Starting phenix.real_space_refine on Sat Feb 7 15:47:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdi_71534/02_2026/9pdi_71534.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdi_71534/02_2026/9pdi_71534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pdi_71534/02_2026/9pdi_71534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdi_71534/02_2026/9pdi_71534.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pdi_71534/02_2026/9pdi_71534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdi_71534/02_2026/9pdi_71534.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 14 5.49 5 Mg 3 5.21 5 S 183 5.16 5 C 21123 2.51 5 N 5813 2.21 5 O 6411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 172 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33548 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3053 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 369} Chain: "D" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3040 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 362} Chain: "E" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2887 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 346} Chain: "G" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1867 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1933 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1860 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1813 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1876 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 229} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1890 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "v" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3146 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 24, 'TRANS': 374} Chain breaks: 2 Chain: "B" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3075 Classifications: {'peptide': 392} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 370} Chain breaks: 2 Chain: "F" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2803 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 341} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2220 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 270} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.80, per 1000 atoms: 0.23 Number of scatterers: 33548 At special positions: 0 Unit cell: (131, 189.688, 154.056, 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) Zn 1 29.99 S 183 16.00 P 14 15.00 Mg 3 11.99 O 6411 8.00 N 5813 7.00 C 21123 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 113 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 115 " 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7978 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 24 sheets defined 47.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'C' and resid 21 through 66 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 154 through 166 removed outlier: 3.680A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 171 through 179 removed outlier: 4.299A pdb=" N PHE C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.594A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 373 removed outlier: 3.721A pdb=" N GLU C 373 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 391 Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'D' and resid 40 through 83 removed outlier: 3.832A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.612A pdb=" N LEU D 123 " --> pdb=" O ASP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 182 removed outlier: 3.835A pdb=" N ALA D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.799A pdb=" N TYR D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 232 through 236 removed outlier: 4.092A pdb=" N VAL D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 232 through 236' Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 267 through 270 Processing helix chain 'D' and resid 279 through 298 Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 337 through 350 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 371 through 389 Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'D' and resid 414 through 418 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 34 through 51 removed outlier: 3.618A pdb=" N LYS E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 116 through 124 Processing helix chain 'E' and resid 138 through 155 Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 155 through 163 removed outlier: 3.829A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 192 Processing helix chain 'E' and resid 209 through 225 removed outlier: 3.542A pdb=" N ARG E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 265 Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 305 through 317 Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 340 through 357 removed outlier: 3.784A pdb=" N ILE E 355 " --> pdb=" O GLY E 351 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 379 Processing helix chain 'G' and resid 17 through 21 removed outlier: 3.688A pdb=" N ARG G 21 " --> pdb=" O PRO G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.807A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 66 removed outlier: 3.645A pdb=" N VAL G 66 " --> pdb=" O SER G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 171 through 184 Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'H' and resid 19 through 31 removed outlier: 4.023A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 3.595A pdb=" N TYR H 83 " --> pdb=" O MET H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 121 removed outlier: 3.708A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 183 through 198 removed outlier: 4.202A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 234 Processing helix chain 'I' and resid 18 through 28 removed outlier: 3.874A pdb=" N ILE I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 79 through 102 Processing helix chain 'I' and resid 106 through 124 removed outlier: 3.724A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'I' and resid 229 through 251 Processing helix chain 'J' and resid 16 through 25 Processing helix chain 'J' and resid 26 through 29 Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'J' and resid 76 through 99 Processing helix chain 'J' and resid 103 through 119 Processing helix chain 'J' and resid 164 through 176 Processing helix chain 'J' and resid 178 through 182 removed outlier: 3.510A pdb=" N ILE J 181 " --> pdb=" O ASP J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 199 removed outlier: 3.961A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 240 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.508A pdb=" N ARG K 10 " --> pdb=" O SER K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 30 Processing helix chain 'K' and resid 31 through 34 Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 81 through 103 Processing helix chain 'K' and resid 108 through 120 Processing helix chain 'K' and resid 125 through 129 removed outlier: 3.867A pdb=" N ALA K 128 " --> pdb=" O GLU K 125 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP K 129 " --> pdb=" O GLU K 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 125 through 129' Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.792A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 230 through 241 removed outlier: 3.884A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 29 removed outlier: 3.859A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 77 through 99 Processing helix chain 'L' and resid 104 through 122 removed outlier: 3.768A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix Processing helix chain 'L' and resid 164 through 175 removed outlier: 4.423A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 182 removed outlier: 5.573A pdb=" N MET L 180 " --> pdb=" O SER L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 Processing helix chain 'L' and resid 229 through 235 removed outlier: 3.952A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 32 Processing helix chain 'M' and resid 80 through 103 Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 168 through 178 removed outlier: 3.719A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 201 removed outlier: 4.317A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLU M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 219 through 221 No H-bonds generated for 'chain 'M' and resid 219 through 221' Processing helix chain 'M' and resid 228 through 244 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 41 through 64 removed outlier: 3.951A pdb=" N GLY A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 180 through 197 Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 197 through 204 removed outlier: 3.873A pdb=" N PHE A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 252 through 267 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 347 through 361 removed outlier: 4.282A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 Processing helix chain 'A' and resid 381 through 399 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 427 through 431 removed outlier: 4.053A pdb=" N THR A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 427 through 431' Processing helix chain 'B' and resid 58 through 85 Processing helix chain 'B' and resid 95 through 104 Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.606A pdb=" N LEU B 143 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 208 through 214 removed outlier: 3.908A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 261 through 277 Processing helix chain 'B' and resid 287 through 290 Processing helix chain 'B' and resid 299 through 319 removed outlier: 3.721A pdb=" N PHE B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.914A pdb=" N ILE B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 415 through 427 removed outlier: 3.619A pdb=" N GLU B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 84 removed outlier: 3.923A pdb=" N ASP F 71 " --> pdb=" O GLN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 175 Processing helix chain 'F' and resid 191 through 208 removed outlier: 4.664A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 208 through 216 Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 267 through 274 removed outlier: 3.970A pdb=" N LEU F 274 " --> pdb=" O ASP F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 277 No H-bonds generated for 'chain 'F' and resid 275 through 277' Processing helix chain 'F' and resid 303 through 318 removed outlier: 3.776A pdb=" N GLN F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 Processing helix chain 'F' and resid 359 through 370 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 393 through 410 Processing helix chain 'F' and resid 417 through 427 Processing helix chain 'F' and resid 428 through 431 removed outlier: 4.572A pdb=" N LYS F 431 " --> pdb=" O GLN F 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 428 through 431' Processing helix chain 'c' and resid 35 through 48 Processing helix chain 'c' and resid 88 through 103 Processing helix chain 'c' and resid 123 through 137 removed outlier: 3.702A pdb=" N LEU c 136 " --> pdb=" O SER c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 171 removed outlier: 3.894A pdb=" N GLY c 171 " --> pdb=" O MET c 167 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 