Starting phenix.real_space_refine on Fri Oct 23 14:57:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xj7_66930/10_2026/9xj7_66930.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xj7_66930/10_2026/9xj7_66930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xj7_66930/10_2026/9xj7_66930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xj7_66930/10_2026/9xj7_66930.map" model { file = "/net/cci-nas-00/data/ceres_data/9xj7_66930/10_2026/9xj7_66930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xj7_66930/10_2026/9xj7_66930.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 6429 2.51 5 N 1717 2.21 5 O 1855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10068 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2867 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 336} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2595 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 427 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1761 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "R" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2359 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 9, 'TRANS': 278} Time building chain proxies: 2.17, per 1000 atoms: 0.22 Number of scatterers: 10068 At special positions: 0 Unit cell: (104.854, 123.178, 136.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1855 8.00 N 1717 7.00 C 6429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 173 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 374.4 milliseconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2402 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 13 sheets defined 41.7% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 5 through 37 removed outlier: 3.604A pdb=" N ASP A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 68 through 98 removed outlier: 3.618A pdb=" N LYS A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.600A pdb=" N ASP A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.532A pdb=" N GLN A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.542A pdb=" N TYR A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.810A pdb=" N VAL A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 212 through 218 removed outlier: 4.126A pdb=" N TRP A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N HIS A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 233 through 236 removed outlier: 4.098A pdb=" N ASP A 236 " --> pdb=" O SER A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.509A pdb=" N PHE A 264 " --> pdb=" O TYR A 261 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 275 through 286 removed outlier: 3.534A pdb=" N GLU A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 4.097A pdb=" N TYR A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 4.560A pdb=" N ALA A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 356 removed outlier: 3.704A pdb=" N LYS A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.517A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.625A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.643A pdb=" N ALA C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'R' and resid 25 through 59 removed outlier: 3.549A pdb=" N ASN R 30 " --> pdb=" O THR R 26 " (cutoff:3.500A) Proline residue: R 34 - end of helix Processing helix chain 'R' and resid 66 through 96 removed outlier: 3.670A pdb=" N VAL R 70 " --> pdb=" O CYS R 66 " (cutoff:3.500A) Proline residue: R 87 - end of helix Processing helix chain 'R' and resid 101 through 103 No H-bonds generated for 'chain 'R' and resid 101 through 103' Processing helix chain 'R' and resid 104 through 134 Processing helix chain 'R' and resid 140 through 164 Proline residue: R 161 - end of helix removed outlier: 3.893A pdb=" N MET R 164 " --> pdb=" O ILE R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 196 removed outlier: 3.622A pdb=" N MET R 193 " --> pdb=" O ASN R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 217 removed outlier: 3.957A pdb=" N VAL R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 256 removed outlier: 3.500A pdb=" N ILE R 226 " --> pdb=" O HIS R 222 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU R 230 " --> pdb=" O ILE R 226 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE R 231 " --> pdb=" O VAL R 227 " (cutoff:3.500A) Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 262 through 280 removed outlier: 3.916A pdb=" N LEU R 269 " --> pdb=" O PHE R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 