Starting phenix.real_space_refine on Sat Sep 12 18:52:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yzp_14393/09_2026/7yzp_14393.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yzp_14393/09_2026/7yzp_14393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yzp_14393/09_2026/7yzp_14393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yzp_14393/09_2026/7yzp_14393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yzp_14393/09_2026/7yzp_14393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yzp_14393/09_2026/7yzp_14393.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yzp_14393/09_2026/7yzp_14393.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yzp_14393/09_2026/7yzp_14393.cif" } resolution = 4.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4320 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 63 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 8650 2.51 5 N 2499 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14107 Number of models: 1 Model: "" Number of chains: 9 Chain: "F" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1211 Classifications: {'DNA': 59} Link IDs: {'rna3p': 58} Chain: "A" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3013 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 20, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2819 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 20, 'TRANS': 335} Chain breaks: 4 Chain: "C" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3502 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 8, 'TRANS': 439} Chain breaks: 1 Chain: "D" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3502 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 8, 'TRANS': 439} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 21 residue: pdb=" N GLY A 284 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 284 " occ=0.50 residue: pdb=" N ALA A 287 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 287 " occ=0.60 residue: pdb=" N THR A 290 " occ=0.70 ... (5 atoms not shown) pdb=" CG2 THR A 290 " occ=0.70 residue: pdb=" N ALA A 291 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 291 " occ=0.60 residue: pdb=" N GLN A 292 " occ=0.70 ... (7 atoms not shown) pdb=" NE2 GLN A 292 " occ=0.70 residue: pdb=" N LEU A 293 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 293 " occ=0.80 residue: pdb=" N PRO A 303 " occ=0.61 ... (5 atoms not shown) pdb=" CD PRO A 303 " occ=0.61 residue: pdb=" N PRO A 304 " occ=0.68 ... (5 atoms not shown) pdb=" CD PRO A 304 " occ=0.68 residue: pdb=" N VAL A 305 " occ=0.88 ... (5 atoms not shown) pdb=" CG2 VAL A 305 " occ=0.88 residue: pdb=" N TRP A 306 " occ=0.97 ... (12 atoms not shown) pdb=" CH2 TRP A 306 " occ=0.97 residue: pdb=" N LEU A 307 " occ=0.87 ... (6 atoms not shown) pdb=" CD2 LEU A 307 " occ=0.87 residue: pdb=" N ILE A 309 " occ=0.89 ... (6 atoms not shown) pdb=" CD1 ILE A 309 " occ=0.89 ... (remaining 9 not shown) Time building chain proxies: 2.73, per 1000 atoms: 0.19 Number of scatterers: 14107 At special positions: 0 Unit cell: (100.605, 140.847, 139.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 38 16.00 P 63 15.00 Mg 2 11.99 O 2851 8.00 N 2499 7.00 C 8650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 588.2 milliseconds 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 15 sheets defined 45.6% alpha, 14.9% beta 27 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 39 Processing helix chain 'A' and resid 56 through 74 removed outlier: 3.618A pdb=" N GLN A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 98 removed outlier: 4.450A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.744A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 173 removed outlier: 3.533A pdb=" N GLN A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 295 through 298 removed outlier: 3.948A pdb=" N ASP A 298 " --> pdb=" O GLN A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 319 through 329 removed outlier: 3.848A pdb=" N GLN A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.609A pdb=" N LEU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 393 removed outlier: 4.180A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 Processing helix chain 'B' and resid 56 through 74 removed outlier: 3.692A pdb=" N ARG B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.883A pdb=" N LEU B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 152 through 173 Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.574A pdb=" N GLU B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 316 through 329 removed outlier: 4.091A pdb=" N ARG B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 378 through 395 removed outlier: 4.138A pdb=" N ALA B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 removed outlier: 4.461A pdb=" N ILE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 104 Processing helix chain 'C' and resid 128 through 141 removed outlier: 4.247A pdb=" N GLU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 149 removed outlier: 3.913A pdb=" N ARG C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 165 through 177 Processing helix chain 'C' and resid 180 through 201 removed outlier: 3.691A pdb=" N PHE C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 210 removed outlier: 3.584A pdb=" N VAL C 210 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 235 removed outlier: 4.108A pdb=" N GLU