb=" N GLU B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.711A pdb=" N GLU B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.874A pdb=" N ILE B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 221 removed outlier: 3.971A pdb=" N ALA B 201 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.632A pdb=" N SER B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 303 removed outlier: 3.661A pdb=" N VAL B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 55 Processing helix chain 'C' and resid 67 through 74 removed outlier: 3.643A pdb=" N HIS C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 106 through 115 removed outlier: 3.593A pdb=" N LEU C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 143 removed outlier: 3.690A pdb=" N ILE C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 178 removed outlier: 4.340A pdb=" N ARG C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 164 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 removed outlier: 3.695A pdb=" N LEU C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 217 removed outlier: 4.491A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.525A pdb=" N LYS C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 290 through 305 removed outlier: 3.780A pdb=" N VAL C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 55 Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.724A pdb=" N LEU D 71 " --> pdb=" O ASP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.684A pdb=" N ALA D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.947A pdb=" N GLU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 removed outlier: 4.151A pdb=" N VAL D 136 " --> pdb=" O GLY D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 178 removed outlier: 4.239A pdb=" N ARG D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU D 164 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 177 " --> pdb=" O GLN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 191 removed outlier: 4.014A pdb=" N ILE D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 190 " --> pdb=" O ASN D 186 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 185 through 191' Processing helix chain 'D' and resid 197 through 221 removed outlier: 4.488A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU D 204 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU D 209 " --> pdb=" O ALA D 205 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 217 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.565A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.562A pdb=" N SER D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.768A pdb=" N LYS D 275 " --> pdb=" O ASP D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 304 removed outlier: 3.941A pdb=" N VAL D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 302 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D 304 " --> pdb=" O CYS D 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 81 removed outlier: 4.058A pdb=" N ASN A 65 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE A 35 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL A 62 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 37 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 64 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A 39 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR A 36 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR A 122 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 38 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N GLY A 124 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL A 40 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 119 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A 151 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 121 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N THR A 153 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N CYS A 123 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 180 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 250 removed outlier: 3.568A pdb=" N ALA A 248 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 327 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 250 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 279 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.895A pdb=" N THR B 36 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR B 122 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 38 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 245 through 246 Processing sheet with id=AA5, first strand: chain 'B' and resid 249 through 250 removed outlier: 3.651A pdb=" N SER B 250 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 282 through 285 removed outlier: 6.676A pdb=" N LEU B 283 " --> pdb=" O ILE B 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 78 through 80 removed outlier: 6.904A pdb=" N THR C 61 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE C 80 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA C 63 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE C 35 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL C 62 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL C 37 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL C 64 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLY C 39 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR C 36 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR C 122 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE C 38 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N GLY C 124 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL C 40 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE C 119 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE C 151 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 121 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THR C 153 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N CYS C 123 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 314 through 315 removed outlier: 4.288A pdb=" N THR C 328 " --> pdb=" O ASN C 282 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 78 through 81 removed outlier: 3.991A pdb=" N ASN D 65 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE D 35 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL D 62 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL D 37 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL D 64 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLY D 39 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR D 36 " --> pdb=" O PHE D 120 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR D 122 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE D 38 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE D 119 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE D 151 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE D 121 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER D 180 " --> pdb=" O THR D 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 244 through 250 362 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3000 1.35 - 1.47: 1652 1.47 - 1.60: 4264 1.60 - 1.72: 12 1.72 - 1.85: 64 Bond restraints: 8992 Sorted by residual: bond pdb=" CA GLY D 39 " pdb=" C GLY D 39 " ideal model delta sigma weight residual 1.520 1.513 0.007 7.30e-03 1.88e+04 9.96e-01 bond pdb=" CA VAL B 271 " pdb=" CB VAL B 271 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.34e-02 5.57e+03 8.09e-01 bond pdb=" CA GLU C 143 " pdb=" CB GLU C 143 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.31e-02 5.83e+03 7.00e-01 bond pdb=" C ALA B 134 " pdb=" N PRO B 135 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.30e-02 5.92e+03 4.97e-01 bond pdb=" N LYS A 104 " pdb=" CA LYS A 104 " ideal model delta sigma weight residual 1.462 1.471 -0.009 1.54e-02 4.22e+03 3.78e-01 ... (remaining 8987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 11708 1.02 - 2.04: 377 2.04 - 3.05: 65 3.05 - 4.07: 25 4.07 - 5.09: 13 Bond angle restraints: 12188 Sorted by residual: angle pdb=" N ILE D 226 " pdb=" CA ILE D 226 " pdb=" C ILE D 226 " ideal model delta sigma weight residual 112.35 108.20 4.15 1.41e+00 5.03e-01 8.66e+00 angle pdb=" C THR A 87 " pdb=" N LYS A 88 " pdb=" CA LYS A 88 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 7.00e+00 angle pdb=" C ILE C 226 " pdb=" N ASN C 227 " pdb=" CA ASN C 227 " ideal model delta sigma weight residual 121.56 124.80 -3.24 1.56e+00 4.11e-01 4.30e+00 angle pdb=" C ILE B 226 " pdb=" N ASN B 227 " pdb=" CA ASN B 227 " ideal model delta sigma weight residual 121.56 124.70 -3.14 1.56e+00 4.11e-01 4.04e+00 angle pdb=" C PHE C 221 " pdb=" N LYS C 222 " pdb=" CA LYS C 222 " ideal model delta sigma weight residual 121.80 126.65 -4.85 2.44e+00 1.68e-01 3.95e+00 ... (remaining 12183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5172 17.43 - 34.86: 311 34.86 - 52.29: 69 52.29 - 69.72: 18 69.72 - 87.15: 6 Dihedral angle restraints: 5576 sinusoidal: 2232 harmonic: 3344 Sorted by residual: dihedral pdb=" CA LYS C 240 " pdb=" C LYS C 240 " pdb=" N GLY C 241 " pdb=" CA GLY C 241 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLY C 215 " pdb=" C GLY C 215 " pdb=" N ILE C 216 " pdb=" CA ILE C 216 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LEU D 280 " pdb=" C LEU D 280 " pdb=" N ILE D 281 " pdb=" CA ILE D 281 " ideal model delta harmonic sigma weight residual 180.00 -164.05 -15.95 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 943 0.028 - 0.057: 350 0.057 - 0.085: 99 0.085 - 0.113: 90 0.113 - 0.142: 30 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE C 316 " pdb=" N ILE C 316 " pdb=" C ILE C 316 " pdb=" CB ILE C 316 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE B 316 " pdb=" N ILE B 316 " pdb=" C ILE B 316 " pdb=" CB ILE B 316 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1509 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 134 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO D 135 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 135 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 135 