Starting phenix.real_space_refine on Sat Jul 4 15:59:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umv_42385/07_2026/8umv_42385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umv_42385/07_2026/8umv_42385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8umv_42385/07_2026/8umv_42385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umv_42385/07_2026/8umv_42385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8umv_42385/07_2026/8umv_42385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umv_42385/07_2026/8umv_42385.map" } resolution = 2.75 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= 0.001 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 329 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 61 5.49 5 Mg 4 5.21 5 S 138 5.16 5 C 13599 2.51 5 N 3772 2.21 5 O 4286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21860 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4319 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 512} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2591 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2541 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "I" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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} Time building chain proxies: 3.88, per 1000 atoms: 0.18 Number of scatterers: 21860 At special positions: 0 Unit cell: (116.748, 128.34, 138.276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 61 15.00 Mg 4 11.99 O 4286 8.00 N 3772 7.00 C 13599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 840.0 milliseconds 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5038 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 14 sheets defined 52.3% alpha, 14.4% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.690A pdb=" N LEU A 294 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.646A pdb=" N LEU A 351 " --> pdb=" O HIS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.508A pdb=" N ARG A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 440 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 498 through 503 removed outlier: 4.093A pdb=" N GLN A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.911A pdb=" N SER A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.699A pdb=" N VAL A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 627 through 643 removed outlier: 4.056A pdb=" N GLY A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 656 Processing helix chain 'A' and resid 666 through 690 Processing helix chain 'A' and resid 691 through 698 removed outlier: 3.686A pdb=" N LEU A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG A 696 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 697 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Proline residue: A 698 - end of helix Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.652A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 744 removed outlier: 3.617A pdb=" N GLY A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 744 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.565A pdb=" N SER A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 777 through 781 Processing helix chain 'A' and resid 782 through 799 removed outlier: 3.841A pdb=" N TYR A 799 " --> pdb=" O THR A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.545A pdb=" N ILE B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.686A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.587A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 255 removed outlier: 3.925A pdb=" N VAL B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 272 removed outlier: 4.230A pdb=" N LEU B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.901A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 removed outlier: 3.555A pdb=" N LYS B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.591A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.517A pdb=" N MET C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 86' Processing helix chain 'C' and resid 97 through 103 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.749A pdb=" N ARG C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.546A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.554A pdb=" N VAL C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.993A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.592A pdb=" N GLN C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 289 removed outlier: 3.897A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.514A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 83 through 97 removed outlier: 3.596A pdb=" N ILE D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 115 through 128 removed outlier: 3.802A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 187 through 194 