184 removed outlier: 3.587A pdb=" N LEU c 184 " --> pdb=" O LEU c 181 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 194 removed outlier: 3.648A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 219 removed outlier: 3.665A pdb=" N ASN c 219 " --> pdb=" O LYS c 215 " (cutoff:3.500A) Processing helix chain 'c' and resid 233 through 264 removed outlier: 4.295A pdb=" N LYS c 264 " --> pdb=" O GLU c 260 " (cutoff:3.500A) Processing helix chain 'c' and resid 279 through 309 removed outlier: 3.555A pdb=" N HIS c 283 " --> pdb=" O ASP c 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 71 through 78 removed outlier: 7.549A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 93 through 99 current: chain 'C' and resid 122 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 122 through 126 current: chain 'D' and resid 100 through 105 removed outlier: 3.530A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 109 through 114 current: chain 'D' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 139 through 142 current: chain 'E' and resid 69 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 81 current: chain 'E' and resid 107 through 110 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 107 through 110 current: chain 'A' and resid 111 through 115 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 123 current: chain 'A' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 152 current: chain 'B' and resid 120 through 125 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 134 current: chain 'B' and resid 159 through 162 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 159 through 162 current: chain 'F' and resid 121 through 126 removed outlier: 3.658A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 130 through 134 current: chain 'F' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'C' and resid 210 through 213 removed outlier: 6.107A pdb=" N THR C 210 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE C 247 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE C 292 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE C 246 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA C 294 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET C 248 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 337 through 338 removed outlier: 6.927A pdb=" N ASN C 337 " --> pdb=" O VAL C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 226 through 231 removed outlier: 6.224A pdb=" N ALA D 260 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE D 308 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE D 262 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA D 310 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE D 264 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 194 through 199 removed outlier: 6.878A pdb=" N ASN E 194 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHE E 231 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU E 196 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP E 233 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL E 198 " --> pdb=" O ASP E 233 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS E 228 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE E 276 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE E 230 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA E 278 " --> pdb=" O ILE E 230 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET E 232 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY E 169 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ILE E 299 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU E 171 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.515A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU G 216 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.594A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR G 81 " --> pdb=" O CYS G 137 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY G 162 " --> pdb=" O ASP H 58 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AA9, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.845A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 161 through 164 Processing sheet with id=AB2, first strand: chain 'I' and resid 65 through 69 removed outlier: 6.136A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 158 through 161 Processing sheet with id=AB4, first strand: chain 'J' and resid 62 through 66 removed outlier: 6.638A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 167 through 170 Processing sheet with id=AB6, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.430A pdb=" N ILE K 67 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N MET K 78 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU K 69 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS K 76 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP K 71 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 159 through 161 removed outlier: 3.534A pdb=" N MET L 159 " --> pdb=" O GLY L 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 63 through 65 removed outlier: 3.565A pdb=" N ASP L 138 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.873A pdb=" N GLY M 44 " --> pdb=" O CYS M 41 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU M 212 " --> pdb=" O VAL M 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 66 through 70 removed outlier: 6.448A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY M 138 " --> pdb=" O GLY M 74 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR M 158 " --> pdb=" O MET M 150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 236 through 240 removed outlier: 8.192A pdb=" N LEU A 318 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE A 272 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA A 320 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE A 274 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 212 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY A 211 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A 341 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 213 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 246 through 250 removed outlier: 6.179A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 250 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER B 280 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE B 328 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL B 282 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA B 330 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE B 284 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 223 " --> pdb=" O ILE B 351 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 223 through 226 Processing sheet with id=AC5, first strand: chain 'F' and resid 247 through 250 removed outlier: 5.416A pdb=" N THR F 247 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE F 284 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU F 249 " --> pdb=" O PHE F 284 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 30 through 34 removed outlier: 6.912A pdb=" N ASP c 71 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL c 67 " --> pdb=" O VAL c 62 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL c 62 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL c 69 " --> pdb=" O GLU c 60 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU c 60 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL c 145 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS c 113 " --> pdb=" O VAL c 145 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) 1661 hydrogen bonds defined for protein. 4782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.29 Time building geometry restraints manager: 4.19 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: 11236 1.34 - 1.46: 6826 1.46 - 1.58: 15704 1.58 - 1.70: 16 1.70 - 1.82: 308 Bond restraints: 34090 Sorted by residual: bond pdb=" CA SER E 248 " pdb=" CB SER E 248 " ideal model delta sigma weight residual 1.529 1.481 0.048 1.58e-02 4.01e+03 9.27e+00 bond pdb=" N ILE K 82 " pdb=" CA ILE K 82 " ideal model delta sigma weight residual 1.461 1.492 -0.030 1.17e-02 7.31e+03 6.74e+00 bond pdb=" N GLY E 266 " pdb=" CA GLY E 266 " ideal model delta sigma weight residual 1.447 1.471 -0.024 9.30e-03 1.16e+04 6.67e+00 bond pdb=" N ILE E 230 " pdb=" CA ILE E 230 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.15e-02 7.56e+03 6.20e+00 bond pdb=" CA PHE E 231 " pdb=" C PHE E 231 " ideal model delta sigma weight residual 1.525 1.494 0.031 1.28e-02 6.10e+03 5.74e+00 ... (remaining 34085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 45416 2.89 - 5.78: 545 5.78 - 8.67: 68 8.67 - 11.56: 17 11.56 - 14.45: 9 Bond angle restraints: 46055 Sorted by residual: angle pdb=" C GLU E 245 " pdb=" CA GLU E 245 " pdb=" CB GLU E 245 " ideal model delta sigma weight residual 116.54 109.13 7.41 1.15e+00 7.56e-01 4.16e+01 angle pdb=" N MET A 299 " pdb=" CA MET A 299 " pdb=" CB MET A 299 " ideal model delta sigma weight residual 110.30 117.87 -7.57 1.54e+00 4.22e-01 2.42e+01 angle pdb=" CA MET A 299 " pdb=" CB MET A 299 " pdb=" CG MET A 299 " ideal model delta sigma weight residual 114.10 123.84 -9.74 2.00e+00 2.50e-01 2.37e+01 angle pdb=" N LEU E 257 " pdb=" CA LEU E 257 " pdb=" C LEU E 257 " ideal model delta sigma weight residual 111.28 106.47 4.81 1.09e+00 8.42e-01 1.95e+01 angle pdb=" CA GLU H 200 " pdb=" CB GLU H 200 " pdb=" CG GLU H 200 " ideal model delta sigma weight residual 114.10 122.91 -8.81 2.00e+00 2.50e-01 1.94e+01 ... (remaining 46050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.72: 19357 27.72 - 55.43: 1517 55.43 - 83.15: 126 83.15 - 110.87: 23 110.87 - 138.58: 3 Dihedral angle restraints: 21026 sinusoidal: 8672 harmonic: 12354 Sorted by residual: dihedral pdb=" CA ALA F 279 " pdb=" C ALA F 279 " pdb=" N PRO F 280 " pdb=" CA PRO F 280 " ideal model delta harmonic sigma weight residual 180.00 125.86 54.14 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CD ARG E 242 " pdb=" NE ARG E 242 " pdb=" CZ ARG E 242 " pdb=" NH1 ARG E 242 " ideal model delta sinusoidal sigma weight residual 0.00 60.50 -60.50 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" O2A ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PA ADP E 501 " pdb=" PB ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 78.58 -138.58 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 21023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4084 0.051 - 0.101: 960 0.101 - 0.152: 175 0.152 - 0.203: 18 0.203 - 0.253: 8 Chirality restraints: 5245 Sorted by residual: chirality pdb=" CA GLU E 245 " pdb=" N GLU E 245 " pdb=" C GLU E 245 " pdb=" CB GLU E 245 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE E 276 " pdb=" N ILE E 276 " pdb=" C ILE E 276 " pdb=" CB ILE E 276 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE E 229 " pdb=" N ILE E 229 " pdb=" C ILE E 229 " pdb=" CB ILE E 229 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 5242 not shown) Planarity restraints: 5947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 242 " 0.976 9.50e-02 1.11e+02 4.37e-01 1.16e+02 pdb=" NE ARG E 242 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG E 242 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 242 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 242 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 241 " 0.825 9.50e-02 1.11e+02 3.70e-01 8.32e+01 pdb=" NE ARG E 241 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG E 241 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 241 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 241 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 251 " -0.709 9.50e-02 1.11e+02 3.18e-01 6.15e+01 pdb=" NE ARG E 251 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG E 251 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 251 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 251 " -0.022 2.00e-02 2.50e+03 ... (remaining 5944 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 329 2.51 - 3.11: 25997 3.11 - 3.71: 56016 3.71 - 4.30: 75302 4.30 - 4.90: 124853 Nonbonded interactions: 282497 Sorted by model distance: nonbonded pdb=" O2G ATP C 501 " pdb="MG MG C 502 " model vdw 1.913 2.170 nonbonded pdb=" OG1 THR C 197 " pdb="MG MG C 502 " model vdw 1.927 2.170 nonbonded pdb=" OG1 THR B 233 " pdb="MG MG B 502 " model vdw 1.953 2.170 nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 501 " model vdw 1.984 2.230 nonbonded pdb=" O LYS E 34 " pdb=" OG1 THR E 37 " model vdw 2.019 3.040 ... (remaining 282492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.460 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 : 0.006 0.897 34093 Z= 0.525 Angle : 0.813 14.447 46055 Z= 0.439 Chirality : 0.046 0.253 5245 Planarity : 0.010 0.437 5947 Dihedral : 18.178 138.582 13048 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.64 % Favored : 93.09 % Rotamer: Outliers : 3.43 % Allowed : 34.64 % Favored : 61.