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 222 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO D 223 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 280 " -0.005 2.00e-02 2.50e+03 9.87e-03 9.75e-01 pdb=" C LEU C 280 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU C 280 " -0.006 2.00e-02 2.50e+03 pdb=" N ILE C 281 " -0.006 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 5462 3.03 - 3.50: 9458 3.50 - 3.97: 13629 3.97 - 4.43: 15897 4.43 - 4.90: 25028 Nonbonded interactions: 69474 Sorted by model distance: nonbonded pdb=" N THR C 242 " pdb=" OG1 THR C 242 " model vdw 2.567 2.496 nonbonded pdb=" C THR C 131 " pdb=" OG1 THR C 131 " model vdw 2.586 2.616 nonbonded pdb=" C4 G2P B 401 " pdb=" N1 G2P B 401 " model vdw 2.586 2.672 nonbonded pdb=" C4 G2P A 401 " pdb=" N1 G2P A 401 " model vdw 2.588 2.672 nonbonded pdb=" C4 G2P C 401 " pdb=" N1 G2P C 401 " model vdw 2.588 2.672 ... (remaining 69469 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.460 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 0.019 8992 Z= 0.091 Angle : 0.480 5.090 12188 Z= 0.252 Chirality : 0.042 0.142 1512 Planarity : 0.002 0.040 1536 Dihedral : 12.362 87.146 3424 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.88 % Allowed : 9.40 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.26), residues: 1188 helix: 0.71 (0.25), residues: 476 sheet: -1.22 (0.31), residues: 312 loop : -1.26 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 50 PHE 0.010 0.001 PHE D 120 TRP 0.005 0.001 TRP A 313 HIS 0.002 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 8992) covalent geometry : angle 0.48038 (12188) hydrogen bonds : bond 0.18781 ( 362) hydrogen bonds : angle 6.46461 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.367 Fit side-chains REVERT: A 67 ASP cc_start: 0.8064 (t70) cc_final: 0.6637 (p0) REVERT: A 159 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6520 (mm-30) REVERT: A 173 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7395 (pp30) REVERT: A 178 CYS cc_start: 0.7571 (m) cc_final: 0.7318 (t) REVERT: A 188 ARG cc_start: 0.8291 (tpt170) cc_final: 0.8064 (tpt170) REVERT: B 45 ASN cc_start: 0.8140 (m-40) cc_final: 0.7836 (m-40) REVERT: B 85 GLN cc_start: 0.8218 (mp-120) cc_final: 0.7853 (tm-30) REVERT: C 45 ASN cc_start: 0.8520 (m110) cc_final: 0.8112 (t0) REVERT: C 53 MET cc_start: 0.8812 (tpp) cc_final: 0.8589 (tpp) REVERT: C 56 VAL cc_start: 0.8315 (t) cc_final: 0.7940 (m) REVERT: C 296 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7639 (mm-30) REVERT: D 196 LEU cc_start: 0.7808 (mt) cc_final: 0.7585 (mp) REVERT: D 299 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7982 (ttp80) outliers start: 27 outliers final: 6 residues processed: 164 average time/residue: 0.0902 time to fit residues: 20.8647 Evaluate side-chains 108 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain D residue 269 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** C 94 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 = 0.4123 r_free = 0.4123 target = 0.121226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.098625 restraints weight = 15317.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.102644 restraints weight = 8960.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.105536 restraints weight = 6084.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.107574 restraints weight = 4531.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.109263 restraints weight = 3603.983| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8992 Z= 0.173 Angle : 0.589 7.698 12188 Z= 0.300 Chirality : 0.044 0.152 1512 Planarity : 0.003 0.038 1536 Dihedral : 8.927 79.196 1369 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 3.21 % Allowed : 16.24 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.26), residues: 1188 helix: 0.69 (0.25), residues: 484 sheet: -1.18 (0.31), residues: 292 loop : -1.69 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 50 PHE 0.008 0.001 PHE B 221 TRP 0.007 0.001 TRP D 313 HIS 0.003 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8992) covalent geometry : angle 0.58857 (12188) hydrogen bonds : bond 0.03811 ( 362) hydrogen bonds : angle 5.03542 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.392 Fit side-chains REVERT: A 45 ASN cc_start: 0.8747 (m-40) cc_final: 0.8288 (m-40) REVERT: A 67 ASP cc_start: 0.7842 (t70) cc_final: 0.6433 (p0) REVERT: B 45 ASN cc_start: 0.8440 (m-40) cc_final: 0.8147 (m110) REVERT: B 67 ASP cc_start: 0.6907 (t0) cc_final: 0.6624 (t0) REVERT: B 85 GLN cc_start: 0.8284 (mp-120) cc_final: 0.7677 (tm-30) REVERT: B 296 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7574 (mm-30) REVERT: C 67 ASP cc_start: 0.7306 (t0) cc_final: 0.7097 (t0) REVERT: C 296 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7706 (mm-30) REVERT: D 196 LEU cc_start: 0.7866 (mt) cc_final: 0.7564 (mp) REVERT: D 310 GLU cc_start: 0.7966 (pm20) cc_final: 0.7684 (mm-30) outliers start: 30 outliers final: 18 residues processed: 114 average time/residue: 0.0879 time to fit residues: 14.6104 Evaluate side-chains 106 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 290 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.120729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.098068 restraints weight = 15274.