292 removed outlier: 4.214A pdb=" N CYS R 285 " --> pdb=" O PHE R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.538A pdb=" N TYR R 291 " --> pdb=" O ASN R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 310 removed outlier: 4.087A pdb=" N ARG R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196 removed outlier: 3.795A pdb=" N MET A 203 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N SER A 225 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS A 41 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 43 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU A 45 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ALA A 231 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 226 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE A 272 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE A 228 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ASN A 274 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 230 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.872A pdb=" N LEU A 239 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU A 245 " --> pdb=" O LEU A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.515A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.836A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.017A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.931A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.904A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.497A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.613A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.773A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136 removed outlier: 3.988A pdb=" N GLY D 213 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN D 182 " --> pdb=" O TYR D 178 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1413 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: 1.50 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3255 1.35 - 1.47: 2554 1.47 - 1.59: 4382 1.59 - 1.71: 0 1.71 - 1.83: 98 Bond restraints: 10289 Sorted by residual: bond pdb=" C ILE R 160 " pdb=" N PRO R 161 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.42e+00 bond pdb=" N ILE A 324 " pdb=" CA ILE A 324 " ideal model delta sigma weight residual 1.462 1.473 -0.011 1.32e-02 5.74e+03 7.07e-01 bond pdb=" CA ARG A 181 " pdb=" C ARG A 181 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 6.74e-01 bond pdb=" C VAL A 184 " pdb=" O VAL A 184 " ideal model delta sigma weight residual 1.232 1.239 -0.007 8.90e-03 1.26e+04 6.28e-01 bond pdb=" CA LEU R 86 " pdb=" C LEU R 86 " ideal model delta sigma weight residual 1.520 1.530 -0.009 1.23e-02 6.61e+03 5.71e-01 ... (remaining 10284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 13589 1.40 - 2.81: 297 2.81 - 4.21: 46 4.21 - 5.61: 15 5.61 - 7.01: 4 Bond angle restraints: 13951 Sorted by residual: angle pdb=" C LYS A 120 " pdb=" N VAL A 121 " pdb=" CA VAL A 121 " ideal model delta sigma weight residual 121.97 126.28 -4.31 1.80e+00 3.09e-01 5.73e+00 angle pdb=" N PHE B 292 " pdb=" CA PHE B 292 " pdb=" CB PHE B 292 " ideal model delta sigma weight residual 113.65 110.29 3.36 1.47e+00 4.63e-01 5.24e+00 angle pdb=" N ILE A 62 " pdb=" CA ILE A 62 " pdb=" C ILE A 62 " ideal model delta sigma weight residual 111.00 113.27 -2.27 1.09e+00 8.42e-01 4.33e+00 angle pdb=" N ILE A 61 " pdb=" CA ILE A 61 " pdb=" C ILE A 61 " ideal model delta sigma weight residual 111.58 109.40 2.18 1.06e+00 8.90e-01 4.24e+00 angle pdb=" CA LEU B 70 " pdb=" CB LEU B 70 " pdb=" CG LEU B 70 " ideal model delta sigma weight residual 116.30 123.31 -7.01 3.50e+00 8.16e-02 4.02e+00 ... (remaining 13946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5645 17.53 - 35.05: 361 35.05 - 52.58: 97 52.58 - 70.10: 19 70.10 - 87.63: 7 Dihedral angle restraints: 6129 sinusoidal: 2407 harmonic: 3722 Sorted by residual: dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 263 " pdb=" CB CYS R 263 " ideal model delta sinusoidal sigma weight residual -86.00 -130.03 44.03 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR D 101 " pdb=" C TYR D 101 " pdb=" N TYR D 102 " pdb=" CA TYR D 102 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 852 0.028 - 0.056: 459 0.056 - 0.083: 163 0.083 - 0.111: 75 0.111 - 0.139: 24 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA VAL D 37 " pdb=" N VAL D 37 " pdb=" C VAL D 37 " pdb=" CB VAL D 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1570 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 