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 235 removed outlier: 3.855A pdb=" N GLU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 266 Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.519A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 362 removed outlier: 4.204A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.927A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.839A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 30 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.894A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 65 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 6.920A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 118 removed outlier: 3.812A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 115 " --> pdb=" O MET E 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER E 118 " --> pdb=" O THR E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 removed outlier: 3.792A pdb=" N ARG E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG E 150 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.796A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.547A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.551A pdb=" N VAL E 253 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.119A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.516A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 removed outlier: 3.671A pdb=" N ILE F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.774A pdb=" N ILE F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.721A pdb=" N SER F 222 " --> pdb=" O THR F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 Processing helix chain 'G' and resid 72 through 81 removed outlier: 4.040A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.710A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 74 through 82 removed outlier: 3.655A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 152 through 154 No H-bonds generated for 'chain 'H' and resid 152 through 154' Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.625A pdb=" N GLU H 193 " --> pdb=" O LYS H 190 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA H 194 " --> pdb=" O GLU H 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 190 through 194' Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 222 Proline residue: H 220 - end of helix No H-bonds generated for 'chain 'H' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 397 removed outlier: 6.130A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU A 508 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 371 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 806 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.113A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.184A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.377A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.758A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS E 37 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL E 182 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 57 through 62 removed outlier: 6.558A pdb=" N ARG F 5 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR F 60 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU F 3 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL G 167 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.909A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 177 through 180 removed outlier: 3.507A pdb=" N ILE F 180 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE F 169 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 61 through 62 removed outlier: 3.806A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS H 181 " --> pdb=" O VAL G 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.790A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 59 through 62 removed outlier: 4.102A pdb=" N THR H 59 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 67 through 71 removed outlier: 6.809A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 3174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7147 1.35 - 1.50: 5639 1.50 - 1.65: 9315 1.65 - 1.80: 85 1.80 - 1.95: 123 Bond restraints: 22309 Sorted by residual: bond pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" O3B AGS A1202 " pdb=" PB AGS A1202 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " ideal model delta sigma weight residual 1.664 1.581 0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 22304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 29759 2.31 - 4.61: 544 4.61 - 6.92: 60 6.92 - 9.22: 28 9.22 - 11.53: 7 Bond angle restraints: 30398 Sorted by residual: angle pdb=" N MET F 119 " pdb=" CA MET F 119 " pdb=" C MET F 119 " ideal model delta sigma weight residual 109.95 100.50 9.45 1.59e+00 3.96e-01 3.53e+01 angle pdb=" N ARG E 234 " pdb=" CA ARG E 234 " pdb=" C ARG E 234 " ideal model delta sigma weight residual 111.36 105.24 6.12 1.09e+00 8.42e-01 3.16e+01 angle pdb=" N PRO A 819 " pdb=" CA PRO A 819 " pdb=" C PRO A 819 " ideal model delta sigma weight residual 112.47 100.94 11.53 2.06e+00 2.36e-01 3.13e+01 angle pdb=" N VAL G 158 " pdb=" CA VAL G 158 " pdb=" C VAL G 158 " ideal model delta sigma weight residual 107.75 114.37 -6.62 1.46e+00 4.69e-01 2.06e+01 angle pdb=" N GLU F 124 " pdb=" CA GLU F 124 " pdb=" C GLU F 124 " ideal model delta sigma weight residual 110.32 103.18 7.14 1.59e+00 3.96e-01 2.01e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.05: 13183 34.05 - 68.09: 490 68.09 - 102.14: 23 102.14 - 136.18: 6 136.18 - 170.23: 5 Dihedral angle restraints: 13707 sinusoidal: 5967 harmonic: 7740 Sorted by residual: dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 146.37 153.63 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" CA LEU F 79 " pdb=" C LEU F 79 " pdb=" N LYS F 80 " pdb=" CA LYS F 80 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA MET G 199 " pdb=" C MET G 199 " pdb=" N ASN G 200 " pdb=" CA ASN G 200 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 13704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2973 0.061 - 0.121: 486 0.121 - 0.182: 57 0.182 - 0.242: 8 0.242 - 0.303: 4 Chirality restraints: 3528 Sorted by residual: chirality pdb=" C3' AGS B 402 " pdb=" C2' AGS B 402 " pdb=" C4' AGS B 402 " pdb=" O3' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.67 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' AGS C 402 " pdb=" C2' AGS C 402 " pdb=" C4' AGS C 402 " pdb=" O3' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' AGS D 402 " pdb=" C2' AGS D 402 " pdb=" C4' AGS D 402 " pdb=" O3' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3525 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " 0.067 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO A 699 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 162 " -0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C CYS F 162 " 0.061 2.00e-02 2.50e+03 pdb=" O CYS F 162 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA F 163 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 119 " -0.015 2.00e-02 2.50e+03 3.16e-02 9.98e+00 pdb=" C MET F 119 " 0.055 2.00e-02 2.50e+03 pdb=" O MET F 119 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP F 120 " -0.019 2.00e-02 2.50e+03 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 219 2.63 - 3.20: 17570 3.20 - 3.76: 34742 3.76 - 4.33: 48344 4.33 - 4.90: 79185 Nonbonded interactions: 180060 Sorted by model distance: nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.062 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.071 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.082 2.170 nonbonded pdb=" OG1 THR D 85 " pdb="MG MG D 401 " model vdw 2.084 2.170 nonbonded pdb=" OG1 THR C 67 " pdb="MG MG C 401 " model vdw 2.090 2.170 ... (remaining 180055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 258) selection = (chain 'H' and resid 1 through 258) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.300 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 22309 Z= 0.280 Angle : 0.764 11.525 30398 Z= 0.457 Chirality : 0.047 0.303 3528 Planarity : 0.007 0.122 3723 Dihedral : 16.232 170.230 8669 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.69 % Allowed : 9.22 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 2623 helix: -1.15 (0.12), residues: 1249 sheet: -0.46 (0.22), residues: 540 loop : -0.85 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 193 TYR 0.017 0.002 TYR E 279 PHE 0.015 0.002 PHE A 409 TRP 0.006 0.001 TRP C 253 HIS 0.003 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.28 (22309) covalent geometry : angle 0.76352 / 0.46 (30398) hydrogen bonds : bond 0.14520 / 9.74 ( 1143) hydrogen bonds : angle 5.96248 / 4.27 ( 3258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 436 time to evaluate : 0.721 Fit side-chains REVERT: A 644 GLU cc_start: 0.6576 (mp0) cc_final: 0.6370 (mp0) REVERT: B 66 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7617 (mt-10) REVERT: B 99 LYS cc_start: 0.8446 (mttt) cc_final: 0.8236 (mmtt) REVERT: B 307 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7443 (tm-30) REVERT: C 51 ASP cc_start: 0.7092 (t0) cc_final: 0.6816 (t0) REVERT: C 133 ASP cc_start: 0.7616 (m-30) cc_final: 0.7309 (m-30) REVERT: C 182 MET cc_start: 0.8468 (ttt) cc_final: 0.8216 (ttt) REVERT: D 56 GLU cc_start: 0.7840 (mp0) cc_final: 0.7537 (mp0) REVERT: D 275 ASP cc_start: 0.7523 (m-30) cc_final: 0.7226 (m-30) REVERT: D 294 LYS cc_start: 0.8134 (mttt) cc_final: 0.7892 (tttp) REVERT: D 356 MET cc_start: 0.8586 (ttp) cc_final: 0.8284 (ttp) REVERT: E 9 ARG cc_start: 0.8551 (ttp-170) cc_final: 0.8261 (ttt180) REVERT: E 31 GLN cc_start: 0.7410 (mt0) cc_final: 0.7084 (pt0) REVERT: F 150 ASP cc_start: 0.7626 (m-30) cc_final: 0.7396 (m-30) REVERT: F 199 MET cc_start: 0.7025 (ppp) cc_final: 0.6788 (ppp) REVERT: F 209 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6883 (mt) REVERT: F 213 ASN cc_start: 0.6575 (m-40) cc_final: 0.6357 (m-40) REVERT: F 248 LYS cc_start: 0.8103 (mttt) cc_final: 0.7598 (mptt) REVERT: G 23 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8124 (mm) REVERT: H 116 MET cc_start: 0.6385 (mtm) cc_final: 0.6173 (mtt) REVERT: H 196 THR cc_start: 0.7450 (p) cc_final: 0.7178 (t) outliers start: 39 outliers final: 9 residues processed: 460 average time/residue: 0.6460 time to fit residues: 334.9159 Evaluate side-chains 325 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 314 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 298 ASN B 332 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 194 HIS F 38 GLN F 65 ASN G 38 GLN G 108 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.131995 restraints weight = 25032.912| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.70 r_work: 0.3351 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22309 Z= 0.175 Angle : 0.575 7.034 30398 Z= 0.305 Chirality : 0.042 0.193 3528 Planarity : 0.005 0.084 3723 Dihedral : 16.542 177.488 3542 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.98 % Allowed : 14.42 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2623 helix: 0.23 (0.14), residues: 1269 sheet: -0.60 (0.21), residues: 547 loop : -0.48 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 807 TYR 0.014 0.002 TYR B 279 PHE 0.015 0.002 PHE C 119 TRP 0.010 0.001 TRP G 28 HIS 0.005 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (22309) covalent geometry : angle 0.57550 / 0.30 (30398) hydrogen bonds : bond 0.04298 / 2.90 ( 1143) hydrogen bonds : angle 4.48170 / 3.19 ( 3258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 328 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 772 LYS cc_start: 0.7750 (mtmm) cc_final: 0.7519 (tttt) REVERT: A 830 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7729 (mm) REVERT: B 66 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8122 (mt-10) REVERT: B 72 ILE cc_start: 0.8759 (mt) cc_final: 0.8311 (pt) REVERT: B 99 LYS cc_start: 0.8822 (mttt) cc_final: 0.8345 (mmtt) REVERT: B 307 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7664 (tm-30) REVERT: C 51 ASP cc_start: 0.7565 (t0) cc_final: 0.7252 (t0) REVERT: C 133 ASP cc_start: 0.7903 (m-30) cc_final: 0.7660 (m-30) REVERT: C 233 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: C 320 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8412 (mm) REVERT: D 56 GLU cc_start: 0.8081 (mp0) cc_final: 0.7786 (mp0) REVERT: D 107 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: D 121 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: D 209 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: D 275 ASP cc_start: 0.7865 (m-30) cc_final: 0.7609 (m-30) REVERT: D 294 LYS cc_start: 0.8295 (mttt) cc_final: 0.7791 (tttp) REVERT: D 356 MET cc_start: 0.8668 (ttp) cc_final: 0.8400 (ttp) REVERT: E 9 ARG cc_start: 0.8647 (ttp-170) cc_final: 0.8335 (ttt180) REVERT: E 31 GLN cc_start: 0.7485 (mt0) cc_final: 0.7102 (pt0) REVERT: F 68 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7833 (mpp) REVERT: F 209 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7266 (mt) REVERT: F 214 PHE cc_start: 0.7298 (m-10) cc_final: 0.7011 (m-80) REVERT: F 215 PHE cc_start: 0.8300 (m-10) cc_final: 0.7886 (m-80) REVERT: F 248 LYS cc_start: 0.8169 (mttt) cc_final: 0.7491 (mptt) REVERT: G 23 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8127 (mm) REVERT: G 114 TYR cc_start: 0.8232 (m-10) cc_final: 0.7956 (m-10) REVERT: G 214 PHE cc_start: 0.8381 (m-10) cc_final: 0.8151 (m-10) REVERT: G 238 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.5909 (mt-10) REVERT: G 244 MET cc_start: 0.7471 (mpt) cc_final: 0.6866 (tpp) REVERT: G 248 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8255 (mmtt) REVERT: H 40 MET cc_start: 0.8403 (ttp) cc_final: 0.8169 (ttp) REVERT: H 196 THR cc_start: 0.6649 (p) cc_final: 0.6392 (t) REVERT: H 248 LYS cc_start: 0.7243 (tttt) cc_final: 0.6876 (tttm) outliers start: 92 outliers final: 36 residues processed: 379 average time/residue: 0.6251 time to fit residues: 268.0706 Evaluate side-chains 359 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 139 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 252 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN A 595 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN B 332 ASN C 256 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS E 213 HIS F 38 GLN F 65 ASN G 38 GLN G 246 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.174454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133156 