C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 887 removed outlier: 3.588A pdb=" N GLN C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP C 879 " --> pdb=" O GLN C 875 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP C 880 " --> pdb=" O GLN C 876 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 882 " --> pdb=" O GLU C 878 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU C 883 " --> pdb=" O ASP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 900 Processing helix chain 'C' and resid 900 through 917 removed outlier: 3.843A pdb=" N ASN C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 971 removed outlier: 3.982A pdb=" N VAL C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 989 removed outlier: 3.962A pdb=" N THR C 988 " --> pdb=" O GLY C 985 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU C 989 " --> pdb=" O PHE C 986 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 985 through 989' Processing helix chain 'C' and resid 990 through 1005 Processing helix chain 'C' and resid 1017 through 1024 Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 44 through 56 removed outlier: 4.908A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 165 through 176 removed outlier: 4.292A pdb=" N GLU D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 208 removed outlier: 3.916A pdb=" N GLN D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 234 Processing helix chain 'D' and resid 836 through 885 removed outlier: 3.760A pdb=" N ARG D 840 " --> pdb=" O HIS D 836 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 875 " --> pdb=" O ALA D 871 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN D 876 " --> pdb=" O GLN D 872 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP D 879 " --> pdb=" O GLN D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 919 removed outlier: 4.733A pdb=" N LEU D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 913 " --> pdb=" O HIS D 909 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 949 through 951 No H-bonds generated for 'chain 'D' and resid 949 through 951' Processing helix chain 'D' and resid 952 through 971 removed outlier: 3.762A pdb=" N VAL D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1006 removed outlier: 3.528A pdb=" N ASP D 995 " --> pdb=" O SER D 991 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR D 996 " --> pdb=" O GLU D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1021 removed outlier: 4.118A pdb=" N MET D1020 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1043 through 1046 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.208A pdb=" N LEU A 77 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG A 2 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE A 44 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU A 4 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 3 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 255 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN A 270 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU A 257 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL A 268 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR A 259 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 removed outlier: 8.331A pdb=" N ILE A 180 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL A 125 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N THR A 182 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N CYS A 127 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 179 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA A 219 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA A 181 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 236 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 283 removed outlier: 6.819A pdb=" N ALA A 280 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLU A 310 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 282 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.364A pdb=" N LEU B 77 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG B 2 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE B 44 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B 4 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B 256 " --> pdb=" O HIS B 5 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER B 261 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 116 removed outlier: 3.671A pdb=" N GLN B 113 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N ILE B 180 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 125 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR B 182 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N CYS B 127 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 179 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA B 219 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B 181 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 218 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.214A pdb=" N VAL B 305 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL B 335 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 307 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 337 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2 through 3 removed outlier: 3.639A pdb=" N LEU C 80 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU C 84 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3 removed outlier: 