201 " 0.022 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C LEU R 201 " -0.075 2.00e-02 2.50e+03 pdb=" O LEU R 201 " 0.028 2.00e-02 2.50e+03 pdb=" N SER R 202 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO B 236 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 59 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO C 60 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.026 5.00e-02 4.00e+02 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 170 2.67 - 3.23: 9341 3.23 - 3.78: 15226 3.78 - 4.34: 20722 4.34 - 4.90: 35020 Nonbonded interactions: 80479 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.112 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 323 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 159 " pdb=" OD1 ASP A 178 " model vdw 2.253 3.040 nonbonded pdb=" O ARG A 210 " pdb=" NE ARG A 210 " model vdw 2.263 3.120 ... (remaining 80474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 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 : 0.003 0.028 10293 Z= 0.136 Angle : 0.544 7.014 13959 Z= 0.299 Chirality : 0.042 0.139 1573 Planarity : 0.004 0.053 1769 Dihedral : 13.120 87.627 3715 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 4.01 % Allowed : 10.12 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.08 (0.24), residues: 1256 helix: 1.46 (0.24), residues: 480 sheet: 0.25 (0.31), residues: 273 loop : -1.47 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 63 TYR 0.011 0.001 TYR D 223 PHE 0.018 0.002 PHE B 151 TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (10289) covalent geometry : angle 0.54363 / 0.30 (13951) SS BOND : bond 0.00291 / 0.14 ( 4) SS BOND : angle 0.94858 / 0.53 ( 8) hydrogen bonds : bond 0.13752 / 9.27 ( 486) hydrogen bonds : angle 5.76434 / 4.50 ( 1413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7160 (ttp80) cc_final: 0.6709 (ttt-90) REVERT: A 79 VAL cc_start: 0.8424 (t) cc_final: 0.8142 (t) REVERT: A 99 ILE cc_start: 0.6641 (mt) cc_final: 0.6413 (mt) REVERT: A 178 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6671 (t70) REVERT: A 209 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7690 (tp-100) REVERT: A 256 ARG cc_start: 0.7002 (ptm-80) cc_final: 0.6770 (ptm160) REVERT: A 307 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: B 96 ARG cc_start: 0.7198 (mtt-85) cc_final: 0.6911 (mtm-85) REVERT: B 219 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7711 (mtm180) REVERT: D 180 MET cc_start: 0.6139 (tpt) cc_final: 0.5771 (tpt) REVERT: R 115 MET cc_start: 0.5931 (ttt) cc_final: 0.5473 (mtm) REVERT: R 157 ILE cc_start: 0.7354 (mt) cc_final: 0.7113 (mt) REVERT: R 164 MET cc_start: 0.3547 (pp-130) cc_final: 0.1240 (ttt) REVERT: R 193 MET cc_start: 0.6401 (tmm) cc_final: 0.6187 (tmm) outliers start: 44 outliers final: 16 residues processed: 225 average time/residue: 0.5196 time to fit residues: 125.9785 Evaluate side-chains 153 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain R residue 247 THR Chi-restraints excluded: chain R residue 252 THR Chi-restraints excluded: chain R residue 294 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 GLN A 176 GLN A 209 GLN A 222 ASN A 274 ASN A 287 HIS B 17 GLN B 156 GLN B 295 ASN B 340 ASN D 3 GLN R 219 GLN R 222 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.239459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.181131 restraints weight = 11829.018| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.03 r_work: 0.3894 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10293 Z= 0.126 Angle : 0.570 12.464 13959 Z= 0.298 Chirality : 0.042 0.139 1573 Planarity : 0.004 0.053 1769 Dihedral : 6.015 54.480 1437 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 4.10 % Allowed : 17.41 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.15 (0.24), residues: 1256 helix: 1.53 (0.24), residues: 491 sheet: 0.18 (0.30), residues: 290 loop : -1.49 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 190 TYR 0.015 0.001 TYR A 151 PHE 0.013 0.001 PHE B 151 TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (10289) covalent geometry : angle 0.56943 / 0.30 (13951) SS BOND : bond 0.00279 / 0.14 ( 4) SS BOND : angle 0.76106 / 0.37 ( 8) hydrogen bonds : bond 0.04138 / 2.75 ( 486) hydrogen bonds : angle 4.66939 / 3.54 ( 1413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7037 (ttp80) cc_final: 0.6483 (ttt-90) REVERT: A 90 MET cc_start: 0.7968 (mmm) cc_final: 0.7714 (ptp) REVERT: A 101 TYR cc_start: 