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.102148 restraints weight = 8957.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.105041 restraints weight = 6074.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.107108 restraints weight = 4523.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.108762 restraints weight = 3595.502| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8992 Z= 0.155 Angle : 0.560 6.900 12188 Z= 0.283 Chirality : 0.043 0.154 1512 Planarity : 0.003 0.039 1536 Dihedral : 8.832 78.293 1367 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.53 % Allowed : 18.59 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.26), residues: 1188 helix: 0.73 (0.25), residues: 484 sheet: -1.25 (0.31), residues: 292 loop : -1.69 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 PHE 0.009 0.001 PHE B 221 TRP 0.006 0.001 TRP A 313 HIS 0.003 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8992) covalent geometry : angle 0.56032 (12188) hydrogen bonds : bond 0.03478 ( 362) hydrogen bonds : angle 4.79837 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.360 Fit side-chains REVERT: A 45 ASN cc_start: 0.8743 (m-40) cc_final: 0.8382 (m-40) REVERT: A 67 ASP cc_start: 0.7712 (t70) cc_final: 0.6157 (p0) REVERT: B 45 ASN cc_start: 0.8428 (m-40) cc_final: 0.8042 (m110) REVERT: B 67 ASP cc_start: 0.6886 (t0) cc_final: 0.6575 (t0) REVERT: B 85 GLN cc_start: 0.8203 (mp-120) cc_final: 0.7759 (tm-30) REVERT: B 296 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7553 (mm-30) REVERT: C 67 ASP cc_start: 0.7403 (t0) cc_final: 0.7165 (t0) REVERT: C 296 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7761 (mm-30) REVERT: D 196 LEU cc_start: 0.7836 (mt) cc_final: 0.7522 (mp) REVERT: D 310 GLU cc_start: 0.7938 (pm20) cc_final: 0.7603 (mm-30) outliers start: 33 outliers final: 24 residues processed: 113 average time/residue: 0.0791 time to fit residues: 13.5490 Evaluate side-chains 112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 331 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.118504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.096390 restraints weight = 15636.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.100203 restraints weight = 9367.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.102942 restraints weight = 6467.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.104963 restraints weight = 4882.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.106436 restraints weight = 3899.846| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8992 Z= 0.199 Angle : 0.607 7.600 12188 Z= 0.307 Chirality : 0.044 0.168 1512 Planarity : 0.004 0.040 1536 Dihedral : 8.940 76.303 1367 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 5.56 % Allowed : 17.52 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.26), residues: 1188 helix: 0.59 (0.25), residues: 484 sheet: -1.46 (0.31), residues: 292 loop : -1.75 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 306 PHE 0.010 0.001 PHE C 230 TRP 0.007 0.001 TRP D 313 HIS 0.003 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8992) covalent geometry : angle 0.60664 (12188) hydrogen bonds : bond 0.03516 ( 362) hydrogen bonds : angle 4.85736 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 94 time to evaluate : 0.360 Fit side-chains REVERT: A 45 ASN cc_start: 0.8657 (m-40) cc_final: 0.8169 (m-40) REVERT: A 67 ASP cc_start: 0.7780 (t70) cc_final: 0.6292 (p0) REVERT: B 45 ASN cc_start: 0.8469 (m-40) cc_final: 0.8097 (m110) REVERT: B 67 ASP cc_start: 0.6992 (t0) cc_final: 0.6598 (t0) REVERT: B 71 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8519 (mm) REVERT: B 85 GLN cc_start: 0.8219 (mp-120) cc_final: 0.7780 (tm-30) REVERT: C 296 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7725 (mm-30) REVERT: D 196 LEU cc_start: 0.7799 (mt) cc_final: 0.7504 (mp) REVERT: D 299 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8106 (ttp80) REVERT: D 310 GLU cc_start: 0.7920 (pm20) cc_final: 0.7626 (mm-30) outliers start: 52 outliers final: 41 residues processed: 132 average time/residue: 0.0788 time to fit residues: 15.5544 Evaluate side-chains 133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 300 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 16 optimal weight: 5.9990 chunk 93 optimal weight: 0.0050 chunk 114 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 ASN C 94 ASN D 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.122949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.100505 restraints weight = 15152.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.104542 restraints weight = 8915.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.107453 restraints weight = 6062.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.109528 restraints weight = 4518.