3.631A pdb=" N GLU C 115 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 116 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 979 through 982 removed outlier: 6.305A pdb=" N LEU C 980 " --> pdb=" O GLY C1012 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE C1014 " --> pdb=" O LEU C 980 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C 982 " --> pdb=" O ILE C1014 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE C 33 " --> pdb=" O VAL C1013 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 922 through 926 Processing sheet with id=AB3, first strand: chain 'C' and resid 1031 through 1032 Processing sheet with id=AB4, first strand: chain 'D' and resid 18 through 21 removed outlier: 6.272A pdb=" N ILE D 3 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU D 86 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 116 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG D 118 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE D 124 " --> pdb=" O ARG D 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.722A pdb=" N LEU D 980 " --> pdb=" O GLY D1012 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE D1014 " --> pdb=" O LEU D 980 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU D 982 " --> pdb=" O ILE D1014 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE D 33 " --> pdb=" O VAL D1013 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA D 34 " --> pdb=" O ILE D1028 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL D1030 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 36 " --> pdb=" O VAL D1030 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LYS D1032 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 922 through 926 removed outlier: 3.510A pdb=" N ARG D 946 " --> pdb=" O VAL D 936 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4471 1.34 - 1.46: 2318 1.46 - 1.58: 7491 1.58 - 1.70: 123 1.70 - 1.82: 60 Bond restraints: 14463 Sorted by residual: bond pdb=" C4 ADP D1101 " pdb=" C5 ADP D1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP C1101 " pdb=" C5 ADP C1101 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C5 ADP D1101 " pdb=" C6 ADP D1101 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C5 ADP C1101 " pdb=" C6 ADP C1101 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C3' DG F 34 " pdb=" C2' DG F 34 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 14458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 19705 2.80 - 5.59: 128 5.59 - 8.39: 19 8.39 - 11.19: 8 11.19 - 13.99: 1 Bond angle restraints: 19861 Sorted by residual: angle pdb=" O4' DT F 35 " pdb=" C4' DT F 35 " pdb=" C3' DT F 35 " ideal model delta sigma weight residual 106.00 102.70 3.30 6.00e-01 2.78e+00 3.03e+01 angle pdb=" PA ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sigma weight residual 120.50 134.49 -13.99 3.00e+00 1.11e-01 2.17e+01 angle pdb=" C ASN D 12 " pdb=" CA ASN D 12 " pdb=" CB ASN D 12 " ideal model delta sigma weight residual 116.63 111.67 4.96 1.16e+00 7.43e-01 1.83e+01 angle pdb=" N ASN A 83 " pdb=" CA ASN A 83 " pdb=" C ASN A 83 " ideal model delta sigma weight residual 113.12 107.86 5.26 1.25e+00 6.40e-01 1.77e+01 angle pdb=" N VAL C 971 " pdb=" CA VAL C 971 " pdb=" C VAL C 971 " ideal model delta sigma weight residual 112.29 108.37 3.92 9.40e-01 1.13e+00 1.74e+01 ... (remaining 19856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.90: 7984 28.90 - 57.80: 570 57.80 - 86.70: 46 86.70 - 115.60: 3 115.60 - 144.50: 1 Dihedral angle restraints: 8604 sinusoidal: 3868 harmonic: 4736 Sorted by residual: dihedral pdb=" C ASP B 376 " pdb=" N ASP B 376 " pdb=" CA ASP B 376 " pdb=" CB ASP B 376 " ideal model delta harmonic sigma weight residual -122.60 -135.45 12.85 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N ASP B 376 " pdb=" C ASP B 376 " pdb=" CA ASP B 376 " pdb=" CB ASP B 376 " ideal model delta harmonic sigma weight residual 122.80 133.54 -10.74 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C4' DG F 34 " pdb=" C3' DG F 34 " pdb=" O3' DG F 34 " pdb=" P DT F 35 " ideal model delta sinusoidal sigma weight residual 220.00 75.50 144.50 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 8601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2110 0.079 - 0.159: 178 0.159 - 0.238: 5 0.238 - 0.318: 0 0.318 - 0.397: 1 Chirality restraints: 2294 Sorted by residual: chirality pdb=" CA ASP B 376 " pdb=" N ASP B 376 " pdb=" C ASP B 376 " pdb=" CB ASP B 376 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C3' ADP D1101 " pdb=" C2' ADP D1101 " pdb=" C4' ADP D1101 " pdb=" O3' ADP D1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ASP A 85 " pdb=" N ASP A 85 " pdb=" C ASP A 85 " pdb=" CB ASP A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 2291 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 895 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C PHE D 895 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE D 895 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG D 896 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C1034 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C ASN C1034 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN C1034 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY C1035 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 87 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C VAL D 87 