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4199 helix: 0.99 (0.12), residues: 1830 sheet: -0.86 (0.18), residues: 722 loop : -0.82 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG c 208 TYR 0.033 0.002 TYR A 249 PHE 0.028 0.002 PHE B 319 TRP 0.009 0.001 TRP I 159 HIS 0.009 0.001 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00405 (34090) covalent geometry : angle 0.81331 (46055) hydrogen bonds : bond 0.15443 ( 1661) hydrogen bonds : angle 6.46607 ( 4782) metal coordination : bond 0.00281 ( 2) Misc. bond : bond 0.89654 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 387 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 GLU cc_start: 0.8806 (tp30) cc_final: 0.8591 (tt0) REVERT: D 98 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8022 (tp-100) REVERT: D 170 MET cc_start: 0.9154 (ptp) cc_final: 0.8715 (ptp) REVERT: D 395 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8650 (mp) REVERT: D 408 LYS cc_start: 0.8401 (tptp) cc_final: 0.8201 (tppp) REVERT: E 28 GLU cc_start: 0.7274 (pp20) cc_final: 0.6522 (tt0) REVERT: E 232 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.8864 (mtp) REVERT: E 234 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8507 (mm-30) REVERT: E 250 ASP cc_start: 0.8504 (m-30) cc_final: 0.8123 (m-30) REVERT: E 254 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: E 258 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8999 (mtt) REVERT: G 150 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: H 123 GLN cc_start: 0.8537 (mm110) cc_final: 0.8297 (mm110) REVERT: I 26 GLU cc_start: 0.8439 (mp0) cc_final: 0.8022 (mp0) REVERT: J 23 GLN cc_start: 0.8542 (tt0) cc_final: 0.8265 (pt0) REVERT: J 106 TYR cc_start: 0.9062 (t80) cc_final: 0.8641 (t80) REVERT: K 9 ASP cc_start: 0.6721 (m-30) cc_final: 0.6295 (m-30) REVERT: K 10 ARG cc_start: 0.8635 (tpp-160) cc_final: 0.8228 (mmt-90) REVERT: K 118 ASN cc_start: 0.8943 (m-40) cc_final: 0.8360 (m-40) REVERT: L 26 MET cc_start: 0.8879 (mtm) cc_final: 0.8654 (mmm) REVERT: L 41 LYS cc_start: 0.8431 (mptp) cc_final: 0.8208 (mppt) REVERT: L 137 TYR cc_start: 0.8297 (t80) cc_final: 0.8079 (t80) REVERT: L 226 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: M 3 ILE cc_start: 0.5514 (OUTLIER) cc_final: 0.5061 (mp) REVERT: M 43 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7707 (p0) REVERT: M 117 MET cc_start: 0.8736 (tpp) cc_final: 0.8379 (mmp) REVERT: M 177 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: M 221 ASN cc_start: 0.9372 (t0) cc_final: 0.9062 (t0) REVERT: A 163 MET cc_start: 0.7211 (ppp) cc_final: 0.6773 (ppp) REVERT: A 164 MET cc_start: 0.7868 (tmm) cc_final: 0.6765 (tmm) REVERT: A 236 CYS cc_start: 0.8735 (p) cc_final: 0.7456 (t) REVERT: A 249 TYR cc_start: 0.6127 (t80) cc_final: 0.5710 (t80) REVERT: A 256 MET cc_start: 0.8476 (mtp) cc_final: 0.8249 (mtp) REVERT: A 319 MET cc_start: 0.8252 (mmt) cc_final: 0.8017 (tpt) REVERT: A 394 MET cc_start: 0.9308 (mmm) cc_final: 0.8999 (mmm) REVERT: B 66 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6857 (tm-30) REVERT: B 74 MET cc_start: 0.7071 (mtp) cc_final: 0.6652 (mtt) REVERT: B 85 MET cc_start: 0.7471 (mmm) cc_final: 0.6245 (ptt) REVERT: B 145 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8185 (tm-30) REVERT: B 275 GLU cc_start: 0.8859 (tp30) cc_final: 0.8525 (mm-30) REVERT: B 306 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8149 (tp-100) REVERT: B 373 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8433 (p) REVERT: B 412 MET cc_start: 0.9014 (tpt) cc_final: 0.8738 (tpt) REVERT: F 74 LYS cc_start: 0.8320 (mmmt) cc_final: 0.7706 (ttmm) REVERT: F 145 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8256 (mm) REVERT: F 186 SER cc_start: 0.8488 (t) cc_final: 0.8118 (p) REVERT: F 259 MET cc_start: 0.8252 (mtp) cc_final: 0.7660 (ttm) REVERT: F 310 MET cc_start: 0.7295 (mmt) cc_final: 0.7009 (mtt) REVERT: F 356 MET cc_start: 0.9251 (mtp) cc_final: 0.8807 (mtp) REVERT: F 373 MET cc_start: 0.8391 (mtp) cc_final: 0.7899 (pmm) REVERT: c 98 MET cc_start: 0.8088 (ttt) cc_final: 0.7774 (ttt) REVERT: c 168 MET cc_start: 0.7545 (tpp) cc_final: 0.7008 (tpt) REVERT: c 198 ARG cc_start: 0.9056 (ttp80) cc_final: 0.8609 (ttp80) REVERT: c 233 ASP cc_start: 0.8592 (t0) cc_final: 0.8322 (t0) outliers start: 124 outliers final: 84 residues processed: 490 average time/residue: 0.6164 time to fit residues: 367.8459 Evaluate side-chains 456 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 360 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 230 ILE Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 254 GLN Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 171 LYS Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 39 LEU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 36 ASN C 41 ASN ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 HIS H 166 ASN I 30 HIS ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN ** J 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN M 68 ASN M 170 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS B 181 GLN B 425 ASN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.089235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066142 restraints weight = 86929.700| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.16 r_work: 0.2966 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34093 Z= 0.184 Angle : 0.715 22.197 46055 Z= 0.353 Chirality : 0.045 0.170 5245 Planarity : 0.004 0.068 5947 Dihedral : 9.022 134.683 4901 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.19 % Favored : 93.59 % Rotamer: Outliers : 5.83 % Allowed : 29.39 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.02 % 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: 0.01 (0.13), residues: 4199 helix: 1.17 (0.12), residues: 1856 sheet: -0.93 (0.18), residues: 721 loop : -0.80 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 40 TYR 0.027 0.002 TYR L 137 PHE 0.021 0.002 PHE B 319 TRP 0.009 0.001 TRP L 13 HIS 0.008 0.001 HIS L 143 Details of bonding type rmsd covalent geometry : bond 0.00423 (34090) covalent geometry : angle 0.71543 (46055) hydrogen bonds : bond 0.04189 ( 1661) hydrogen bonds : angle 5.19887 ( 4782) metal coordination : bond 0.00342 ( 2) Misc. bond : bond 0.00311 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 394 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.8796 (t0) cc_final: 0.8587 (t0) REVERT: C 399 MET cc_start: 0.8736 (tpp) cc_final: 0.8462 (tpp) REVERT: D 77 GLU cc_start: 0.8810 (tp30) cc_final: 0.8535 (tt0) REVERT: D 98 GLN cc_start: 0.8603 (tp-100) cc_final: 0.8066 (tp-100) REVERT: D 170 MET cc_start: 0.9173 (ptp) cc_final: 0.8810 (ptp) REVERT: D 249 ASP cc_start: 0.8968 (m-30) cc_final: 0.8755 (m-30) REVERT: D 374 ASP cc_start: 0.8837 (m-30) cc_final: 0.8515 (m-30) REVERT: D 395 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8462 (mp) REVERT: D 408 LYS cc_start: 0.8394 (tptp) cc_final: 0.8133 (tppp) REVERT: E 47 LEU cc_start: 0.8295 (mm) cc_final: 0.7661 (mm) REVERT: E 161 ARG cc_start: 0.8168 (tpm170) cc_final: 0.7707 (tpm170) REVERT: E 232 MET cc_start: 0.9339 (mtp) cc_final: 0.8986 (mtm) REVERT: E 234 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8374 (tp30) REVERT: E 250 ASP cc_start: 0.8387 (m-30) cc_final: 0.8011 (m-30) REVERT: E 316 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.8600 (m170) REVERT: G 80 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7513 (mtp) REVERT: G 131 MET cc_start: 0.8713 (tpp) cc_final: 0.8509 (tpp) REVERT: G 150 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7576 (mp-120) REVERT: H 102 GLN cc_start: 0.9051 (mm110) cc_final: 0.8036 (pt0) REVERT: H 123 GLN cc_start: 0.8648 (mm110) cc_final: 0.8300 (mm110) REVERT: H 171 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8564 (tppp) REVERT: I 72 MET cc_start: 0.8345 (tpt) cc_final: 0.8119 (mmt) REVERT: I 137 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8691 (pt) REVERT: I 167 ASN cc_start: 0.8992 (m-40) cc_final: 0.8775 (m110) REVERT: J 239 ASN cc_start: 0.7871 (t0) cc_final: 0.6867 (p0) REVERT: K 9 ASP cc_start: 0.6688 (m-30) cc_final: 0.6279 (m-30) REVERT: L 26 MET cc_start: 0.8916 (mtm) cc_final: 0.8382 (mmm) REVERT: L 159 MET cc_start: 0.9020 (tpt) cc_final: 0.8538 (tpt) REVERT: L 180 MET cc_start: 0.8721 (tpp) cc_final: 0.8396 (tpp) REVERT: L 226 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: M 3 ILE cc_start: 0.5431 (OUTLIER) cc_final: 0.5155 (mp) REVERT: M 27 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7887 (mpm) REVERT: M 117 MET cc_start: 0.8725 (tpp) cc_final: 0.8425 (mmp) REVERT: M 221 ASN cc_start: 0.9416 (t0) cc_final: 0.9030 (t0) REVERT: A 57 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8557 (tmmt) REVERT: A 146 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8610 (pmtt) REVERT: A 163 MET cc_start: 0.7159 (ppp) cc_final: 0.6700 (ppp) REVERT: A 164 MET cc_start: 0.8019 (tmm) cc_final: 0.7566 (tmm) REVERT: A 166 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 236 CYS cc_start: 0.8956 (p) cc_final: 0.7961 (t) REVERT: A 394 MET cc_start: 0.9254 (mmm) cc_final: 0.8957 (mmm) REVERT: B 66 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6870 (tm-30) REVERT: B 74 MET cc_start: 0.6665 (mtp) cc_final: 0.6340 (mtt) REVERT: B 85 MET cc_start: 0.7788 (mmm) cc_final: 0.6803 (ptt) REVERT: B 211 TYR cc_start: 0.8496 (m-80) cc_final: 0.8251 (m-80) REVERT: B 246 THR cc_start: 0.9165 (m) cc_final: 0.8883 (p) REVERT: B 306 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8202 (tp-100) REVERT: B 412 MET cc_start: 0.9052 (tpt) cc_final: 0.8815 (tpt) REVERT: F 69 MET cc_start: 0.3521 (OUTLIER) cc_final: 0.3222 (tmt) REVERT: F 145 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8396 (mm) REVERT: F 259 MET cc_start: 0.8219 (mtp) cc_final: 0.7573 (ttm) REVERT: F 356 MET cc_start: 0.9260 (mtp) cc_final: 0.8853 (mtm) REVERT: c 85 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: c 98 MET cc_start: 0.7870 (ttt) cc_final: 0.7614 (ttt) REVERT: c 168 MET cc_start: 0.7523 (tpp) cc_final: 0.7030 (tpt) REVERT: c 198 ARG cc_start: 0.9075 (ttp80) cc_final: 0.8658 (ttp80) REVERT: c 233 ASP cc_start: 0.8571 (t0) cc_final: 0.8304 (t0) outliers start: 211 outliers final: 86 residues processed: 557 average time/residue: 0.6019 time to fit residues: 409.3654 Evaluate side-chains 442 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 341 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 171 LYS Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 137 ILE Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 202 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 318 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 329 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 HIS I 30 HIS ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN ** J 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 HIS M 32 ASN M 170 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 425 ASN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.090547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067927 restraints weight = 86658.504| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.14 r_work: 0.3000 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34093 Z= 0.131 Angle : 0.665 16.990 46055 Z= 0.329 Chirality : 0.043 0.210 5245 Planarity : 0.004 0.056 5947 Dihedral : 8.319 131.815 4809 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.83 % Favored : 93.95 % Rotamer: Outliers : 5.33 % Allowed : 29.28 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.02 % 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: 0.17 (0.13), residues: 4199 helix: 1.31 (0.12), residues: 1855 sheet: -0.98 (0.18), residues: 723 loop : -0.67 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 208 TYR 0.024 0.001 TYR L 137 PHE 0.018 0.001 PHE F 260 TRP 0.014 0.001 TRP I 159 HIS 0.007 0.001 HIS F 417 Details of bonding type rmsd covalent geometry : bond 0.00292 (34090) covalent geometry : angle 0.66469 (46055) hydrogen bonds : bond 0.03825 ( 1661) hydrogen bonds : angle 4.92682 ( 4782) metal coordination : bond 0.00178 ( 2) Misc. bond : bond 0.00148 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 414 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLN cc_start: 0.9291 (tm-30) cc_final: 0.9016 (tm-30) REVERT: C 90 HIS cc_start: 0.8510 (t-90) cc_final: 0.8310 (t70) REVERT: C 102 ASN cc_start: 0.8804 (t0) cc_final: 0.8526 (t0) REVERT: C 118 ASN cc_start: 0.8147 (t0) cc_final: 0.7940 (m-40) REVERT: C 130 LYS cc_start: 0.9279 (tppt) cc_final: 0.9048 (tppt) REVERT: C 248 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.8982 (mmt) REVERT: D 77 GLU cc_start: 0.8826 (tp30) cc_final: 0.8514 (tt0) REVERT: D 98 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8029 (tp-100) REVERT: D 170 MET cc_start: 0.9132 (ptp) cc_final: 0.8788 (ptp) REVERT: D 249 ASP cc_start: 0.9010 (m-30) cc_final: 0.8722 (m-30) REVERT: D 374 ASP cc_start: 0.8783 (m-30) cc_final: 0.8454 (m-30) REVERT: D 395 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8458 (mp) REVERT: D 408 LYS cc_start: 0.8347 (tptp) cc_final: 0.8108 (tppp) REVERT: E 53 VAL cc_start: 0.8534 (p) cc_final: 0.8164 (t) REVERT: E 232 MET cc_start: 0.9223 (mtp) cc_final: 0.8889 (mtm) REVERT: E 234 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8360 (tp30) REVERT: E 250 ASP cc_start: 0.8376 (m-30) cc_final: 0.7995 (m-30) REVERT: E 316 HIS cc_start: 0.8883 (OUTLIER) cc_final: 0.8527 (m170) REVERT: E 352 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7836 (ttp) REVERT: G 42 VAL cc_start: 0.9122 (t) cc_final: 0.8676 (m) REVERT: G 80 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7384 (mtp) REVERT: G 147 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8447 (tm-30) REVERT: G 150 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7333 (mp-120) REVERT: H 49 GLU cc_start: 0.8639 (pt0) cc_final: 0.8395 (pt0) REVERT: H 102 GLN cc_start: 0.9031 (mm110) cc_final: 0.7948 (pt0) REVERT: H 123 GLN cc_start: 0.8640 (mm110) cc_final: 0.8194 (mm110) REVERT: H 183 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8493 (tp30) REVERT: H 219 ARG cc_start: 0.8401 (tmm-80) cc_final: 0.7896 (tmm-80) REVERT: I 167 ASN cc_start: 0.8957 (m-40) cc_final: 0.8736 (m110) REVERT: J 106 TYR cc_start: 0.8984 (t80) cc_final: 0.8763 (t80) REVERT: J 227 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8918 (ttpp) REVERT: J 239 ASN cc_start: 0.7873 (t0) cc_final: 0.7034 (p0) REVERT: K 9 ASP cc_start: 0.6705 (m-30) cc_final: 0.6324 (m-30) REVERT: K 10 ARG cc_start: 0.8588 (tpp-160) cc_final: 0.8164 (mmt-90) REVERT: K 41 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8518 (tp40) REVERT: K 86 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8935 (mtmm) REVERT: L 26 MET cc_start: 0.8774 (mtm) cc_final: 0.8559 (mtm) REVERT: L 41 LYS cc_start: 0.8892 (mptt) cc_final: 0.8602 (mppt) REVERT: L 159 MET cc_start: 0.8889 (tpt) cc_final: 0.8416 (tpt) REVERT: L 180 MET cc_start: 0.8696 (tpp) cc_final: 0.8097 (mmm) REVERT: L 226 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: M 117 MET cc_start: 0.8670 (tpp) cc_final: 0.8396 (mmp) REVERT: M 221 ASN cc_start: 0.9382 (t0) cc_final: 0.8961 (t0) REVERT: A 57 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8571 (tmmt) REVERT: A 146 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8579 (pmtt) REVERT: A 163 MET cc_start: 0.7342 (ppp) cc_final: 0.6905 (ppp) REVERT: A 236 CYS cc_start: 0.8637 (p) cc_final: 0.8062 (t) REVERT: A 394 MET cc_start: 0.9259 (mmm) cc_final: 0.8922 (mmm) REVERT: B 66 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6873 (tm-30) REVERT: B 74 MET cc_start: 0.6594 (mtp) cc_final: 0.6287 (mtt) REVERT: B 85 MET cc_start: 0.7704 (mmm) cc_final: 0.6932 (ptt) REVERT: B 211 TYR cc_start: 0.8495 (m-80) cc_final: 0.8142 (m-80) REVERT: B 246 THR cc_start: 0.9178 (m) cc_final: 0.8955 (p) REVERT: B 294 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7852 (tpt-90) REVERT: B 306 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8203 (tp-100) REVERT: F 144 LYS cc_start: 0.9462 (mmmt) cc_final: 0.9243 (mppt) REVERT: F 145 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8416 (mm) REVERT: F 259 MET cc_start: 0.7964 (mtp) cc_final: 0.7455 (ttm) REVERT: F 310 MET cc_start: 0.7144 (mmt) cc_final: 0.6818 (mtt) REVERT: F 356 MET cc_start: 0.9264 (mtp) cc_final: 0.8848 (mtm) REVERT: F 421 MET cc_start: 0.9026 (mmt) cc_final: 0.8800 (mmm) REVERT: c 85 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: c 98 MET cc_start: 0.7443 (ttt) cc_final: 0.7224 (ttt) REVERT: c 168 MET cc_start: 0.7503 (tpp) cc_final: 0.7009 (tpt) REVERT: c 198 ARG cc_start: 0.9077 (ttp80) cc_final: 0.8667 (ttp80) REVERT: c 233 ASP cc_start: 0.8529 (t0) cc_final: 0.8251 (t0) outliers start: 193 outliers final: 73 residues processed: 567 average time/residue: 0.6179 time to fit residues: 426.0139 Evaluate side-chains 444 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 354 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 352 MET Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 160 PHE Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain c residue 234 TYR Chi-restraints excluded: chain c residue 300 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 198 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 278 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 HIS I 30 HIS I 123 GLN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN ** J 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 ASN M 170 GLN A 148 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 131 HIS B 181 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 287 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.087208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064054 restraints weight = 86956.866| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.14 r_work: 0.2927 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 34093 Z= 0.238 Angle : 0.704 15.357 46055 Z= 0.350 Chirality : 0.045 0.193 5245 Planarity : 0.004 0.057 5947 Dihedral : 8.126 133.859 4791 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.00 % Favored : 93.78 % Rotamer: Outliers : 6.88 % Allowed : 28.09 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.02 % 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: 0.17 (0.13), residues: 4199 helix: 1.31 (0.12), residues: 1860 sheet: -0.95 (0.18), residues: 709 loop : -0.70 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 21 TYR 0.022 0.002 TYR F 132 PHE 0.024 0.002 PHE B 319 TRP 0.010 0.002 TRP L 13 HIS 0.009 0.001 HIS E 124 Details of bonding type rmsd covalent geometry : bond 0.00552 (34090) covalent geometry : angle 0.70369 (46055) hydrogen bonds : bond 0.03865 ( 1661) hydrogen bonds : angle 4.87874 ( 4782) metal coordination : bond 0.00522 ( 2) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 356 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.8942 (t0) cc_final: 0.8702 (t0) REVERT: D 98 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8075 (tp-100) REVERT: D 170 MET cc_start: 0.9173 (ptp) cc_final: 0.8812 (ptp) REVERT: D 374 ASP cc_start: 0.8859 (m-30) cc_final: 0.8531 (m-30) REVERT: D 395 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8441 (mp) REVERT: D 408 LYS cc_start: 0.8366 (tptp) cc_final: 0.8162 (tppp) REVERT: E 28 GLU cc_start: 0.7138 (pp20) cc_final: 0.6387 (mp0) REVERT: E 33 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7657 (mt) REVERT: E 47 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7369 (mm) REVERT: E 51 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8323 (mp10) REVERT: E 53 VAL cc_start: 0.8735 (p) cc_final: 0.8462 (t) REVERT: E 124 HIS cc_start: 0.8795 (m-70) cc_final: 0.8430 (m90) REVERT: E 196 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9277 (mp) REVERT: E 221 TYR cc_start: 0.9452 (t80) cc_final: 0.9242 (t80) REVERT: E 232 MET cc_start: 0.9325 (mtp) cc_final: 0.8957 (mtm) REVERT: E 234 GLU cc_start: 0.8967 (tp30) cc_final: 0.8486 (tp30) REVERT: E 250 ASP cc_start: 0.8436 (m-30) cc_final: 0.8050 (m-30) REVERT: E 316 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.8495 (m170) REVERT: E 339 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7874 (p0) REVERT: E 345 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8464 (m-40) REVERT: E 352 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7878 (ttp) REVERT: G 80 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7670 (mtp) REVERT: G 147 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8539 (tm-30) REVERT: G 150 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7252 (mp-120) REVERT: H 123 GLN cc_start: 0.8750 (mm110) cc_final: 0.8400 (mm110) REVERT: H 219 ARG cc_start: 0.8388 (tmm-80) cc_final: 0.7862 (tmm-80) REVERT: I 220 ASN cc_start: 0.9238 (t0) cc_final: 0.9035 (t0) REVERT: J 227 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8874 (ttpp) REVERT: K 41 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: L 137 TYR cc_start: 0.8309 (t80) cc_final: 0.7901 (t80) REVERT: L 159 MET cc_start: 