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.111238 restraints weight = 3586.905| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8992 Z= 0.102 Angle : 0.540 8.397 12188 Z= 0.272 Chirality : 0.043 0.183 1512 Planarity : 0.003 0.041 1536 Dihedral : 8.731 77.389 1367 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.06 % Allowed : 19.76 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.26), residues: 1188 helix: 0.85 (0.24), residues: 512 sheet: -1.38 (0.31), residues: 300 loop : -1.80 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 306 PHE 0.006 0.001 PHE B 120 TRP 0.007 0.001 TRP B 313 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8992) covalent geometry : angle 0.53971 (12188) hydrogen bonds : bond 0.02877 ( 362) hydrogen bonds : angle 4.47431 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.339 Fit side-chains REVERT: A 45 ASN cc_start: 0.8583 (m-40) cc_final: 0.8177 (m-40) REVERT: A 56 VAL cc_start: 0.7897 (t) cc_final: 0.7656 (m) REVERT: A 67 ASP cc_start: 0.7685 (t70) cc_final: 0.6165 (p0) REVERT: B 45 ASN cc_start: 0.8321 (m-40) cc_final: 0.7994 (m110) REVERT: B 67 ASP cc_start: 0.6821 (t0) cc_final: 0.6455 (t0) REVERT: B 85 GLN cc_start: 0.8144 (mp-120) cc_final: 0.7706 (tm-30) REVERT: B 280 LEU cc_start: 0.7011 (tt) cc_final: 0.6547 (tt) REVERT: B 296 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7347 (mm-30) REVERT: C 163 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.5568 (mpt-90) REVERT: C 296 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7702 (mm-30) REVERT: D 196 LEU cc_start: 0.7742 (mt) cc_final: 0.7508 (mp) REVERT: D 310 GLU cc_start: 0.7929 (pm20) cc_final: 0.7586 (mm-30) outliers start: 38 outliers final: 28 residues processed: 130 average time/residue: 0.0781 time to fit residues: 15.1320 Evaluate side-chains 116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 331 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 0.0050 chunk 83 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN D 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.123413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.100905 restraints weight = 15177.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.104923 restraints weight = 8963.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.107844 restraints weight = 6109.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.109955 restraints weight = 4551.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.111612 restraints weight = 3606.241| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8992 Z= 0.103 Angle : 0.536 10.168 12188 Z= 0.272 Chirality : 0.042 0.160 1512 Planarity : 0.003 0.040 1536 Dihedral : 8.644 77.584 1367 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.63 % Allowed : 21.05 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.26), residues: 1188 helix: 0.91 (0.24), residues: 512 sheet: -1.46 (0.30), residues: 316 loop : -1.71 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 50 PHE 0.009 0.001 PHE B 221 TRP 0.004 0.001 TRP C 313 HIS 0.001 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8992) covalent geometry : angle 0.53615 (12188) hydrogen bonds : bond 0.02789 ( 362) hydrogen bonds : angle 4.42976 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.410 Fit side-chains REVERT: A 45 ASN cc_start: 0.8503 (m-40) cc_final: 0.8124 (m-40) REVERT: A 56 VAL cc_start: 0.7821 (t) cc_final: 0.7597 (m) REVERT: A 67 ASP cc_start: 0.7766 (t70) cc_final: 0.6231 (p0) REVERT: B 45 ASN cc_start: 0.8283 (m-40) cc_final: 0.7946 (m110) REVERT: B 67 ASP cc_start: 0.6763 (t0) cc_final: 0.6343 (t0) REVERT: B 85 GLN cc_start: 0.8200 (mp-120) cc_final: 0.7655 (tm-30) REVERT: B 280 LEU cc_start: 0.7008 (tt) cc_final: 0.6490 (tt) REVERT: B 296 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7322 (mm-30) REVERT: C 163 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.5589 (mpt-90) REVERT: C 296 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7675 (mm-30) REVERT: D 196 LEU cc_start: 0.7751 (mt) cc_final: 0.7457 (mp) REVERT: D 310 GLU cc_start: 0.7773 (pm20) cc_final: 0.7573 (mm-30) outliers start: 34 outliers final: 27 residues processed: 119 average time/residue: 0.0731 time to fit residues: 13.3684 Evaluate side-chains 117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 331 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 107 optimal weight: 0.0010 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.126572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.104642 restraints weight = 15418.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.108776 restraints weight = 8911.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.111490 restraints weight = 5968.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.113790 restraints weight = 4486.