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL D 87 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS D 88 " 0.009 2.00e-02 2.50e+03 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 20 2.25 - 2.92: 5542 2.92 - 3.58: 21296 3.58 - 4.24: 31935 4.24 - 4.90: 52744 Nonbonded interactions: 111537 Sorted by model distance: nonbonded pdb=" OD1 ASN A 83 " pdb="MN MN A 502 " model vdw 1.593 2.320 nonbonded pdb=" N ASN B 83 " pdb="MN MN B 502 " model vdw 2.004 2.400 nonbonded pdb=" OD1 ASP B 8 " pdb="MN MN B 501 " model vdw 2.006 2.320 nonbonded pdb=" OD1 ASN B 83 " pdb="MN MN B 502 " model vdw 2.023 2.320 nonbonded pdb=" CD2 HIS A 222 " pdb="MN MN A 502 " model vdw 2.051 2.540 ... (remaining 111532 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 105 or resid 109 through 137 or resid 151 throug \ h 188 or resid 205 through 342 or resid 354 through 502)) selection = (chain 'B' and (resid 1 through 188 or resid 205 through 502)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.28 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.130 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 14463 Z= 0.262 Angle : 0.655 13.986 19861 Z= 0.400 Chirality : 0.042 0.397 2294 Planarity : 0.003 0.036 2364 Dihedral : 17.725 144.499 5524 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.22), residues: 1611 helix: 1.67 (0.21), residues: 686 sheet: 0.15 (0.35), residues: 225 loop : -0.56 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.013 0.001 TYR B 63 PHE 0.013 0.001 PHE A 366 TRP 0.019 0.001 TRP B 30 HIS 0.008 0.001 HIS D 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.26 (14463) covalent geometry : angle 0.65473 / 0.40 (19861) hydrogen bonds : bond 0.16883 / 19.14 ( 654) hydrogen bonds : angle 5.73899 / 7.05 ( 1841) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.548 Fit side-chains REVERT: C 1020 MET cc_start: 0.7360 (ttp) cc_final: 0.6408 (ttp) REVERT: D 13 SER cc_start: 0.8825 (t) cc_final: 0.8415 (p) REVERT: D 990 ASP cc_start: 0.7422 (p0) cc_final: 0.7162 (p0) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0833 time to fit residues: 19.9841 Evaluate side-chains 94 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS D 192 GLN D 842 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.096534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.080203 restraints weight = 40363.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081272 restraints weight = 27639.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082567 restraints weight = 21756.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082660 restraints weight = 16465.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082785 restraints weight = 14993.568| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (13 function evaluations) r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14463 Z= 0.135 Angle : 0.609 8.461 19861 Z= 0.310 Chirality : 0.042 0.212 2294 Planarity : 0.004 0.037 2364 Dihedral : 17.803 144.229 2417 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.86 % Allowed : 7.28 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.22), residues: 1611 helix: 1.62 (0.20), residues: 683 sheet: 0.20 (0.34), residues: 243 loop : -0.46 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.025 0.002 TYR C 144 PHE 0.016 0.001 PHE A 27 TRP 0.030 0.002 TRP B 30 HIS 0.009 0.001 HIS D 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (14463) covalent geometry : angle 0.60914 / 0.31 (19861) hydrogen bonds : bond 0.04644 / 5.27 ( 654) hydrogen bonds : angle 4.58857 / 5.78 ( 1841) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.509 Fit side-chains REVERT: C 151 MET cc_start: 0.8963 (ptm) cc_final: 0.8518 (ptm) REVERT: C 188 MET cc_start: 0.7746 (tmm) cc_final: 0.7478 (tmm) REVERT: D 13 SER cc_start: 0.8923 (t) cc_final: 0.8466 (p) REVERT: D 990 ASP cc_start: 0.7451 (p0) cc_final: 0.7210 (p0) REVERT: D 992 GLU cc_start: 0.7661 (mp0) cc_final: 0.7302 (mp0) outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 0.0872 time to fit residues: 15.5213 Evaluate side-chains 98 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 905 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 101 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.0030 chunk 154 optimal weight: 0.7980 chunk 68 optimal weight: 0.0370 chunk 72 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 0.5268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 GLN D1027 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.095704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.079461 restraints weight = 40337.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079839 restraints weight = 26173.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.080495 restraints weight = 21894.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080800 restraints weight = 18998.