0.4237 (m-10) cc_final: 0.4033 (m-10) REVERT: A 222 ASN cc_start: 0.7221 (m-40) cc_final: 0.7012 (m-40) REVERT: A 248 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6089 (mmt) REVERT: A 256 ARG cc_start: 0.6797 (ptm-80) cc_final: 0.6519 (ptm160) REVERT: A 307 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: A 341 PHE cc_start: 0.7323 (t80) cc_final: 0.6919 (t80) REVERT: B 96 ARG cc_start: 0.7785 (mtt-85) cc_final: 0.7341 (mtm-85) REVERT: B 219 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7712 (mtm180) REVERT: B 226 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: C 46 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7009 (mppt) REVERT: R 115 MET cc_start: 0.5680 (ttt) cc_final: 0.5069 (mtm) REVERT: R 164 MET cc_start: 0.3627 (pp-130) cc_final: 0.3206 (tmm) REVERT: R 174 MET cc_start: 0.4827 (ptp) cc_final: 0.3961 (mmm) REVERT: R 299 ARG cc_start: 0.4602 (OUTLIER) cc_final: 0.4196 (mtp180) outliers start: 45 outliers final: 18 residues processed: 181 average time/residue: 0.5332 time to fit residues: 103.7760 Evaluate side-chains 162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 299 ARG Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: [101, 8, 122, 114, 111, 70, 42, 112, 9, 75, 93] chunk 101 optimal weight: 5.9990 chunk 8 optimal weight: 0.0670 chunk 122 optimal weight: 7.9990 chunk 114 optimal weight: 0.0170 chunk 111 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 274 ASN B 125 ASN R 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.226961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.4087 r_free = 0.4087 target = 0.181658 restraints weight = 11864.219| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.38 r_work: 0.3756 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10293 Z= 0.105 Angle : 0.538 10.609 13959 Z= 0.278 Chirality : 0.042 0.276 1573 Planarity : 0.004 0.052 1769 Dihedral : 5.293 53.599 1426 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.39 % Favored : 97.53 % Rotamer: Outliers : 3.46 % Allowed : 19.05 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.29 (0.24), residues: 1256 helix: 1.69 (0.24), residues: 492 sheet: 0.27 (0.30), residues: 290 loop : -1.50 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 190 TYR 0.019 0.001 TYR A 151 PHE 0.013 0.001 PHE R 197 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (10289) covalent geometry : angle 0.53812 / 0.28 (13951) SS BOND : bond 0.00314 / 0.16 ( 4) SS BOND : angle 0.63230 / 0.31 ( 8) hydrogen bonds : bond 0.03588 / 2.38 ( 486) hydrogen bonds : angle 4.37426 / 3.31 ( 1413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7035 (ttp80) cc_final: 0.6548 (ttp-110) REVERT: A 222 ASN cc_start: 0.7097 (m-40) cc_final: 0.6850 (m110) REVERT: A 256 ARG cc_start: 0.6869 (ptm-80) cc_final: 0.6591 (ptm160) REVERT: A 307 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: A 341 PHE cc_start: 0.7415 (t80) cc_final: 0.7133 (t80) REVERT: A 357 ASN cc_start: 0.7615 (t0) cc_final: 0.7284 (t0) REVERT: B 172 GLU cc_start: 0.6999 (tp30) cc_final: 0.6461 (tp30) REVERT: R 115 MET cc_start: 0.5658 (ttt) cc_final: 0.5181 (mtm) REVERT: R 164 MET cc_start: 0.3534 (pp-130) cc_final: 0.3195 (tmm) REVERT: R 174 MET cc_start: 0.4453 (ptp) cc_final: 0.3764 (mmm) outliers start: 38 outliers final: 20 residues processed: 169 average time/residue: 0.5375 time to fit residues: 97.7322 Evaluate side-chains 159 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: [97, 122, 70, 9, 88, 31, 19, 23, 37, 102, 69] chunk 97 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 162 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN R 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.220742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.175889 restraints weight = 11806.664| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.39 r_work: 0.3712 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10293 Z= 0.286 Angle : 0.763 10.667 13959 Z= 0.399 Chirality : 0.049 0.153 1573 Planarity : 0.005 0.056 1769 Dihedral : 5.781 51.399 1418 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 6.20 % Allowed : 18.14 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.46 (0.23), residues: 1256 helix: 1.07 (0.23), residues: 491 sheet: -0.23 (0.31), residues: 279 loop : -1.80 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 134 TYR 0.025 0.003 TYR D 50 PHE 0.028 0.003 PHE B 151 TRP 0.021 0.003 TRP B 211 HIS 0.009 0.002 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.29 (10289) covalent geometry : angle 0.76250 / 0.40 (13951) SS BOND : bond 0.00228 / 0.11 ( 4) SS BOND : angle 1.48978 / 0.74 ( 8) hydrogen bonds : bond 0.05557 / 3.68 ( 486) hydrogen bonds : angle 5.00012 / 3.74 ( 1413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 141 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7231 (ttp80) cc_final: 0.6819 (ttp-110) REVERT: A 77 LYS cc_start: 0.8272 (tttm) cc_final: 0.7795 (tptp) REVERT: A 81 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8035 (mt0) REVERT: A 158 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8232 (mtmm) REVERT: A 177 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7837 (tp40) REVERT: A 248 MET cc_start: 0.6721 (OUTLIER) cc_final: 0.6073 (mmt) REVERT: A 256 ARG cc_start: 0.6857 (ptm-80) cc_final: 0.6613 (ptm160) REVERT: A 307 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: B 51 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6263 (mt) REVERT: B 226 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: D 62 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6404 (m-30) REVERT: R 115 MET cc_start: 0.6079 (ttt) cc_final: 0.5334 (ttp) REVERT: R 136 MET cc_start: 0.6935 (mtm) cc_final: 0.6643 (mtp) REVERT: R 164 MET cc_start: 0.3600 (pp-130) cc_final: 0.1983 (ttt) REVERT: R 174 MET cc_start: 0.4144 (ptp) cc_final: 0.3456 (mmp) REVERT: R 244 TYR cc_start: 0.7300 (t80) cc_final: 0.6889 (t80) REVERT: R 299 ARG cc_start: 0.4853 (OUTLIER) cc_final: 0.4406 (mtp180) outliers start: 68 outliers final: 36 residues processed: 186 average time/residue: 0.5279 time to fit residues: 105.7527 Evaluate side-chains 179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 165 VAL Chi-restraints excluded: chain R residue 299 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: [72, 0, 41, 80, 8, 43, 70, 25, 7, 99, 97] chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 chunk 97 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.223840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.184410 restraints weight = 11824.431| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.49 r_work: 0.3775 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10293 Z= 0.123 Angle : 0.597 10.362 13959 Z= 0.306 Chirality : 0.043 0.231 1573 Planarity : 0.004 0.056 1769 Dihedral : 5.373 54.025 1418 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 3.92 % Allowed : 21.70 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.09 (0.23), residues: 1256 helix: 1.46 (0.23), residues: 489 sheet: 0.02 (0.30), residues: 281 loop : -1.73 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.019 0.001 TYR A 151 PHE 0.013 0.001 PHE B 199 TRP 0.014 0.002 TRP B 169 HIS 0.008 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10289) covalent geometry : angle 0.59713 / 0.31 (13951) SS BOND : bond 0.00345 / 0.17 ( 4) SS BOND : angle 0.78896 / 0.39 ( 8) hydrogen bonds : bond 0.03968 / 2.63 ( 486) hydrogen bonds : angle 4.56052 / 3.44 ( 1413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7195 (ttp80) cc_final: 0.6713 (ttp-110) REVERT: A 158 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8282 (mtmm) REVERT: A 256 ARG cc_start: 0.6924 (ptm-80) cc_final: 0.6611 (ptm160) REVERT: A 341 PHE cc_start: 0.7282 (t80) cc_final: 0.6973 (t80) REVERT: D 62 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6433 (m-30) REVERT: D 180 MET cc_start: 0.5904 (tpt) cc_final: 0.5703 (tpt) REVERT: R 115 MET cc_start: 0.6039 (ttt) cc_final: 0.5360 (mtm) REVERT: R 136 MET cc_start: 0.6860 (mtm) cc_final: 0.6607 (mtp) REVERT: R 164 MET cc_start: 0.3548 (pp-130) cc_final: 0.3127 (tmm) REVERT: R 174 MET cc_start: 0.4102 (ptp) cc_final: 0.3449 (mmp) REVERT: R 244 TYR cc_start: 0.7368 (t80) cc_final: 0.6969 (t80) outliers start: 43 outliers final: 27 residues processed: 163 average time/residue: 0.5558 time to fit residues: 97.4206 Evaluate side-chains 158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: [60, 78, 73, 2, 96, 50, 72, 54, 106, 98, 116] chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 0.0470 chunk 2 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 0.0770 chunk 116 optimal weight: 2.