0.9057 (tpt) cc_final: 0.8585 (tpt) REVERT: L 166 GLN cc_start: 0.8212 (tp-100) cc_final: 0.8001 (tp-100) REVERT: L 226 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: M 3 ILE cc_start: 0.5556 (OUTLIER) cc_final: 0.5326 (mp) REVERT: M 27 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7706 (mpm) REVERT: M 117 MET cc_start: 0.8735 (tpp) cc_final: 0.8443 (mmp) REVERT: M 177 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: M 221 ASN cc_start: 0.9392 (t0) cc_final: 0.8989 (t0) REVERT: A 57 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8598 (tmmt) REVERT: A 146 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8571 (pmtt) REVERT: A 249 TYR cc_start: 0.6046 (t80) cc_final: 0.5787 (t80) REVERT: A 256 MET cc_start: 0.8824 (ttt) cc_final: 0.8012 (ttt) REVERT: A 394 MET cc_start: 0.9291 (mmm) cc_final: 0.8964 (mmm) REVERT: A 418 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.6788 (mmmt) REVERT: B 66 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6830 (tm-30) REVERT: B 74 MET cc_start: 0.6758 (mtp) cc_final: 0.6416 (mtt) REVERT: B 85 MET cc_start: 0.7772 (mmm) cc_final: 0.7008 (ptt) REVERT: B 195 GLN cc_start: 0.8603 (tt0) cc_final: 0.8398 (tt0) REVERT: B 211 TYR cc_start: 0.8693 (m-80) cc_final: 0.8374 (m-80) REVERT: B 246 THR cc_start: 0.9189 (m) cc_final: 0.8892 (p) REVERT: B 294 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8254 (tpt-90) REVERT: F 145 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8560 (mm) REVERT: F 186 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8251 (p) REVERT: F 259 MET cc_start: 0.8150 (mtp) cc_final: 0.7593 (ttm) REVERT: F 356 MET cc_start: 0.9342 (mtp) cc_final: 0.8904 (mtm) REVERT: c 85 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: c 98 MET cc_start: 0.7391 (ttt) cc_final: 0.7158 (ttt) REVERT: c 168 MET cc_start: 0.7581 (tpp) cc_final: 0.7064 (tpt) REVERT: c 233 ASP cc_start: 0.8610 (t0) cc_final: 0.8354 (t0) REVERT: c 263 ASP cc_start: 0.8422 (t0) cc_final: 0.8165 (p0) outliers start: 249 outliers final: 116 residues processed: 558 average time/residue: 0.5502 time to fit residues: 377.3953 Evaluate side-chains 464 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 325 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 352 MET Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 177 GLU Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain c residue 234 TYR Chi-restraints excluded: chain c residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 386 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 390 optimal weight: 30.0000 chunk 252 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 318 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 308 optimal weight: 20.0000 chunk 233 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 124 HIS ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN K 23 GLN M 32 ASN M 170 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS B 181 GLN B 425 ASN F 436 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065189 restraints weight = 86622.597| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.16 r_work: 0.2952 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34093 Z= 0.161 Angle : 0.678 15.538 46055 Z= 0.332 Chirality : 0.044 0.215 5245 Planarity : 0.004 0.060 5947 Dihedral : 7.976 132.286 4788 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.95 % Favored : 93.83 % Rotamer: Outliers : 5.22 % Allowed : 30.00 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.02 % 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: 0.28 (0.13), residues: 4199 helix: 1.39 (0.12), residues: 1859 sheet: -0.92 (0.18), residues: 735 loop : -0.59 (0.17), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG c 208 TYR 0.021 0.001 TYR F 437 PHE 0.021 0.001 PHE F 260 TRP 0.011 0.001 TRP I 159 HIS 0.009 0.001 HIS E 124 Details of bonding type rmsd covalent geometry : bond 0.00368 (34090) covalent geometry : angle 0.67836 (46055) hydrogen bonds : bond 0.03672 ( 1661) hydrogen bonds : angle 4.78201 ( 4782) metal coordination : bond 0.00336 ( 2) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 368 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8650 (tttp) REVERT: C 102 ASN cc_start: 0.8940 (t0) cc_final: 0.8695 (t0) REVERT: C 141 GLU cc_start: 0.8597 (pm20) cc_final: 0.8391 (pm20) REVERT: D 77 GLU cc_start: 0.8778 (tp30) cc_final: 0.8478 (tt0) REVERT: D 98 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8101 (tp-100) REVERT: D 170 MET cc_start: 0.9134 (ptp) cc_final: 0.8787 (ptp) REVERT: D 249 ASP cc_start: 0.9048 (m-30) cc_final: 0.8659 (m-30) REVERT: D 374 ASP cc_start: 0.8844 (m-30) cc_final: 0.8487 (m-30) REVERT: D 395 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8427 (mp) REVERT: D 408 LYS cc_start: 0.8337 (tptp) cc_final: 0.8122 (tppp) REVERT: E 53 VAL cc_start: 0.8676 (p) cc_final: 0.8405 (t) REVERT: E 124 HIS cc_start: 0.8685 (m90) cc_final: 0.8324 (m90) REVERT: E 161 ARG cc_start: 0.8259 (tpm170) cc_final: 0.7402 (tpm170) REVERT: E 232 MET cc_start: 0.9250 (mtp) cc_final: 0.8893 (mtm) REVERT: E 234 GLU cc_start: 0.8968 (tp30) cc_final: 0.8472 (tp30) REVERT: E 250 ASP cc_start: 0.8424 (m-30) cc_final: 0.8023 (m-30) REVERT: E 316 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8441 (m170) REVERT: E 339 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7825 (p0) REVERT: G 80 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7556 (mtp) REVERT: G 147 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8620 (tm-30) REVERT: G 150 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7247 (mp-120) REVERT: H 49 GLU cc_start: 0.8646 (pt0) cc_final: 0.8440 (pt0) REVERT: H 123 GLN cc_start: 0.8763 (mm110) cc_final: 0.8363 (mm110) REVERT: I 167 ASN cc_start: 0.8976 (m-40) cc_final: 0.8754 (m110) REVERT: I 220 ASN cc_start: 0.9242 (t0) cc_final: 0.8985 (t0) REVERT: J 227 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8918 (ttpp) REVERT: K 41 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: L 41 LYS cc_start: 0.9039 (mptt) cc_final: 0.8684 (mptt) REVERT: L 137 TYR cc_start: 0.8493 (t80) cc_final: 0.8050 (t80) REVERT: L 159 MET cc_start: 0.9036 (tpt) cc_final: 0.8559 (tpt) REVERT: L 166 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7912 (tp-100) REVERT: L 180 MET cc_start: 0.8649 (tpp) cc_final: 0.8000 (mmm) REVERT: L 226 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: M 3 ILE cc_start: 0.5575 (OUTLIER) cc_final: 0.5339 (mp) REVERT: M 117 MET cc_start: 0.8684 (tpp) cc_final: 0.8393 (mmp) REVERT: M 221 ASN cc_start: 0.9345 (t0) cc_final: 0.8964 (t0) REVERT: A 57 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8566 (tmmt) REVERT: A 146 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8510 (pmtt) REVERT: A 163 MET cc_start: 0.7667 (ppp) cc_final: 0.7050 (ppp) REVERT: A 394 MET cc_start: 0.9290 (mmm) cc_final: 0.8920 (mmm) REVERT: A 418 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.6785 (mmmt) REVERT: B 41 LYS cc_start: 0.8433 (pptt) cc_final: 0.8039 (pptt) REVERT: B 66 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6944 (tm-30) REVERT: B 74 MET cc_start: 0.6900 (mtp) cc_final: 0.6591 (mtt) REVERT: B 85 MET cc_start: 0.7702 (mmm) cc_final: 0.7001 (ptt) REVERT: B 195 GLN cc_start: 0.8574 (tt0) cc_final: 0.8350 (tt0) REVERT: B 211 TYR cc_start: 0.8681 (m-80) cc_final: 0.8270 (m-80) REVERT: B 246 THR cc_start: 0.9196 (m) cc_final: 0.8889 (p) REVERT: B 294 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7936 (tpt-90) REVERT: B 405 MET cc_start: 0.9229 (mmm) cc_final: 0.8966 (mmm) REVERT: F 145 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8529 (mm) REVERT: F 186 SER cc_start: 0.8531 (t) cc_final: 0.8255 (p) REVERT: F 259 MET cc_start: 0.7968 (mtp) cc_final: 0.7458 (ttm) REVERT: F 310 MET cc_start: 0.7128 (mmt) cc_final: 0.6922 (mtt) REVERT: F 356 MET cc_start: 0.9315 (mtp) cc_final: 0.8925 (mtm) REVERT: c 85 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: c 168 MET cc_start: 0.7529 (tpp) cc_final: 0.7027 (tpt) REVERT: c 208 ARG cc_start: 0.8374 (mtp-110) cc_final: 0.8149 (mmm160) REVERT: c 233 ASP cc_start: 0.8620 (t0) cc_final: 0.8349 (t0) REVERT: c 263 ASP cc_start: 0.8492 (t0) cc_final: 0.8127 (p0) outliers start: 189 outliers final: 96 residues processed: 524 average time/residue: 0.5676 time to fit residues: 363.3201 Evaluate side-chains 443 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 331 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 68 HIS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain c residue 234 TYR Chi-restraints excluded: chain c residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 147 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 410 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 364 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS I 198 ASN I 240 HIS ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN M 32 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS B 181 GLN B 277 HIS ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.066163 restraints weight = 86432.167| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.10 r_work: 0.2961 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34093 Z= 0.149 Angle : 0.678 15.813 46055 Z= 0.330 Chirality : 0.043 0.246 5245 Planarity : 0.004 0.062 5947 Dihedral : 7.835 131.225 4783 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 5.25 % Allowed : 29.64 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 0.33 (0.13), residues: 4199 helix: 1.42 (0.12), residues: 1864 sheet: -0.95 (0.18), residues: 739 loop : -0.53 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG c 208 TYR 0.022 0.001 TYR F 88 PHE 0.025 0.001 PHE B 78 TRP 0.011 0.001 TRP I 159 HIS 0.007 0.001 HIS c 172 Details of bonding type rmsd covalent geometry : bond 0.00346 (34090) covalent geometry : angle 0.67774 (46055) hydrogen bonds : bond 0.03575 ( 1661) hydrogen bonds : angle 4.69611 ( 4782) metal coordination : bond 0.00256 ( 2) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 381 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLN cc_start: 0.9304 (tm-30) cc_final: 0.9082 (tm-30) REVERT: C 88 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8680 (tttp) REVERT: C 102 ASN cc_start: 0.8942 (t0) cc_final: 0.8692 (t0) REVERT: C 141 GLU cc_start: 0.8575 (pm20) cc_final: 0.8367 (pm20) REVERT: C 176 GLU cc_start: 0.9205 (tp30) cc_final: 0.8994 (tp30) REVERT: D 77 GLU cc_start: 0.8759 (tp30) cc_final: 0.8456 (tt0) REVERT: D 98 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8097 (tp-100) REVERT: D 170 MET cc_start: 0.9133 (ptp) cc_final: 0.8799 (ptp) REVERT: D 249 ASP cc_start: 0.9023 (m-30) cc_final: 0.8629 (m-30) REVERT: D 374 ASP cc_start: 0.8857 (m-30) cc_final: 0.8495 (m-30) REVERT: D 395 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8457 (mp) REVERT: D 408 LYS cc_start: 0.8328 (tptp) cc_final: 0.8118 (tppp) REVERT: E 28 GLU cc_start: 0.7184 (pp20) cc_final: 0.6063 (mp0) REVERT: E 53 VAL cc_start: 0.8737 (p) cc_final: 0.8493 (t) REVERT: E 124 HIS cc_start: 0.8765 (m90) cc_final: 0.8538 (m-70) REVERT: E 161 ARG cc_start: 0.8300 (tpm170) cc_final: 0.7352 (tpm170) REVERT: E 232 MET cc_start: 0.9249 (mtp) cc_final: 0.8861 (mtm) REVERT: E 234 GLU cc_start: 0.8960 (tp30) cc_final: 0.8471 (tp30) REVERT: E 277 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8832 (mtt) REVERT: E 316 HIS cc_start: 0.8911 (OUTLIER) cc_final: 0.8533 (OUTLIER) REVERT: E 345 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8422 (m-40) REVERT: G 147 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8582 (tm-30) REVERT: G 150 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7291 (mp-120) REVERT: H 49 GLU cc_start: 0.8651 (pt0) cc_final: 0.8438 (pt0) REVERT: H 123 GLN cc_start: 0.8782 (mm110) cc_final: 0.8390 (mm110) REVERT: H 163 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8669 (pmt) REVERT: I 167 ASN cc_start: 0.8970 (m-40) cc_final: 0.8753 (m110) REVERT: I 220 ASN cc_start: 0.9231 (t0) cc_final: 0.8948 (t0) REVERT: J 227 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8895 (ttpp) REVERT: K 10 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8269 (mmt-90) REVERT: K 41 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: L 143 HIS cc_start: 0.7991 (m90) cc_final: 0.7644 (m90) REVERT: L 159 MET cc_start: 0.9058 (tpt) cc_final: 0.8609 (tpt) REVERT: L 166 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7946 (tp-100) REVERT: L 226 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: M 3 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5406 (mt) REVERT: M 117 MET cc_start: 0.8684 (tpp) cc_final: 0.8393 (mmp) REVERT: M 221 ASN cc_start: 0.9325 (t0) cc_final: 0.8929 (t0) REVERT: A 57 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8567 (tmmt) REVERT: A 146 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8490 (pmtt) REVERT: A 394 MET cc_start: 0.9298 (mmm) cc_final: 0.8918 (mmm) REVERT: A 418 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.6863 (mmmt) REVERT: B 66 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 74 MET cc_start: 0.6836 (mtp) cc_final: 0.6540 (mtt) REVERT: B 195 GLN cc_start: 0.8587 (tt0) cc_final: 0.8349 (tt0) REVERT: B 211 TYR cc_start: 0.8687 (m-80) cc_final: 0.8304 (m-80) REVERT: B 246 THR cc_start: 0.9182 (m) cc_final: 0.8950 (p) REVERT: B 294 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7927 (tpt-90) REVERT: B 425 ASN cc_start: 0.8798 (t0) cc_final: 0.8569 (t160) REVERT: F 145 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8526 (mm) REVERT: F 158 TYR cc_start: 0.7170 (m-10) cc_final: 0.6797 (m-10) REVERT: F 186 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8262 (p) REVERT: F 259 MET cc_start: 0.7991 (mtp) cc_final: 0.7605 (ttm) REVERT: F 310 MET cc_start: 0.7247 (mmt) cc_final: 0.6955 (mtt) REVERT: F 356 MET cc_start: 0.9287 (mtp) cc_final: 0.8895 (mtm) REVERT: c 85 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: c 168 MET cc_start: 0.7539 (tpp) cc_final: 0.7128 (tpt) REVERT: c 198 ARG cc_start: 0.8993 (ttp80) cc_final: 0.8611 (ttp80) REVERT: c 208 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.7902 (mmm-85) REVERT: c 233 ASP cc_start: 0.8632 (t0) cc_final: 0.8359 (t0) REVERT: c 262 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8930 (tp30) outliers start: 190 outliers final: 115 residues processed: 537 average time/residue: 0.5791 time to fit residues: 379.6483 Evaluate side-chains 466 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 334 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 68 HIS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain c residue 234 TYR Chi-restraints excluded: chain c residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 359 optimal weight: 6.9990 chunk 16 optimal weight: 0.0770 chunk 348 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 340 optimal weight: 4.9990 chunk 157 optimal weight: 0.0070 chunk 233 optimal weight: 10.0000 chunk 326 optimal weight: 8.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN I 30 HIS J 120 GLN M 32 ASN A 103 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS B 154 HIS B 181 GLN B 277 HIS ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.089645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067081 restraints weight = 86603.737| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.11 r_work: 0.2984 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34093 Z= 0.131 Angle : 0.684 16.083 46055 Z= 0.332 Chirality : 0.043 0.267 5245 Planarity : 0.004 0.062 5947 Dihedral : 7.763 130.602 4781 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.91 % Favored : 93.93 % Rotamer: Outliers : 4.67 % Allowed : 31.08 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 0.38 (0.13), residues: 4199 helix: 1.46 (0.12), residues: 1861 sheet: -0.92 (0.18), residues: 737 loop : -0.51 (0.17), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 239 TYR 0.020 0.001 TYR F 437 PHE 0.026 0.001 PHE B 319 TRP 0.013 0.001 TRP I 159 HIS 0.006 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00299 (34090) covalent geometry : angle 0.68430 (46055) hydrogen bonds : bond 0.03495 ( 1661) hydrogen bonds : angle 4.63303 ( 4782) metal coordination : bond 0.00171 ( 2) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 364 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLN cc_start: 0.9293 (tm-30) cc_final: 0.9070 (tm-30) REVERT: C 88 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8656 (tttp) REVERT: C 102 ASN cc_start: 0.8939 (t0) cc_final: 0.8700 (t0) REVERT: C 176 GLU cc_start: 0.9231 (tp30) cc_final: 0.9024 (tp30) REVERT: C 248 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8998 (mmt) REVERT: C 284 GLU cc_start: 0.8881 (tp30) cc_final: 0.8664 (mm-30) REVERT: D 77 GLU cc_start: 0.8771 (tp30) cc_final: 0.8434 (tt0) REVERT: D 98 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8090 (tp-100) REVERT: D 170 MET cc_start: 0.9114 (ptp) cc_final: 0.8728 (ptp) REVERT: D 229 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8578 (ttp80) REVERT: D 249 ASP cc_start: 0.9015 (m-30) cc_final: 0.8613 (m-30) REVERT: D 374 ASP cc_start: 0.8827 (m-30) cc_final: 0.8464 (m-30) REVERT: D 395 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8448 (mp) REVERT: D 408 LYS cc_start: 0.8305 (tptp) cc_final: 0.8096 (tppp) REVERT: E 28 GLU cc_start: 0.7289 (pp20) cc_final: 0.6246 (mp0) REVERT: E 53 VAL cc_start: 0.8742 (p) cc_final: 0.8511 (t) REVERT: E 124 HIS cc_start: 0.8797 (m90) cc_final: 0.8527 (m-70) REVERT: E 161 ARG cc_start: 0.8230 (tpm170) cc_final: 0.7314 (tpm170) REVERT: E 234 GLU cc_start: 0.8930 (tp30) cc_final: 0.8397 (tp30) REVERT: E 316 HIS cc_start: 0.8869 (OUTLIER) cc_final: 0.8418 (m170) REVERT: G 80 MET cc_start: 0.7722 (mtp) cc_final: 0.7269 (mtp) REVERT: G 147 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: G 150 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7182 (mp-120) REVERT: H 49 GLU cc_start: 0.8618 (pt0) cc_final: 0.8418 (pt0) REVERT: H 123 GLN cc_start: 0.8750 (mm110) cc_final: 0.8314 (mm110) REVERT: H 163 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8550 (pmt) REVERT: I 167 ASN cc_start: 0.8963 (m-40) cc_final: 0.8754 (m110) REVERT: I 220 ASN cc_start: 0.9255 (t0) cc_final: 0.8981 (t0) REVERT: J 224 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8259 (pm20) REVERT: J 227 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8897 (ttpp) REVERT: K 10 ARG cc_start: 0.8603 (tpp-160) cc_final: 0.8255 (mmt-90) REVERT: K 41 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: L 26 MET cc_start: 0.8724 (mtm) cc_final: 0.8337 (mmm) REVERT: L 41 LYS cc_start: 0.8929 (mptt) cc_final: 0.8598 (mptt) REVERT: L 137 TYR cc_start: 0.8404 (t80) cc_final: 0.7927 (t80) REVERT: L 143 HIS cc_start: 0.7876 (m90) cc_final: 0.7462 (m90) REVERT: L 159 MET cc_start: 0.9053 (tpt) cc_final: 0.8600 (tpt) REVERT: L 166 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7935 (tp-100) REVERT: L 180 MET cc_start: 0.8596 (tpp) cc_final: 0.7803 (mmm) REVERT: L 226 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: M 117 MET cc_start: 0.8663 (tpp) cc_final: 0.8378 (mmp) REVERT: M 221 ASN cc_start: 0.9316 (t0) cc_final: 0.8931 (t0) REVERT: A 57 LYS cc_start: 0.8846 (ttmt) cc_final: 0.8607 (tmmt) REVERT: A 146 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8475 (pmtt) REVERT: A 321 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.8005 (p) REVERT: A 394 MET cc_start: 0.9293 (mmm) cc_final: 0.8850 (mmm) REVERT: A 418 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.6874 (mmmt) REVERT: B 66 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7003 (tm-30) REVERT: B 74 MET cc_start: 0.6405 (mtp) cc_final: 0.6140 (mtt) REVERT: B 195 GLN cc_start: 0.8592 (tt0) cc_final: 0.8339 (tt0) REVERT: B 211 TYR cc_start: 0.8707 (m-80) cc_final: 0.8280 (m-80) REVERT: B 294 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7909 (tpt-90) REVERT: B 425 ASN cc_start: 0.8799 (t0) cc_final: 0.8539 (t160) REVERT: F 145 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8480 (mm) REVERT: F 186 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8265 (p) REVERT: F 259 MET cc_start: 0.7980 (mtp) cc_final: 0.7586 (ttm) REVERT: F 310 MET cc_start: 0.7145 (mmt) cc_final: 0.6839 (mtt) REVERT: F 356 MET cc_start: 0.9265 (mtp) cc_final: 0.8857 (mtm) REVERT: F 421 MET cc_start: 0.8925 (mmt) cc_final: 0.8704 (mmm) REVERT: c 85 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: c 168 MET cc_start: 0.7587 (tpp) cc_final: 0.7082 (tpt) REVERT: c 198 ARG cc_start: 0.8997 (ttp80) cc_final: 0.8669 (ttp80) REVERT: c 208 ARG cc_start: 0.8393 (mtp-110) cc_final: 0.7896 (mmm-85) REVERT: c 229 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8244 (pp) REVERT: c 233 ASP cc_start: 0.8623 (t0) cc_final: 0.8347 (t0) REVERT: c 262 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8919 (tp30) REVERT: c 286 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8869 (mp0) outliers start: 169 outliers final: 106 residues processed: 504 average time/residue: 0.5824 time to fit residues: 359.8310 Evaluate side-chains 469 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 342 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 352 MET Chi-restraints excluded: chain E residue 367 PHE Chi-restraints excluded: chain G residue 16 PHE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain L residue 21 GLN Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 160 PHE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 234 TYR Chi-restraints excluded: chain c residue 286 GLU Chi-restraints excluded: chain c residue 300 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 267 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 328 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 chunk 90 optimal weight: 0.0980 chunk 122 optimal weight: 0.0470 chunk 155 optimal weight: 5.