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080962 restraints weight = 16555.360| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14463 Z= 0.112 Angle : 0.569 10.370 19861 Z= 0.288 Chirality : 0.040 0.211 2294 Planarity : 0.003 0.034 2364 Dihedral : 17.834 144.401 2417 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.07 % Allowed : 9.42 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.22), residues: 1611 helix: 1.67 (0.20), residues: 683 sheet: 0.21 (0.34), residues: 243 loop : -0.48 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 2 TYR 0.011 0.001 TYR C 144 PHE 0.012 0.001 PHE C 147 TRP 0.015 0.001 TRP B 30 HIS 0.006 0.001 HIS D 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (14463) covalent geometry : angle 0.56883 / 0.29 (19861) hydrogen bonds : bond 0.04129 / 4.68 ( 654) hydrogen bonds : angle 4.35693 / 5.44 ( 1841) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: B 30 TRP cc_start: 0.8599 (t60) cc_final: 0.8205 (t60) REVERT: C 188 MET cc_start: 0.7809 (tmm) cc_final: 0.7437 (tmm) REVERT: D 13 SER cc_start: 0.8981 (t) cc_final: 0.8498 (p) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 0.0863 time to fit residues: 15.6358 Evaluate side-chains 108 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 851 GLN Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 905 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 chunk 134 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 76 optimal weight: 0.0020 chunk 44 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.5966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 864 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.095463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078697 restraints weight = 40032.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079688 restraints weight = 25933.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080751 restraints weight = 20038.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080941 restraints weight = 16587.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081111 restraints weight = 14904.156| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14463 Z= 0.110 Angle : 0.560 10.251 19861 Z= 0.280 Chirality : 0.040 0.211 2294 Planarity : 0.003 0.032 2364 Dihedral : 17.883 144.719 2417 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.14 % Allowed : 11.85 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.22), residues: 1611 helix: 1.70 (0.21), residues: 683 sheet: 0.13 (0.33), residues: 253 loop : -0.47 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.011 0.001 TYR A 58 PHE 0.030 0.001 PHE C 986 TRP 0.011 0.001 TRP B 30 HIS 0.005 0.001 HIS D 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (14463) covalent geometry : angle 0.55961 / 0.28 (19861) hydrogen bonds : bond 0.03844 / 4.34 ( 654) hydrogen bonds : angle 4.27942 / 5.34 ( 1841) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: B 232 MET cc_start: 0.6419 (tpp) cc_final: 0.6091 (tpp) REVERT: B 234 HIS cc_start: 0.6016 (m-70) cc_final: 0.5580 (m-70) REVERT: C 188 MET cc_start: 0.7829 (tmm) cc_final: 0.7479 (tmm) REVERT: D 168 GLU cc_start: 0.7050 (pt0) cc_final: 0.6787 (tt0) outliers start: 16 outliers final: 15 residues processed: 111 average time/residue: 0.0848 time to fit residues: 15.5896 Evaluate side-chains 108 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 905 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 30 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 18 optimal weight: 0.0470 chunk 108 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 851 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.095268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078958 restraints weight = 40261.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079329 restraints weight = 26481.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.080001 restraints weight = 22024.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080309 restraints weight = 19059.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080521 restraints weight = 16692.934| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14463 Z= 0.113 Angle : 0.564 10.583 19861 Z= 0.281 Chirality : 0.040 0.214 2294 Planarity : 0.003 0.030 2364 Dihedral : 17.921 144.949 2417 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.36 % Allowed : 12.85 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.22), residues: 1611 helix: 1.78 (0.21), residues: 683 sheet: 0.12 (0.33), residues: 253 loop : -0.50 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.012 0.001 TYR A 58 PHE 0.031 0.001 PHE C 986 TRP 0.010 0.001 TRP B 30 HIS 0.004 0.001 HIS D 919 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (14463) covalent geometry : angle 0.56369 / 0.28 (19861) hydrogen bonds : bond 0.03673 / 4.14 ( 654) hydrogen bonds : angle 4.20270 / 5.27 ( 1841) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: B 30 TRP cc_start: 0.8680 (t60) cc_final: 0.8470 (t60) REVERT: B 232 MET cc_start: 0.6541 (tpp) cc_final: 0.6127 (tpp) REVERT: B 234 HIS cc_start: 0.6157 (m-70) cc_final: 0.5658 (m-70) REVERT: C 188 MET cc_start: 0.7810 (tmm) cc_final: 0.7472 (tmm) REVERT: D 168 GLU cc_start: 0.7096 (pt0) cc_final: 0.6849 (tt0) outliers start: 19 outliers final: 16 residues processed: 116 average time/residue: 0.0879 time to fit residues: 16.7047 Evaluate side-chains 112 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 851 GLN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 905 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 95 optimal weight: 0.2980 chunk 131 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.095136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078639 restraints weight = 40046.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.080121 restraints weight = 27335.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.080863 restraints weight = 19860.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.081116 restraints weight = 15510.