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.115300 restraints weight = 3474.077| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8992 Z= 0.102 Angle : 0.539 10.277 12188 Z= 0.272 Chirality : 0.042 0.160 1512 Planarity : 0.003 0.040 1536 Dihedral : 8.259 74.300 1364 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.00 % Favored : 91.92 % Rotamer: Outliers : 3.42 % Allowed : 21.58 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.26), residues: 1188 helix: 1.01 (0.24), residues: 512 sheet: -1.41 (0.30), residues: 316 loop : -1.72 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 50 PHE 0.004 0.001 PHE B 120 TRP 0.004 0.001 TRP A 169 HIS 0.001 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8992) covalent geometry : angle 0.53935 (12188) hydrogen bonds : bond 0.02686 ( 362) hydrogen bonds : angle 4.37769 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.425 Fit side-chains REVERT: A 45 ASN cc_start: 0.8600 (m-40) cc_final: 0.8389 (m-40) REVERT: A 56 VAL cc_start: 0.7828 (t) cc_final: 0.7578 (m) REVERT: A 67 ASP cc_start: 0.7818 (t70) cc_final: 0.6301 (p0) REVERT: B 45 ASN cc_start: 0.8391 (m-40) cc_final: 0.8024 (m110) REVERT: B 85 GLN cc_start: 0.8220 (mp-120) cc_final: 0.7660 (tm-30) REVERT: B 188 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7478 (tpm170) REVERT: B 280 LEU cc_start: 0.6994 (tt) cc_final: 0.6480 (tt) REVERT: B 296 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 163 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.5558 (mpt-90) REVERT: C 296 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7677 (mm-30) REVERT: D 196 LEU cc_start: 0.7803 (mt) cc_final: 0.7494 (mp) outliers start: 32 outliers final: 28 residues processed: 117 average time/residue: 0.0765 time to fit residues: 13.7022 Evaluate side-chains 114 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 331 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 0.0060 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 ASN D 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.127290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.105356 restraints weight = 15257.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.109437 restraints weight = 8862.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.112461 restraints weight = 5945.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.114650 restraints weight = 4337.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.116190 restraints weight = 3387.783| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8992 Z= 0.102 Angle : 0.541 10.471 12188 Z= 0.274 Chirality : 0.042 0.159 1512 Planarity : 0.003 0.040 1536 Dihedral : 8.198 74.519 1364 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.16 % Favored : 91.75 % Rotamer: Outliers : 4.38 % Allowed : 20.94 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.26), residues: 1188 helix: 1.10 (0.25), residues: 508 sheet: -1.41 (0.31), residues: 316 loop : -1.57 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 PHE 0.009 0.001 PHE B 221 TRP 0.004 0.001 TRP C 313 HIS 0.001 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8992) covalent geometry : angle 0.54087 (12188) hydrogen bonds : bond 0.02599 ( 362) hydrogen bonds : angle 4.34004 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.375 Fit side-chains REVERT: A 45 ASN cc_start: 0.8589 (m-40) cc_final: 0.8153 (m110) REVERT: A 56 VAL cc_start: 0.7845 (t) cc_final: 0.7605 (m) REVERT: A 67 ASP cc_start: 0.7866 (t70) cc_final: 0.6342 (p0) REVERT: B 45 ASN cc_start: 0.8340 (m-40) cc_final: 0.7982 (m110) REVERT: B 85 GLN cc_start: 0.8247 (mp-120) cc_final: 0.7671 (tm-30) REVERT: B 188 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7517 (tpm170) REVERT: B 280 LEU cc_start: 0.6963 (tt) cc_final: 0.6435 (tt) REVERT: B 296 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7403 (mm-30) REVERT: C 163 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.5518 (mpt-90) REVERT: C 296 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7701 (mm-30) REVERT: D 196 LEU cc_start: 0.7771 (mt) cc_final: 0.7473 (mp) outliers start: 41 outliers final: 33 residues processed: 117 average time/residue: 0.0742 time to fit residues: 13.2715 Evaluate side-chains 118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 331 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 0.0030 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.127641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.105541 restraints weight = 15312.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.109671 restraints weight = 8812.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.112668 restraints weight = 5912.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.114933 restraints weight = 4322.