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN E 339 ASN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 HIS I 30 HIS M 32 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 154 HIS B 181 GLN B 277 HIS ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.089973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.067493 restraints weight = 86191.914| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.09 r_work: 0.2994 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34093 Z= 0.129 Angle : 0.689 16.853 46055 Z= 0.333 Chirality : 0.043 0.231 5245 Planarity : 0.004 0.062 5947 Dihedral : 7.698 132.188 4779 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.91 % Favored : 93.93 % Rotamer: Outliers : 4.39 % Allowed : 31.24 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 0.40 (0.13), residues: 4199 helix: 1.47 (0.12), residues: 1865 sheet: -0.92 (0.18), residues: 738 loop : -0.49 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG c 46 TYR 0.019 0.001 TYR F 437 PHE 0.027 0.001 PHE B 78 TRP 0.012 0.001 TRP I 159 HIS 0.006 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00293 (34090) covalent geometry : angle 0.68890 (46055) hydrogen bonds : bond 0.03441 ( 1661) hydrogen bonds : angle 4.57348 ( 4782) metal coordination : bond 0.00156 ( 2) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 374 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8687 (tttp) REVERT: C 102 ASN cc_start: 0.8934 (t0) cc_final: 0.8682 (t0) REVERT: C 130 LYS cc_start: 0.9355 (tppt) cc_final: 0.9076 (tppt) REVERT: C 176 GLU cc_start: 0.9248 (tp30) cc_final: 0.9016 (tp30) REVERT: C 248 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.9003 (mmt) REVERT: C 284 GLU cc_start: 0.8841 (tp30) cc_final: 0.8605 (mm-30) REVERT: D 77 GLU cc_start: 0.8775 (tp30) cc_final: 0.8414 (tt0) REVERT: D 98 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8107 (tp-100) REVERT: D 170 MET cc_start: 0.9105 (ptp) cc_final: 0.8719 (ptp) REVERT: D 229 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8589 (ttp80) REVERT: D 249 ASP cc_start: 0.9019 (m-30) cc_final: 0.8616 (m-30) REVERT: D 374 ASP cc_start: 0.8802 (m-30) cc_final: 0.8396 (m-30) REVERT: D 395 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8476 (mp) REVERT: D 408 LYS cc_start: 0.8276 (tptp) cc_final: 0.8028 (tppp) REVERT: E 28 GLU cc_start: 0.7310 (pp20) cc_final: 0.6322 (tt0) REVERT: E 53 VAL cc_start: 0.8781 (p) cc_final: 0.8580 (t) REVERT: E 124 HIS cc_start: 0.8817 (m90) cc_final: 0.8484 (m170) REVERT: E 234 GLU cc_start: 0.8883 (tp30) cc_final: 0.8377 (tp30) REVERT: E 316 HIS cc_start: 0.8861 (OUTLIER) cc_final: 0.8424 (OUTLIER) REVERT: G 42 VAL cc_start: 0.9048 (t) cc_final: 0.8600 (m) REVERT: G 80 MET cc_start: 0.7734 (mtp) cc_final: 0.7343 (mtp) REVERT: G 147 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8459 (tm-30) REVERT: G 150 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7131 (mp-120) REVERT: H 49 GLU cc_start: 0.8615 (pt0) cc_final: 0.8355 (pt0) REVERT: H 123 GLN cc_start: 0.8728 (mm110) cc_final: 0.8294 (mm110) REVERT: H 163 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8452 (pmt) REVERT: I 72 MET cc_start: 0.7544 (mmt) cc_final: 0.7302 (mmt) REVERT: I 151 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8512 (t0) REVERT: I 167 ASN cc_start: 0.8962 (m-40) cc_final: 0.8752 (m110) REVERT: I 220 ASN cc_start: 0.9258 (t0) cc_final: 0.8994 (t0) REVERT: J 36 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.6856 (ptt-90) REVERT: J 224 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: J 227 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8888 (ttpp) REVERT: K 10 ARG cc_start: 0.8552 (tpp-160) cc_final: 0.8131 (mmt-90) REVERT: K 41 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8604 (tp40) REVERT: K 106 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8742 (t) REVERT: L 26 MET cc_start: 0.8738 (mtm) cc_final: 0.8392 (mmm) REVERT: L 100 ASP cc_start: 0.8833 (m-30) cc_final: 0.8304 (m-30) REVERT: L 137 TYR cc_start: 0.8379 (t80) cc_final: 0.7935 (t80) REVERT: L 143 HIS cc_start: 0.7721 (m90) cc_final: 0.7310 (m90) REVERT: L 159 MET cc_start: 0.9044 (tpt) cc_final: 0.8607 (tpt) REVERT: L 166 GLN cc_start: 0.8205 (tp-100) cc_final: 0.7925 (tp-100) REVERT: L 180 MET cc_start: 0.8521 (tpp) cc_final: 0.8213 (mmm) REVERT: M 3 ILE cc_start: 0.5729 (OUTLIER) cc_final: 0.5493 (mt) REVERT: M 117 MET cc_start: 0.8675 (tpp) cc_final: 0.8426 (mmp) REVERT: M 221 ASN cc_start: 0.9324 (t0) cc_final: 0.8947 (t0) REVERT: M 243 LEU cc_start: 0.9320 (tm) cc_final: 0.8753 (pp) REVERT: A 57 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8585 (tmmt) REVERT: A 146 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8452 (pmtt) REVERT: A 321 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8039 (p) REVERT: A 337 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5578 (mt) REVERT: A 394 MET cc_start: 0.9285 (mmm) cc_final: 0.8817 (mmm) REVERT: A 418 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.6912 (mmmt) REVERT: B 66 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7012 (tm-30) REVERT: B 74 MET cc_start: 0.6358 (mtp) cc_final: 0.6078 (mtt) REVERT: B 195 GLN cc_start: 0.8595 (tt0) cc_final: 0.8340 (tt0) REVERT: B 211 TYR cc_start: 0.8710 (m-80) cc_final: 0.8258 (m-80) REVERT: B 294 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7891 (tpt-90) REVERT: B 373 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8519 (p) REVERT: B 425 ASN cc_start: 0.8791 (t0) cc_final: 0.8539 (t160) REVERT: F 145 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8474 (mm) REVERT: F 186 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.7924 (p) REVERT: F 259 MET cc_start: 0.8004 (mtp) cc_final: 0.7700 (ttm) REVERT: F 356 MET cc_start: 0.9226 (mtp) cc_final: 0.8782 (mtm) REVERT: F 421 MET cc_start: 0.8937 (mmt) cc_final: 0.8701 (mmm) REVERT: F 426 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8387 (mm-30) REVERT: c 85 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: c 99 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9262 (mm) REVERT: c 168 MET cc_start: 0.7505 (tpp) cc_final: 0.7079 (tpt) REVERT: c 198 ARG cc_start: 0.9009 (ttp80) cc_final: 0.8686 (ttp80) REVERT: c 229 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8376 (pp) REVERT: c 233 ASP cc_start: 0.8610 (t0) cc_final: 0.8341 (t0) REVERT: c 261 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8865 (tm-30) REVERT: c 262 GLU cc_start: 0.9393 (mt-10) cc_final: 0.9030 (tp30) REVERT: c 286 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8943 (mp0) outliers start: 159 outliers final: 102 residues processed: 504 average time/residue: 0.5939 time to fit residues: 366.6936 Evaluate side-chains 472 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 343 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 352 MET Chi-restraints excluded: chain E residue 367 PHE Chi-restraints excluded: chain G residue 16 PHE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 68 HIS Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 163 MET Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 160 PHE Chi-restraints excluded: chain c residue 172 HIS Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 234 TYR Chi-restraints excluded: chain c residue 286 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 152 optimal weight: 6.9990 chunk 339 optimal weight: 0.7980 chunk 296 optimal weight: 0.8980 chunk 326 optimal weight: 4.9990 chunk 316 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 419 optimal weight: 7.9990 chunk 304 optimal weight: 8.9990 chunk 372 optimal weight: 7.9990 chunk 410 optimal weight: 0.8980 chunk 395 optimal weight: 10.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS J 205 ASN L 21 GLN M 32 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 277 HIS ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.088594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066098 restraints weight = 86491.330| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.07 r_work: 0.2958 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34093 Z= 0.185 Angle : 0.726 18.256 46055 Z= 0.354 Chirality : 0.044 0.219 5245 Planarity : 0.004 0.061 5947 Dihedral : 7.703 135.174 4777 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.10 % Favored : 93.74 % Rotamer: Outliers : 4.56 % Allowed : 31.44 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 0.36 (0.13), residues: 4199 helix: 1.46 (0.12), residues: 1859 sheet: -0.95 (0.18), residues: 745 loop : -0.51 (0.17), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG c 208 TYR 0.023 0.001 TYR A 249 PHE 0.045 0.002 PHE G 16 TRP 0.014 0.002 TRP G 101 HIS 0.008 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00431 (34090) covalent geometry : angle 0.72625 (46055) hydrogen bonds : bond 0.03546 ( 1661) hydrogen bonds : angle 4.61952 ( 4782) metal coordination : bond 0.00377 ( 2) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 355 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.8983 (t0) cc_final: 0.8745 (t0) REVERT: C 130 LYS cc_start: 0.9327 (tppt) cc_final: 0.9082 (tppt) REVERT: C 176 GLU cc_start: 0.9222 (tp30) cc_final: 0.8984 (tp30) REVERT: D 77 GLU cc_start: 0.8790 (tp30) cc_final: 0.8426 (tt0) REVERT: D 98 GLN cc_start: 0.8661 (tp-100) cc_final: 0.8133 (tp-100) REVERT: D 170 MET cc_start: 0.9124 (ptp) cc_final: 0.8801 (ptp) REVERT: D 214 MET cc_start: 0.9096 (ttm) cc_final: 0.8745 (ttm) REVERT: D 229 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8588 (ttp80) REVERT: D 249 ASP cc_start: 0.9001 (m-30) cc_final: 0.8580 (m-30) REVERT: D 374 ASP cc_start: 0.8849 (m-30) cc_final: 0.8463 (m-30) REVERT: D 384 MET cc_start: 0.9038 (mmm) cc_final: 0.8670 (mpp) REVERT: D 395 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8507 (mp) REVERT: D 408 LYS cc_start: 0.8328 (tptp) cc_final: 0.8053 (tppp) REVERT: E 53 VAL cc_start: 0.8839 (p) cc_final: 0.8633 (t) REVERT: E 124 HIS cc_start: 0.8851 (m90) cc_final: 0.8544 (m-70) REVERT: E 234 GLU cc_start: 0.8939 (tp30) cc_final: 0.8411 (tp30) REVERT: E 316 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8303 (m170) REVERT: G 80 MET cc_start: 0.7762 (mtp) cc_final: 0.7525 (mtp) REVERT: G 147 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: G 150 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7188 (mp-120) REVERT: H 49 GLU cc_start: 0.8603 (pt0) cc_final: 0.8384 (pt0) REVERT: H 123 GLN cc_start: 0.8747 (mm110) cc_final: 0.8295 (mm110) REVERT: I 151 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8500 (t0) REVERT: I 167 ASN cc_start: 0.8983 (m-40) cc_final: 0.8782 (m110) REVERT: I 220 ASN cc_start: 0.9262 (t0) cc_final: 0.8948 (t0) REVERT: J 36 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.6910 (ptt-90) REVERT: J 227 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8904 (ttpp) REVERT: K 10 ARG cc_start: 0.8715 (tpp-160) cc_final: 0.8344 (mmt-90) REVERT: K 41 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8641 (tt0) REVERT: K 106 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8841 (t) REVERT: L 26 MET cc_start: 0.8807 (mtm) cc_final: 0.8455 (mmm) REVERT: L 41 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8617 (mptt) REVERT: L 137 TYR cc_start: 0.8474 (t80) cc_final: 0.8075 (t80) REVERT: L 143 HIS cc_start: 0.7886 (m90) cc_final: 0.7477 (m90) REVERT: L 159 MET cc_start: 0.9038 (tpt) cc_final: 0.8605 (tpt) REVERT: L 166 GLN cc_start: 0.8279 (tp-100) cc_final: 0.8009 (tp-100) REVERT: L 180 MET cc_start: 0.8586 (tpp) cc_final: 0.7781 (mmp) REVERT: M 27 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7915 (mpm) REVERT: M 117 MET cc_start: 0.8695 (tpp) cc_final: 0.8407 (mmp) REVERT: M 221 ASN cc_start: 0.9334 (t0) cc_final: 0.8959 (t0) REVERT: M 243 LEU cc_start: 0.9317 (tm) cc_final: 0.8744 (pp) REVERT: A 57 LYS cc_start: 0.8821 (ttmt) cc_final: 0.8557 (tmmt) REVERT: A 146 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8443 (pmtt) REVERT: A 249 TYR cc_start: 0.5676 (t80) cc_final: 0.4597 (t80) REVERT: A 256 MET cc_start: 0.8921 (ttt) cc_final: 0.8151 (ttt) REVERT: A 321 