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.223572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.179442 restraints weight = 11915.702| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.41 r_work: 0.3747 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10293 Z= 0.138 Angle : 0.606 8.713 13959 Z= 0.311 Chirality : 0.043 0.139 1573 Planarity : 0.004 0.055 1769 Dihedral : 4.927 48.483 1413 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 3.92 % Allowed : 22.70 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.10 (0.23), residues: 1256 helix: 1.50 (0.23), residues: 489 sheet: -0.10 (0.30), residues: 285 loop : -1.72 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.020 0.001 TYR A 151 PHE 0.016 0.001 PHE B 151 TRP 0.013 0.002 TRP B 169 HIS 0.007 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10289) covalent geometry : angle 0.60554 / 0.31 (13951) SS BOND : bond 0.00297 / 0.15 ( 4) SS BOND : angle 0.79883 / 0.40 ( 8) hydrogen bonds : bond 0.04009 / 2.66 ( 486) hydrogen bonds : angle 4.51955 / 3.40 ( 1413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7208 (ttp80) cc_final: 0.6722 (ttp-110) REVERT: A 152 GLN cc_start: 0.7278 (tm-30) cc_final: 0.6991 (tm-30) REVERT: A 158 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: A 248 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6091 (mmt) REVERT: A 256 ARG cc_start: 0.6860 (ptm-80) cc_final: 0.6607 (ptm160) REVERT: A 307 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: A 341 PHE cc_start: 0.7192 (t80) cc_final: 0.6920 (t80) REVERT: B 78 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8179 (tppt) REVERT: D 62 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6326 (m-30) REVERT: R 115 MET cc_start: 0.6080 (ttt) cc_final: 0.5338 (ttp) REVERT: R 136 MET cc_start: 0.6835 (mtm) cc_final: 0.6586 (mtp) REVERT: R 164 MET cc_start: 0.3744 (pp-130) cc_final: 0.1832 (ttt) REVERT: R 194 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.5865 (tt) REVERT: R 244 TYR cc_start: 0.7354 (t80) cc_final: 0.6957 (t80) outliers start: 43 outliers final: 28 residues processed: 165 average time/residue: 0.5557 time to fit residues: 98.4187 Evaluate side-chains 166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 236 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: [106, 105, 34, 111, 119, 75, 42, 104, 72, 117, 23] chunk 106 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 111 optimal weight: 0.3980 chunk 119 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.223567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.182269 restraints weight = 11796.898| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.56 r_work: 0.3756 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10293 Z= 0.137 Angle : 0.606 9.083 13959 Z= 0.312 Chirality : 0.043 0.147 1573 Planarity : 0.004 0.056 1769 Dihedral : 4.902 48.708 1413 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 4.74 % Allowed : 22.33 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: -0.06 (0.23), residues: 1256 helix: 1.56 (0.24), residues: 486 sheet: -0.07 (0.30), residues: 290 loop : -1.72 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 168 TYR 0.020 0.001 TYR A 151 PHE 0.015 0.001 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (10289) covalent geometry : angle 0.60595 / 0.31 (13951) SS BOND : bond 0.00303 / 0.15 ( 4) SS BOND : angle 0.80624 / 0.40 ( 8) hydrogen bonds : bond 0.03949 / 2.61 ( 486) hydrogen bonds : angle 4.50545 / 3.39 ( 1413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7279 (ttp80) cc_final: 0.6806 (ttp-110) REVERT: A 77 LYS cc_start: 0.8355 (tttm) cc_final: 0.8018 (tptp) REVERT: A 81 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8365 (mt0) REVERT: A 158 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8256 (mtmm) REVERT: A 248 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6148 (mmt) REVERT: A 256 ARG cc_start: 0.6913 (ptm-80) cc_final: 0.6643 (ptm160) REVERT: A 341 PHE cc_start: 0.7345 (t80) cc_final: 0.7037 (t80) REVERT: B 78 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8151 (tppt) REVERT: B 130 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6561 (mp0) REVERT: R 115 MET cc_start: 0.6135 (ttt) cc_final: 0.5402 (ttp) REVERT: R 136 MET cc_start: 0.6915 (mtm) cc_final: 0.6660 (mtp) REVERT: R 164 MET cc_start: 0.3711 (pp-130) cc_final: 0.1717 (ttt) REVERT: R 174 MET cc_start: 0.4050 (ptp) cc_final: 0.3383 (mmp) REVERT: R 193 MET cc_start: 0.6736 (tmm) cc_final: 0.5842 (ttp) REVERT: R 194 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.5821 (tt) REVERT: R 244 TYR cc_start: 0.7386 (t80) cc_final: 0.7007 (t80) outliers start: 52 outliers final: 33 residues processed: 169 average time/residue: 0.5412 time to fit residues: 98.4691 Evaluate side-chains 170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 214 