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.116425 restraints weight = 3359.948| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8992 Z= 0.099 Angle : 0.549 10.642 12188 Z= 0.275 Chirality : 0.042 0.171 1512 Planarity : 0.003 0.039 1536 Dihedral : 8.159 74.711 1364 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.66 % Favored : 92.26 % Rotamer: Outliers : 3.63 % Allowed : 21.79 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.26), residues: 1188 helix: 0.96 (0.24), residues: 532 sheet: -1.41 (0.31), residues: 316 loop : -1.70 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 PHE 0.008 0.001 PHE B 221 TRP 0.005 0.001 TRP B 313 HIS 0.001 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8992) covalent geometry : angle 0.54877 (12188) hydrogen bonds : bond 0.02556 ( 362) hydrogen bonds : angle 4.31456 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.400 Fit side-chains REVERT: A 45 ASN cc_start: 0.8561 (m-40) cc_final: 0.8130 (m110) REVERT: A 56 VAL cc_start: 0.7822 (t) cc_final: 0.7580 (m) REVERT: A 67 ASP cc_start: 0.7863 (t70) cc_final: 0.6345 (p0) REVERT: B 45 ASN cc_start: 0.8385 (m-40) cc_final: 0.8018 (m110) REVERT: B 85 GLN cc_start: 0.8228 (mp-120) cc_final: 0.7664 (tm-30) REVERT: B 188 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7523 (tpm170) REVERT: B 280 LEU cc_start: 0.6998 (tt) cc_final: 0.6462 (tt) REVERT: B 296 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7405 (mm-30) REVERT: C 163 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.5537 (mpt-90) REVERT: C 296 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7687 (mm-30) REVERT: D 196 LEU cc_start: 0.7735 (mt) cc_final: 0.7450 (mp) outliers start: 34 outliers final: 29 residues processed: 109 average time/residue: 0.0766 time to fit residues: 12.7593 Evaluate side-chains 113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.127517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.105623 restraints weight = 15250.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.109772 restraints weight = 8806.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.112716 restraints weight = 5883.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.114872 restraints weight = 4320.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.116388 restraints weight = 3380.443| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8992 Z= 0.104 Angle : 0.552 13.164 12188 Z= 0.276 Chirality : 0.042 0.160 1512 Planarity : 0.003 0.041 1536 Dihedral : 8.147 74.681 1364 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.16 % Favored : 91.75 % Rotamer: Outliers : 3.63 % Allowed : 21.79 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.27), residues: 1188 helix: 0.99 (0.24), residues: 532 sheet: -1.42 (0.31), residues: 316 loop : -1.71 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 PHE 0.008 0.001 PHE B 221 TRP 0.004 0.001 TRP B 313 HIS 0.001 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8992) covalent geometry : angle 0.55202 (12188) hydrogen bonds : bond 0.02570 ( 362) hydrogen bonds : angle 4.31528 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.320 Fit side-chains REVERT: A 45 ASN cc_start: 0.8552 (m-40) cc_final: 0.8120 (m110) REVERT: A 56 VAL cc_start: 0.7783 (t) cc_final: 0.7524 (m) REVERT: A 67 ASP cc_start: 0.7876 (t70) cc_final: 0.6361 (p0) REVERT: B 45 ASN cc_start: 0.8332 (m-40) cc_final: 0.7976 (m110) REVERT: B 85 GLN cc_start: 0.8249 (mp-120) cc_final: 0.7666 (tm-30) REVERT: B 188 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7530 (tpm170) REVERT: B 280 LEU cc_start: 0.7066 (tt) cc_final: 0.6552 (tt) REVERT: B 296 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7419 (mm-30) REVERT: C 163 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.5442 (mpt-90) REVERT: C 296 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7687 (mm-30) REVERT: D 196 LEU cc_start: 0.7746 (mt) cc_final: 0.7458 (mp) outliers start: 34 outliers final: 30 residues processed: 107 average time/residue: 0.0756 time to fit residues: 12.3218 Evaluate side-chains 113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 227 ASN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.127064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.105320 restraints weight = 15146.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.109393 restraints weight = 8791.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.112364 restraints weight = 5895.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.114530 restraints weight = 4315.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.115997 restraints weight = 3364.410| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8992 Z= 0.113 Angle : 0.557 12.762 12188 Z= 0.278 Chirality : 0.042 0.161 1512 Planarity : 0.003 0.042 1536 Dihedral : 8.168 74.717 1364 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.42 % Favored : 91.50 % Rotamer: Outliers : 3.63 % Allowed : 21.79 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.27), residues: 1188 helix: 1.00 (0.24), residues: 532 sheet: -1.44 (0.31), residues: 316 loop : -1.71 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 50 PHE 0.007 0.001 PHE B 221 TRP 0.003 0.001 TRP D 313 HIS 0.002 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8992) covalent geometry : angle 0.55683 (12188) hydrogen bonds : bond 0.02576 ( 362) hydrogen bonds : angle 4.34938 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1435.61 seconds wall clock time: 25 minutes 40.59 seconds (1540.59 seconds total)