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081182 restraints weight = 14963.768| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14463 Z= 0.113 Angle : 0.566 10.773 19861 Z= 0.280 Chirality : 0.040 0.214 2294 Planarity : 0.003 0.037 2364 Dihedral : 17.945 145.058 2417 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.36 % Allowed : 13.99 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.22), residues: 1611 helix: 1.82 (0.21), residues: 683 sheet: 0.14 (0.33), residues: 251 loop : -0.53 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 850 TYR 0.014 0.001 TYR B 58 PHE 0.034 0.001 PHE C 986 TRP 0.009 0.001 TRP B 30 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (14463) covalent geometry : angle 0.56590 / 0.28 (19861) hydrogen bonds : bond 0.03597 / 4.03 ( 654) hydrogen bonds : angle 4.19424 / 5.24 ( 1841) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.419 Fit side-chains REVERT: C 151 MET cc_start: 0.8923 (ptm) cc_final: 0.8506 (ptm) REVERT: C 188 MET cc_start: 0.7818 (tmm) cc_final: 0.7477 (tmm) REVERT: D 168 GLU cc_start: 0.7071 (pt0) cc_final: 0.6818 (tt0) outliers start: 19 outliers final: 13 residues processed: 113 average time/residue: 0.0872 time to fit residues: 16.2186 Evaluate side-chains 106 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 905 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 165 optimal weight: 0.0870 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 0.1980 chunk 159 optimal weight: 0.3980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.097151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080133 restraints weight = 39899.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.081762 restraints weight = 26756.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.082702 restraints weight = 18173.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082862 restraints weight = 14431.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083095 restraints weight = 13431.725| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14463 Z= 0.104 Angle : 0.571 11.151 19861 Z= 0.280 Chirality : 0.040 0.213 2294 Planarity : 0.003 0.031 2364 Dihedral : 17.952 145.020 2417 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.50 % Allowed : 13.92 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1611 helix: 1.75 (0.20), residues: 691 sheet: 0.14 (0.33), residues: 251 loop : -0.58 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.015 0.001 TYR B 63 PHE 0.018 0.001 PHE A 387 TRP 0.012 0.001 TRP B 30 HIS 0.005 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (14463) covalent geometry : angle 0.57071 / 0.28 (19861) hydrogen bonds : bond 0.03471 / 3.90 ( 654) hydrogen bonds : angle 4.15810 / 5.21 ( 1841) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.504 Fit side-chains REVERT: C 151 MET cc_start: 0.8863 (ptm) cc_final: 0.8443 (ptm) REVERT: C 188 MET cc_start: 0.7785 (tmm) cc_final: 0.7441 (tmm) REVERT: D 168 GLU cc_start: 0.7004 (pt0) cc_final: 0.6786 (tt0) REVERT: D 188 MET cc_start: 0.7972 (tmm) cc_final: 0.7760 (tmm) outliers start: 21 outliers final: 14 residues processed: 120 average time/residue: 0.0854 time to fit residues: 17.0103 Evaluate side-chains 110 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 905 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 43 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 73 optimal weight: 0.0060 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 851 GLN ** C 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.096384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079359 restraints weight = 39986.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.080744 restraints weight = 27498.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.081617 restraints weight = 19074.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.082074 restraints weight = 15810.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082268 restraints weight = 14923.250| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14463 Z= 0.113 Angle : 0.574 10.986 19861 Z= 0.282 Chirality : 0.040 0.217 2294 Planarity : 0.003 0.032 2364 Dihedral : 17.995 145.253 2417 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.36 % Allowed : 14.56 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.22), residues: 1611 helix: 1.82 (0.21), residues: 691 sheet: 0.06 (0.33), residues: 251 loop : -0.60 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.013 0.001 TYR B 58 PHE 0.014 0.001 PHE C 147 TRP 0.011 0.001 TRP B 30 HIS 0.005 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (14463) covalent geometry : angle 0.57437 / 0.28 (19861) hydrogen bonds : bond 0.03464 / 3.87 ( 654) hydrogen bonds : angle 4.14794 / 5.22 ( 1841) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.529 Fit side-chains REVERT: C 151 MET cc_start: 0.8910 (ptm) cc_final: 0.8503 (ptm) REVERT: C 188 MET cc_start: 0.7815 (tmm) cc_final: 0.7474 (tmm) REVERT: C 851 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7880 (pp30) REVERT: D 168 GLU cc_start: 0.7003 (pt0) cc_final: 0.6794 (tt0) outliers start: 19 outliers final: 16 residues processed: 109 average time/residue: 0.0843 time to fit residues: 15.3439 Evaluate side-chains 111 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 851 GLN Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain D residue 192 GLN Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 905 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 143 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 chunk 159 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 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 = 0.3688 r_free = 0.3688 target = 0.096736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.080059 restraints weight = 39933.