ILE Chi-restraints excluded: chain R residue 236 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: [24, 71, 117, 96, 2, 44, 46, 83, 88, 115, 49] chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 46 optimal weight: 0.1980 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.225387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.180242 restraints weight = 11843.415| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.38 r_work: 0.3766 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10293 Z= 0.108 Angle : 0.575 9.884 13959 Z= 0.293 Chirality : 0.041 0.135 1573 Planarity : 0.004 0.055 1769 Dihedral : 4.671 48.373 1413 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 3.92 % Allowed : 23.25 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.11 (0.23), residues: 1256 helix: 1.76 (0.24), residues: 488 sheet: 0.07 (0.30), residues: 290 loop : -1.76 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 13 TYR 0.018 0.001 TYR A 151 PHE 0.011 0.001 PHE R 111 TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10289) covalent geometry : angle 0.57465 / 0.29 (13951) SS BOND : bond 0.00328 / 0.17 ( 4) SS BOND : angle 0.62852 / 0.32 ( 8) hydrogen bonds : bond 0.03461 / 2.29 ( 486) hydrogen bonds : angle 4.34649 / 3.28 ( 1413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7220 (ttp80) cc_final: 0.6754 (ttp-110) REVERT: A 77 LYS cc_start: 0.8332 (tttm) cc_final: 0.7935 (tptp) REVERT: A 87 MET cc_start: 0.8281 (tpp) cc_final: 0.8049 (tpt) REVERT: A 158 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8309 (mtmm) REVERT: A 177 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7742 (tp40) REVERT: A 256 ARG cc_start: 0.6754 (ptm-80) cc_final: 0.6514 (ptm160) REVERT: A 341 PHE cc_start: 0.7296 (t80) cc_final: 0.7018 (t80) REVERT: B 78 LYS cc_start: 0.8369 (ttmm) cc_final: 0.8122 (tppt) REVERT: R 115 MET cc_start: 0.6047 (ttt) cc_final: 0.5370 (mtp) REVERT: R 136 MET cc_start: 0.6794 (mtm) cc_final: 0.6562 (mtp) REVERT: R 164 MET cc_start: 0.3500 (OUTLIER) cc_final: 0.1561 (ttt) REVERT: R 193 MET cc_start: 0.6638 (tmm) cc_final: 0.5736 (ttp) REVERT: R 194 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.5841 (tt) REVERT: R 244 TYR cc_start: 0.7339 (t80) cc_final: 0.6980 (t80) REVERT: R 299 ARG cc_start: 0.5145 (OUTLIER) cc_final: 0.4668 (mtp180) outliers start: 43 outliers final: 27 residues processed: 163 average time/residue: 0.5683 time to fit residues: 99.4382 Evaluate side-chains 160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 164 MET Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 299 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: [97, 53, 35, 72, 116, 56, 21, 118, 87, 41, 16] chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 118 optimal weight: 0.0770 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 81 GLN A 274 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.222908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.176273 restraints weight = 11856.867| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.36 r_work: 0.3760 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10293 Z= 0.109 Angle : 0.577 11.718 13959 Z= 0.293 Chirality : 0.041 0.140 1573 Planarity : 0.004 0.055 1769 Dihedral : 4.609 48.147 1413 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 3.65 % Allowed : 23.70 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.20 (0.24), residues: 1256 helix: 1.83 (0.24), residues: 488 sheet: 0.23 (0.30), residues: 291 loop : -1.78 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 13 TYR 0.018 0.001 TYR A 151 PHE 0.010 0.001 PHE B 151 TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10289) covalent geometry : angle 0.57722 / 0.29 (13951) SS BOND : bond 0.00297 / 0.15 ( 4) SS BOND : angle 0.59168 / 0.30 ( 8) hydrogen bonds : bond 0.03434 / 2.27 ( 486) hydrogen bonds : angle 4.30387 / 3.25 ( 1413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7184 (ttp80) cc_final: 0.6628 (ttp-110) REVERT: A 77 LYS cc_start: 0.8242 (tttm) cc_final: 0.7800 (tptp) REVERT: A 81 GLN cc_start: 0.8509 (mt0) cc_final: 0.8251 (mt0) REVERT: A 158 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8294 (mtmm) REVERT: A 177 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7788 (tp40) REVERT: A 256 ARG cc_start: 0.6738 (ptm-80) cc_final: 0.6485 (ptm160) REVERT: A 341 PHE cc_start: 0.7265 (t80) cc_final: 0.6974 (t80) REVERT: B 78 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8136 (tppt) REVERT: R 115 MET cc_start: 