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8049 (p) REVERT: A 337 LEU cc_start: 0.5822 (OUTLIER) cc_final: 0.5612 (mt) REVERT: A 394 MET cc_start: 0.9307 (mmm) cc_final: 0.8913 (mmm) REVERT: A 418 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.6920 (mmmt) REVERT: B 66 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6983 (tm-30) REVERT: B 74 MET cc_start: 0.6313 (mtp) cc_final: 0.6051 (mtt) REVERT: B 195 GLN cc_start: 0.8628 (tt0) cc_final: 0.8369 (tt0) REVERT: B 211 TYR cc_start: 0.8764 (m-80) cc_final: 0.8432 (m-80) REVERT: B 294 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8007 (tpt-90) REVERT: B 373 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8504 (p) REVERT: B 425 ASN cc_start: 0.8798 (t0) cc_final: 0.8569 (t160) REVERT: F 55 MET cc_start: 0.6411 (mpp) cc_final: 0.6178 (pmm) REVERT: F 145 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8486 (mm) REVERT: F 170 SER cc_start: 0.4552 (t) cc_final: 0.4279 (p) REVERT: F 225 MET cc_start: 0.7842 (pmm) cc_final: 0.7538 (pmm) REVERT: F 259 MET cc_start: 0.8050 (mtp) cc_final: 0.7602 (ttm) REVERT: F 356 MET cc_start: 0.9263 (mtp) cc_final: 0.8819 (mtm) REVERT: F 373 MET cc_start: 0.8428 (mtp) cc_final: 0.7621 (pmm) REVERT: F 421 MET cc_start: 0.8983 (mmt) cc_final: 0.8767 (mmm) REVERT: F 426 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8410 (mm-30) REVERT: c 85 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: c 99 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9263 (mm) REVERT: c 168 MET cc_start: 0.7503 (tpp) cc_final: 0.7052 (tpt) REVERT: c 208 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.7781 (mmm-85) REVERT: c 229 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8293 (pp) REVERT: c 233 ASP cc_start: 0.8680 (t0) cc_final: 0.8405 (t70) REVERT: c 261 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8877 (tm-30) REVERT: c 262 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9051 (tp30) REVERT: c 286 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8880 (mp0) outliers start: 165 outliers final: 102 residues processed: 491 average time/residue: 0.5957 time to fit residues: 358.0469 Evaluate side-chains 467 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 341 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 352 MET Chi-restraints excluded: chain E residue 367 PHE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 68 HIS Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain L residue 41 LYS Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 186 CYS Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 234 TYR Chi-restraints excluded: chain c residue 286 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 171 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 273 optimal weight: 8.9990 chunk 376 optimal weight: 0.0370 chunk 153 optimal weight: 0.0370 chunk 345 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 415 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 overall best weight: 2.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS J 205 ASN J 221 ASN L 21 GLN M 32 ASN M 170 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 181 GLN ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.087981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065358 restraints weight = 86430.758| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.08 r_work: 0.2948 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34093 Z= 0.188 Angle : 0.735 20.150 46055 Z= 0.359 Chirality : 0.044 0.257 5245 Planarity : 0.004 0.073 5947 Dihedral : 7.734 137.491 4777 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.71 % Rotamer: Outliers : 3.70 % Allowed : 32.29 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 0.33 (0.13), residues: 4199 helix: 1.41 (0.12), residues: 1863 sheet: -0.96 (0.18), residues: 740 loop : -0.51 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG c 46 TYR 0.021 0.001 TYR F 437 PHE 0.030 0.001 PHE B 78 TRP 0.016 0.001 TRP G 101 HIS 0.008 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00437 (34090) covalent geometry : angle 0.73507 (46055) hydrogen bonds : bond 0.03588 ( 1661) hydrogen bonds : angle 4.67008 ( 4782) metal coordination : bond 0.00387 ( 2) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8398 Ramachandran restraints generated. 4199 Oldfield, 0 Emsley, 4199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 347 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 ASN cc_start: 0.9058 (t0) cc_final: 0.8808 (t0) REVERT: C 176 GLU cc_start: 0.9206 (tp30) cc_final: 0.8979 (tp30) REVERT: D 77 GLU cc_start: 0.8789 (tp30) cc_final: 0.8448 (tt0) REVERT: D 98 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8149 (tp-100) REVERT: D 170 MET cc_start: 0.9122 (ptp) cc_final: 0.8792 (ptp) REVERT: D 229 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8603 (ttp80) REVERT: D 249 ASP cc_start: 0.9006 (m-30) cc_final: 0.8596 (m-30) REVERT: D 374 ASP cc_start: 0.8855 (m-30) cc_final: 0.8484 (m-30) REVERT: D 384 MET cc_start: 0.9015 (mmm) cc_final: 0.8634 (mpp) REVERT: D 395 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8518 (mp) REVERT: D 408 LYS cc_start: 0.8324 (tptp) cc_final: 0.8045 (tppp) REVERT: E 28 GLU cc_start: 0.7067 (pp20) cc_final: 0.6622 (tt0) REVERT: E 33 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7293 (mt) REVERT: E 53 VAL cc_start: 0.8816 (p) cc_final: 0.8601 (t) REVERT: E 124 HIS cc_start: 0.8893 (m90) cc_final: 0.8555 (m-70) REVERT: E 234 GLU cc_start: 0.8931 (tp30) cc_final: 0.8399 (tp30) REVERT: G 80 MET cc_start: 0.7816 (mtp) cc_final: 0.7553 (mtp) REVERT: G 147 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8486 (tm-30) REVERT: G 150 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7232 (mp-120) REVERT: H 123 GLN cc_start: 0.8780 (mm110) cc_final: 0.8329 (mm110) REVERT: I 151 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8447 (t0) REVERT: I 167 ASN cc_start: 0.8992 (m-40) cc_final: 0.8791 (m110) REVERT: I 220 ASN cc_start: 0.9267 (t0) cc_final: 0.8936 (t0) REVERT: J 36 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.6876 (ptt-90) REVERT: K 9 ASP cc_start: 0.6944 (m-30) cc_final: 0.6553 (m-30) REVERT: K 10 ARG cc_start: 0.8593 (tpp-160) cc_final: 0.8247 (mmt-90) REVERT: K 41 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: K 106 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8832 (t) REVERT: L 26 MET cc_start: 0.8821 (mtm) cc_final: 0.8453 (mmm) REVERT: L 137 TYR cc_start: 0.8575 (t80) cc_final: 0.8140 (t80) REVERT: L 159 MET cc_start: 0.9014 (tpt) cc_final: 0.8576 (tpt) REVERT: L 166 GLN cc_start: 0.8270 (tp-100) cc_final: 0.8060 (tp-100) REVERT: L 180 MET cc_start: 0.8581 (tpp) cc_final: 0.8232 (mmm) REVERT: M 27 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7822 (mpm) REVERT: M 117 MET cc_start: 0.8689 (tpp) cc_final: 0.8391 (mmp) REVERT: M 221 ASN cc_start: 0.9286 (t0) cc_final: 0.8924 (t0) REVERT: M 243 LEU cc_start: 0.9354 (tm) cc_final: 0.8774 (pp) REVERT: A 57 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8562 (tmmt) REVERT: A 146 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8419 (pmtt) REVERT: A 249 TYR cc_start: 0.5719 (t80) cc_final: 0.4571 (t80) REVERT: A 256 MET cc_start: 0.8891 (ttt) cc_final: 0.8161 (ttt) REVERT: A 394 MET cc_start: 0.9291 (mmm) cc_final: 0.8880 (mmm) REVERT: A 418 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.6862 (mmmt) REVERT: B 41 LYS cc_start: 0.8319 (pptt) cc_final: 0.8109 (pptt) REVERT: B 66 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 74 MET cc_start: 0.6439 (mtp) cc_final: 0.6167 (mtt) REVERT: B 195 GLN cc_start: 0.8617 (tt0) cc_final: 0.8340 (tt0) REVERT: B 211 TYR cc_start: 0.8814 (m-80) cc_final: 0.8489 (m-80) REVERT: B 294 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8026 (tpt-90) REVERT: B 373 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8466 (p) REVERT: B 425 ASN cc_start: 0.8815 (t0) cc_final: 0.8605 (t160) REVERT: F 145 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8490 (mm) REVERT: F 170 SER cc_start: 0.4139 (t) cc_final: 0.3856 (p) REVERT: F 225 MET cc_start: 0.7931 (pmm) cc_final: 0.7621 (pmm) REVERT: F 259 MET cc_start: 0.8123 (mtp) cc_final: 0.7673 (ttm) REVERT: F 356 MET cc_start: 0.9279 (mtp) cc_final: 0.8807 (mtm) REVERT: F 373 MET cc_start: 0.8210 (mtp) cc_final: 0.7624 (pmm) REVERT: F 421 MET cc_start: 0.8991 (mmt) cc_final: 0.8791 (mmm) REVERT: F 426 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8409 (mm-30) REVERT: c 85 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: c 99 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9261 (mm) REVERT: c 168 MET cc_start: 0.7559 (tpp) cc_final: 0.7066 (tpt) REVERT: c 198 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8570 (ttp80) REVERT: c 208 ARG cc_start: 0.8435 (mtp-110) cc_final: 0.7800 (mmm-85) REVERT: c 229 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8301 (pp) REVERT: c 233 ASP cc_start: 0.8676 (t0) cc_final: 0.8383 (t0) REVERT: c 262 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9043 (tp30) REVERT: c 265 MET cc_start: 0.5332 (tpt) cc_final: 0.4526 (tpp) REVERT: c 286 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8886 (mp0) outliers start: 134 outliers final: 98 residues processed: 460 average time/residue: 0.6200 time to fit residues: 350.6500 Evaluate side-chains 448 residues out of total 3647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 330 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 88 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 68 HIS Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 165 ILE Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 143 VAL Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 234 TYR Chi-restraints excluded: chain c residue 286 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 399 optimal weight: 0.2980 chunk 261 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 311 optimal weight: 0.8980 chunk 390 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN I 30 HIS L 21 GLN M 32 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS B 154 HIS B 157 HIS B 181 GLN B 241 ASN B 277 HIS ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.067521 restraints weight = 85443.622| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.13 r_work: 0.2993 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34093 Z= 0.131 Angle : 0.728 17.219 46055 Z= 0.354 Chirality : 0.043 0.258 5245 Planarity : 0.004 0.062 5947 Dihedral : 7.666 133.425 4777 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.74 % Favored : 94.09 % Rotamer: Outliers : 3.12 % Allowed : 32.87 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 0.42 (0.13), residues: 4199 helix: 1.46 (0.12), residues: 1863 sheet: -0.92 (0.18), residues: 735 loop : -0.43 (0.17), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG c 46 TYR 0.019 0.001 TYR F 437 PHE 0.034 0.001 PHE B 319 TRP 0.018 0.001 TRP G 101 HIS 0.010 0.001 HIS F 208 Details of bonding type rmsd covalent geometry : bond 0.00297 (34090) covalent geometry : angle 0.72843 (46055) hydrogen bonds : bond 0.03437 ( 1661) hydrogen bonds : angle 4.56995 ( 4782) metal coordination : bond 0.00133 ( 2) Misc. bond : bond 0.00020 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11136.55 seconds wall clock time: 191 minutes 14.91 seconds (11474.91 seconds total)