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081182 restraints weight = 26471.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.082042 restraints weight = 20749.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082312 restraints weight = 16822.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082985 restraints weight = 15500.092| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14463 Z= 0.108 Angle : 0.594 16.591 19861 Z= 0.286 Chirality : 0.040 0.216 2294 Planarity : 0.003 0.031 2364 Dihedral : 17.998 145.235 2417 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.21 % Allowed : 14.56 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1611 helix: 1.79 (0.21), residues: 693 sheet: 0.07 (0.33), residues: 251 loop : -0.62 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.013 0.001 TYR B 63 PHE 0.018 0.001 PHE A 387 TRP 0.012 0.001 TRP B 30 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (14463) covalent geometry : angle 0.59423 / 0.29 (19861) hydrogen bonds : bond 0.03415 / 3.81 ( 654) hydrogen bonds : angle 4.13891 / 5.22 ( 1841) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.582 Fit side-chains REVERT: B 30 TRP cc_start: 0.8757 (t60) cc_final: 0.8236 (t60) REVERT: C 151 MET cc_start: 0.8937 (ptm) cc_final: 0.8610 (ptm) REVERT: C 188 MET cc_start: 0.7800 (tmm) cc_final: 0.7462 (tmm) REVERT: D 168 GLU cc_start: 0.6981 (pt0) cc_final: 0.6752 (tt0) outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.0873 time to fit residues: 15.5482 Evaluate side-chains 108 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 905 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 29 optimal weight: 0.0050 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 98 optimal weight: 0.3980 chunk 126 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.097249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080359 restraints weight = 39811.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081873 restraints weight = 27174.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082874 restraints weight = 18993.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.082986 restraints weight = 15011.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083145 restraints weight = 14012.487| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14463 Z= 0.101 Angle : 0.596 17.890 19861 Z= 0.284 Chirality : 0.040 0.215 2294 Planarity : 0.003 0.030 2364 Dihedral : 17.990 145.129 2417 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.00 % Allowed : 14.85 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.22), residues: 1611 helix: 1.82 (0.21), residues: 693 sheet: 0.11 (0.33), residues: 251 loop : -0.63 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.013 0.001 TYR B 63 PHE 0.015 0.001 PHE C 986 TRP 0.014 0.001 TRP B 30 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (14463) covalent geometry : angle 0.59631 / 0.28 (19861) hydrogen bonds : bond 0.03293 / 3.70 ( 654) hydrogen bonds : angle 4.09331 / 5.16 ( 1841) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.536 Fit side-chains REVERT: B 30 TRP cc_start: 0.8781 (t60) cc_final: 0.8268 (t60) REVERT: C 151 MET cc_start: 0.8863 (ptm) cc_final: 0.8541 (ptm) REVERT: C 188 MET cc_start: 0.7789 (tmm) cc_final: 0.7451 (tmm) outliers start: 14 outliers final: 13 residues processed: 110 average time/residue: 0.0919 time to fit residues: 17.1877 Evaluate side-chains 107 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 905 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 2 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS D 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.096573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079652 restraints weight = 39878.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.081153 restraints weight = 27673.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.082203 restraints weight = 19126.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082330 restraints weight = 14921.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.082600 restraints weight = 15010.173| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14463 Z= 0.113 Angle : 0.600 17.095 19861 Z= 0.288 Chirality : 0.040 0.218 2294 Planarity : 0.003 0.033 2364 Dihedral : 18.016 145.311 2417 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.00 % Allowed : 14.78 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.22), residues: 1611 helix: 1.86 (0.21), residues: 691 sheet: 0.03 (0.33), residues: 251 loop : -0.59 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.012 0.001 TYR B 58 PHE 0.015 0.001 PHE A 387 TRP 0.012 0.001 TRP B 30 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (14463) covalent geometry : angle 0.59969 / 0.29 (19861) hydrogen bonds : bond 0.03338 / 3.73 ( 654) hydrogen bonds : angle 4.09528 / 5.21 ( 1841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.88 seconds wall clock time: 33 minutes 26.90 seconds (2006.90 seconds total)