0.6012 (ttt) cc_final: 0.5340 (mtp) REVERT: R 136 MET cc_start: 0.6799 (mtm) cc_final: 0.6572 (mtp) REVERT: R 174 MET cc_start: 0.3940 (ptp) cc_final: 0.3567 (mmp) REVERT: R 193 MET cc_start: 0.6481 (tmm) cc_final: 0.5717 (ttp) REVERT: R 194 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.5833 (tt) REVERT: R 244 TYR cc_start: 0.7380 (t80) cc_final: 0.7007 (t80) REVERT: R 299 ARG cc_start: 0.5120 (OUTLIER) cc_final: 0.4628 (mtp180) outliers start: 40 outliers final: 29 residues processed: 163 average time/residue: 0.5730 time to fit residues: 100.2980 Evaluate side-chains 163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 299 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: [117, 30, 20, 2, 57, 3, 33, 107, 59, 71, 115] chunk 117 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.223381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.181638 restraints weight = 11800.257| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.39 r_work: 0.3763 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10293 Z= 0.108 Angle : 0.597 11.704 13959 Z= 0.299 Chirality : 0.042 0.220 1573 Planarity : 0.004 0.055 1769 Dihedral : 4.565 47.675 1413 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 3.19 % Allowed : 24.34 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.27 (0.24), residues: 1256 helix: 1.85 (0.24), residues: 489 sheet: 0.31 (0.30), residues: 291 loop : -1.75 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 13 TYR 0.018 0.001 TYR A 151 PHE 0.011 0.001 PHE B 151 TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (10289) covalent geometry : angle 0.59705 / 0.30 (13951) SS BOND : bond 0.00307 / 0.16 ( 4) SS BOND : angle 0.57823 / 0.30 ( 8) hydrogen bonds : bond 0.03362 / 2.23 ( 486) hydrogen bonds : angle 4.26541 / 3.22 ( 1413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.7662 (tpp) cc_final: 0.7309 (tpt) REVERT: A 60 ARG cc_start: 0.7184 (ttp80) cc_final: 0.6655 (ttp-110) REVERT: A 77 LYS cc_start: 0.8267 (tttm) cc_final: 0.7929 (tptp) REVERT: A 158 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8266 (mtmm) REVERT: A 256 ARG cc_start: 0.6705 (ptm-80) cc_final: 0.6442 (ptm160) REVERT: A 341 PHE cc_start: 0.7221 (t80) cc_final: 0.6924 (t80) REVERT: B 78 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8150 (tppt) REVERT: R 115 MET cc_start: 0.5783 (ttt) cc_final: 0.5156 (mtp) REVERT: R 136 MET cc_start: 0.6754 (mtm) cc_final: 0.6528 (mtp) REVERT: R 164 MET cc_start: 0.3866 (pp-130) cc_final: 0.1493 (ttt) REVERT: R 174 MET cc_start: 0.4034 (ptp) cc_final: 0.3647 (mmp) REVERT: R 193 MET cc_start: 0.6419 (tmm) cc_final: 0.5684 (ttp) REVERT: R 194 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.5771 (tt) REVERT: R 244 TYR cc_start: 0.7329 (t80) cc_final: 0.6981 (t80) REVERT: R 299 ARG cc_start: 0.5082 (OUTLIER) cc_final: 0.4602 (mtp180) outliers start: 35 outliers final: 28 residues processed: 160 average time/residue: 0.5687 time to fit residues: 97.6927 Evaluate side-chains 160 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain R residue 110 CYS Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 299 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: [45, 107, 116, 14, 99, 110, 10, 31, 77, 121, 24] chunk 45 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 81 GLN A 176 GLN A 274 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.224917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.183479 restraints weight = 11846.382| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.51 r_work: 0.3783 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10293 Z= 0.122 Angle : 0.606 11.832 13959 Z= 0.306 Chirality : 0.042 0.210 1573 Planarity : 0.004 0.054 1769 Dihedral : 4.597 47.569 1412 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 3.28 % Allowed : 24.07 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 0.20 (0.23), residues: 1256 helix: 1.79 (0.24), residues: 491 sheet: 0.23 (0.30), residues: 291 loop : -1.77 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 13 TYR 0.017 0.001 TYR A 151 PHE 0.014 0.001 PHE B 151 TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10289) covalent geometry : angle 0.60558 / 0.31 (13951) SS BOND : bond 0.00272 / 0.14 ( 4) SS BOND : angle 0.63407 / 0.32 ( 8) hydrogen bonds : bond 0.03610 / 2.39 ( 486) hydrogen bonds : angle 4.32456 / 3.26 ( 1413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4271.67 seconds wall clock time: 73 minutes 24.75 seconds (4404.75 seconds total)