restraints weight = 25111.410| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.72 r_work: 0.3370 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22309 Z= 0.121 Angle : 0.523 6.589 30398 Z= 0.276 Chirality : 0.040 0.180 3528 Planarity : 0.004 0.075 3723 Dihedral : 16.324 179.938 3538 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.42 % Allowed : 16.23 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2623 helix: 0.83 (0.14), residues: 1267 sheet: -0.55 (0.21), residues: 541 loop : -0.36 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 53 TYR 0.013 0.001 TYR D 229 PHE 0.015 0.001 PHE A 632 TRP 0.008 0.001 TRP G 28 HIS 0.003 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (22309) covalent geometry : angle 0.52310 / 0.28 (30398) hydrogen bonds : bond 0.03525 / 2.37 ( 1143) hydrogen bonds : angle 4.23683 / 3.01 ( 3258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 327 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 507 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8328 (tt) REVERT: A 772 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7506 (tttt) REVERT: A 830 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7683 (mm) REVERT: B 66 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8134 (mt-10) REVERT: B 72 ILE cc_start: 0.8756 (mt) cc_final: 0.8355 (pt) REVERT: B 99 LYS cc_start: 0.8803 (mttt) cc_final: 0.8267 (mmtt) REVERT: B 277 GLU cc_start: 0.8205 (mp0) cc_final: 0.7711 (mp0) REVERT: B 307 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7640 (tm-30) REVERT: C 51 ASP cc_start: 0.7520 (t0) cc_final: 0.7181 (t0) REVERT: C 133 ASP cc_start: 0.7883 (m-30) cc_final: 0.7628 (m-30) REVERT: C 320 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8310 (mm) REVERT: D 121 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: D 209 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: D 275 ASP cc_start: 0.7837 (m-30) cc_final: 0.7586 (m-30) REVERT: D 294 LYS cc_start: 0.8258 (mttt) cc_final: 0.7764 (tttp) REVERT: D 356 MET cc_start: 0.8654 (ttp) cc_final: 0.8425 (ttp) REVERT: E 9 ARG cc_start: 0.8628 (ttp-170) cc_final: 0.8293 (ttt180) REVERT: E 31 GLN cc_start: 0.7379 (mt0) cc_final: 0.7014 (pt0) REVERT: E 122 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: E 205 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8170 (mt) REVERT: F 68 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7882 (mpp) REVERT: F 214 PHE cc_start: 0.7253 (m-10) cc_final: 0.6900 (m-80) REVERT: F 215 PHE cc_start: 0.8258 (m-10) cc_final: 0.7932 (m-80) REVERT: F 248 LYS cc_start: 0.8067 (mttt) cc_final: 0.7393 (mptt) REVERT: G 23 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8047 (mm) REVERT: G 214 PHE cc_start: 0.8451 (m-10) cc_final: 0.8208 (m-10) REVERT: G 244 MET cc_start: 0.7431 (mpt) cc_final: 0.6837 (tpp) REVERT: H 88 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.6854 (mm) REVERT: H 196 THR cc_start: 0.6493 (p) cc_final: 0.6240 (t) REVERT: H 244 MET cc_start: 0.5681 (pmm) cc_final: 0.5301 (pmm) REVERT: H 248 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.7047 (tttp) outliers start: 79 outliers final: 28 residues processed: 371 average time/residue: 0.6188 time to fit residues: 260.7589 Evaluate side-chains 349 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 248 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 114 optimal weight: 0.9980 chunk 246 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 172 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 504 GLN A 523 GLN A 591 GLN A 727 GLN B 332 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 194 HIS E 213 HIS F 38 GLN F 44 HIS F 65 ASN F 213 ASN G 246 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.174249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132337 restraints weight = 25071.274| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.95 r_work: 0.3326 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22309 Z= 0.121 Angle : 0.513 6.792 30398 Z= 0.270 Chirality : 0.040 0.176 3528 Planarity : 0.004 0.071 3723 Dihedral : 16.108 178.588 3534 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.72 % Allowed : 16.32 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2623 helix: 1.16 (0.15), residues: 1269 sheet: -0.49 (0.21), residues: 545 loop : -0.25 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 149 TYR 0.014 0.001 TYR D 229 PHE 0.015 0.001 PHE A 632 TRP 0.008 0.001 TRP E 251 HIS 0.003 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (22309) covalent geometry : angle 0.51349 / 0.27 (30398) hydrogen bonds : bond 0.03301 / 2.22 ( 1143) hydrogen bonds : angle 4.09068 / 2.91 ( 3258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 325 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 507 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8359 (tt) REVERT: A 630 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8327 (mm-40) REVERT: A 830 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7677 (mm) REVERT: B 66 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8224 (mt-10) REVERT: B 72 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8415 (pt) REVERT: B 99 LYS cc_start: 0.8842 (mttt) cc_final: 0.8279 (mmtt) REVERT: B 277 GLU cc_start: 0.8295 (mp0) cc_final: 0.7822 (mp0) REVERT: B 307 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 51 ASP cc_start: 0.7636 (t0) cc_final: 0.7291 (t0) REVERT: C 133 ASP cc_start: 0.7993 (m-30) cc_final: 0.7742 (m-30) REVERT: C 320 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8354 (mm) REVERT: D 102 ARG cc_start: 0.8156 (mtm110) cc_final: 0.7905 (mtm-85) REVERT: D 107 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: D 209 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: D 275 ASP cc_start: 0.7942 (m-30) cc_final: 0.7694 (m-30) REVERT: D 294 LYS cc_start: 0.8327 (mttt) cc_final: 0.7852 (tttp) REVERT: D 356 MET cc_start: 0.8679 (ttp) cc_final: 0.8476 (ttp) REVERT: E 9 ARG cc_start: 0.8651 (ttp-170) cc_final: 0.8310 (ttt180) REVERT: E 31 GLN cc_start: 0.7439 (mt0) cc_final: 0.7058 (pt0) REVERT: E 110 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: E 205 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8262 (mt) REVERT: E 218 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8424 (tttt) REVERT: E 304 ASP cc_start: 0.7706 (m-30) cc_final: 0.7126 (t70) REVERT: F 68 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.7946 (mpp) REVERT: F 211 TYR cc_start: 0.8260 (m-80) cc_final: 0.7852 (m-80) REVERT: F 213 ASN cc_start: 0.6593 (m-40) cc_final: 0.6378 (m-40) REVERT: F 214 PHE cc_start: 0.7162 (m-10) cc_final: 0.6937 (m-80) REVERT: F 248 LYS cc_start: 0.8087 (mttt) cc_final: 0.7418 (mptt) REVERT: G 23 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8093 (mm) REVERT: G 214 PHE cc_start: 0.8491 (m-10) cc_final: 0.8244 (m-10) REVERT: G 244 MET cc_start: 0.7623 (mpt) cc_final: 0.7089 (tpp) REVERT: H 1 MET cc_start: 0.4213 (tpp) cc_final: 0.3983 (tpp) REVERT: H 88 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6855 (mm) REVERT: H 153 HIS cc_start: 0.7734 (m90) cc_final: 0.7420 (m-70) REVERT: H 196 THR cc_start: 0.6530 (p) cc_final: 0.6264 (t) REVERT: H 232 ASP cc_start: 0.7190 (p0) cc_final: 0.6859 (m-30) REVERT: H 248 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7123 (tttp) outliers start: 86 outliers final: 30 residues processed: 378 average time/residue: 0.6429 time to fit residues: 276.5531 Evaluate side-chains 358 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 314 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 248 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 60 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 238 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 243 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 504 GLN A 591 GLN B 332 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 102 ASN E 194 HIS E 213 HIS F 65 ASN G 246 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132205 restraints weight = 25049.509| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.72 r_work: 0.3358 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22309 Z= 0.139 Angle : 0.535 7.001 30398 Z= 0.279 Chirality : 0.040 0.166 3528 Planarity : 0.004 0.071 3723 Dihedral : 16.021 179.114 3533 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.68 % Allowed : 17.10 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 2623 helix: 1.24 (0.15), residues: 1273 sheet: -0.41 (0.21), residues: 539 loop : -0.18 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 91 TYR 0.014 0.001 TYR D 229 PHE 0.014 0.001 PHE A 632 TRP 0.008 0.001 TRP E 251 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (22309) covalent geometry : angle 0.53546 / 0.28 (30398) hydrogen bonds : bond 0.03368 / 2.25 ( 1143) hydrogen bonds : angle 4.03875 / 2.88 ( 3258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 325 time to evaluate : 0.874 Fit side-chains REVERT: A 507 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8406 (tt) REVERT: A 630 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8270 (mm-40) REVERT: A 830 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7602 (mm) REVERT: B 66 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8166 (mt-10) REVERT: B 72 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8408 (pt) REVERT: B 99 LYS cc_start: 0.8806 (mttt) cc_final: 0.8277 (mmtt) REVERT: B 277 GLU cc_start: 0.8227 (mp0) cc_final: 0.7761 (mp0) REVERT: B 307 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 51 ASP cc_start: 0.7550 (t0) cc_final: 0.7210 (t0) REVERT: C 133 ASP cc_start: 0.7856 (m-30) cc_final: 0.7604 (m-30) REVERT: C 320 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8369 (mm) REVERT: D 56 GLU cc_start: 0.8098 (mp0) cc_final: 0.7807 (mp0) REVERT: D 107 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: D 209 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: D 275 ASP cc_start: 0.7840 (m-30) cc_final: 0.7599 (m-30) REVERT: D 294 LYS cc_start: 0.8312 (mttt) cc_final: 0.7817 (tttp) REVERT: D 356 MET cc_start: 0.8685 (ttp) cc_final: 0.8478 (ttp) REVERT: E 9 ARG cc_start: 0.8652 (ttp-170) cc_final: 0.8288 (ttt180) REVERT: E 22 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8683 (tt0) REVERT: E 31 GLN cc_start: 0.7393 (mt0) cc_final: 0.7048 (pt0) REVERT: E 110 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: E 122 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: E 205 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8257 (mt) REVERT: E 218 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8358 (tttt) REVERT: E 304 ASP cc_start: 0.7692 (m-30) cc_final: 0.7106 (t70) REVERT: E 310 GLU cc_start: 0.7706 (tp30) cc_final: 0.7461 (tp30) REVERT: F 68 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7963 (mpp) REVERT: F 211 TYR cc_start: 0.8241 (m-80) cc_final: 0.7811 (m-80) REVERT: F 214 PHE cc_start: 0.7129 (m-10) cc_final: 0.6902 (m-80) REVERT: F 215 PHE cc_start: 0.8292 (m-10) cc_final: 0.7972 (m-80) REVERT: F 248 LYS cc_start: 0.8113 (mttt) cc_final: 0.7439 (mptt) REVERT: G 23 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8117 (mm) REVERT: G 214 PHE cc_start: 0.8466 (m-10) cc_final: 0.8223 (m-10) REVERT: G 244 MET cc_start: 0.7481 (mpt) cc_final: 0.7113 (tpp) REVERT: H 88 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.6943 (mm) REVERT: H 153 HIS cc_start: 0.7722 (m90) cc_final: 0.7402 (m-70) REVERT: H 196 THR cc_start: 0.6495 (p) cc_final: 0.6233 (t) REVERT: H 232 ASP cc_start: 0.7198 (p0) cc_final: 0.6867 (m-30) REVERT: H 248 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6979 (tttm) outliers start: 85 outliers final: 32 residues processed: 383 average time/residue: 0.6442 time to fit residues: 280.5496 Evaluate side-chains 367 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 248 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 208 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 239 optimal weight: 0.0980 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 166 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 504 GLN B 332 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 194 HIS E 213 HIS F 213 ASN G 246 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131487 restraints weight = 25052.332| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.76 r_work: 0.3339 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22309 Z= 0.149 Angle : 0.541 7.260 30398 Z= 0.281 Chirality : 0.041 0.141 3528 Planarity : 0.004 0.070 3723 Dihedral : 15.966 179.884 3533 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.90 % Allowed : 17.53 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2623 helix: 1.25 (0.15), residues: 1278 sheet: -0.44 (0.21), residues: 536 loop : -0.15 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 91 TYR 0.014 0.001 TYR D 229 PHE 0.014 0.001 PHE A 632 TRP 0.008 0.001 TRP E 251 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (22309) covalent geometry : angle 0.54136 / 0.28 (30398) hydrogen bonds : bond 0.03415 / 2.29 ( 1143) hydrogen bonds : angle 4.03346 / 2.87 ( 3258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 325 time to evaluate : 0.925 Fit side-chains REVERT: A 507 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8412 (tt) REVERT: A 630 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8262 (mm-40) REVERT: A 830 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7558 (mm) REVERT: B 66 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8172 (mt-10) REVERT: B 72 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8406 (pt) REVERT: B 99 LYS cc_start: 0.8813 (mttt) cc_final: 0.8290 (mmtt) REVERT: B 230 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8862 (mtt90) REVERT: B 277 GLU cc_start: 0.8255 (mp0) cc_final: 0.7798 (mp0) REVERT: B 307 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7627 (tm-30) REVERT: C 51 ASP cc_start: 0.7578 (t0) cc_final: 0.7228 (t0) REVERT: C 133 ASP cc_start: 0.7899 (m-30) cc_final: 0.7655 (m-30) REVERT: C 320 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8424 (mm) REVERT: D 56 GLU cc_start: 0.8154 (mp0) cc_final: 0.7868 (mp0) REVERT: D 107 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: D 209 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: D 275 ASP cc_start: 0.7886 (m-30) cc_final: 0.7647 (m-30) REVERT: D 294 LYS cc_start: 0.8344 (mttt) cc_final: 0.7870 (tttp) REVERT: E 9 ARG cc_start: 0.8664 (ttp-170) cc_final: 0.8365 (ttt180) REVERT: E 31 GLN cc_start: 0.7400 (mt0) cc_final: 0.7053 (pt0) REVERT: E 122 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6761 (tm-30) REVERT: E 205 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8286 (mt) REVERT: E 218 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8395 (tttt) REVERT: E 310 GLU cc_start: 0.7763 (tp30) cc_final: 0.7542 (tp30) REVERT: F 68 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7988 (mpp) REVERT: F 211 TYR cc_start: 0.8279 (m-80) cc_final: 0.7870 (m-80) REVERT: F 214 PHE cc_start: 0.7089 (m-10) cc_final: 0.6857 (m-80) REVERT: F 248 LYS cc_start: 0.8093 (mttt) cc_final: 0.7408 (mptt) REVERT: G 23 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8142 (mm) REVERT: G 214 PHE cc_start: 0.8483 (m-10) cc_final: 0.8250 (m-10) REVERT: G 244 MET cc_start: 0.7528 (mpt) cc_final: 0.7171 (mmt) REVERT: H 88 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.6931 (mm) REVERT: H 232 ASP cc_start: 0.7184 (p0) cc_final: 0.6886 (m-30) REVERT: H 248 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.7068 (tttm) outliers start: 90 outliers final: 39 residues processed: 383 average time/residue: 0.6173 time to fit residues: 268.9641 Evaluate side-chains 367 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 248 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 221 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 250 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 504 GLN B 332 ASN C 91 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 102 ASN E 194 HIS E 213 HIS F 65 ASN ** G 246 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 = 0.4019 r_free = 0.4019 target = 0.173638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131639 restraints weight = 25036.303| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.98 r_work: 0.3300 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22309 Z= 0.122 Angle : 0.529 10.138 30398 Z= 0.275 Chirality : 0.040 0.169 3528 Planarity : 0.004 0.068 3723 Dihedral : 15.821 177.637 3533 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.59 % Allowed : 18.14 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2623 helix: 1.37 (0.15), residues: 1278 sheet: -0.42 (0.21), residues: 536 loop : -0.06 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 91 TYR 0.013 0.001 TYR D 229 PHE 0.015 0.001 PHE F 215 TRP 0.007 0.001 TRP E 251 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (22309) covalent geometry : angle 0.52912 / 0.27 (30398) hydrogen bonds : bond 0.03181 / 2.13 ( 1143) hydrogen bonds : angle 3.98141 / 2.84 ( 3258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 326 time to evaluate : 0.889 Fit side-chains REVERT: A 387 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.7825 (mp) REVERT: A 507 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 630 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: A 830 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7589 (mm) REVERT: B 66 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8230 (mt-10) REVERT: B 72 ILE cc_start: 0.8828 (mt) cc_final: 0.8483 (pt) REVERT: B 99 LYS cc_start: 0.8863 (mttt) cc_final: 0.8313 (mmtt) REVERT: B 277 GLU cc_start: 0.8371 (mp0) cc_final: 0.7889 (mp0) REVERT: B 307 GLN cc_start: 0.8440 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 51 ASP cc_start: 0.7672 (t0) cc_final: 0.7329 (t0) REVERT: C 133 ASP cc_start: 0.8049 (m-30) cc_final: 0.7809 (m-30) REVERT: C 320 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8418 (mm) REVERT: D 56 GLU cc_start: 0.8244 (mp0) cc_final: 0.7948 (mp0) REVERT: D 107 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: D 121 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: D 209 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: D 275 ASP cc_start: 0.7947 (m-30) cc_final: 0.7717 (m-30) REVERT: D 294 LYS cc_start: 0.8358 (mttt) cc_final: 0.7865 (tttp) REVERT: E 9 ARG cc_start: 0.8677 (ttp-170) cc_final: 0.8310 (ttt180) REVERT: E 31 GLN cc_start: 0.7422 (mt0) cc_final: 0.7045 (pt0) REVERT: E 205 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8314 (mt) REVERT: E 218 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8347 (tttt) REVERT: E 310 GLU cc_start: 0.7815 (tp30) cc_final: 0.7583 (tp30) REVERT: F 58 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7027 (t0) REVERT: F 68 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8062 (mpp) REVERT: F 203 VAL cc_start: 0.7677 (p) cc_final: 0.7311 (m) REVERT: F 214 PHE cc_start: 0.7043 (m-10) cc_final: 0.6833 (m-80) REVERT: F 248 LYS cc_start: 0.8154 (mttt) cc_final: 0.7440 (mptt) REVERT: G 23 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8151 (mm) REVERT: G 244 MET cc_start: 0.7712 (mpt) cc_final: 0.7243 (mmt) REVERT: H 88 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.6953 (mm) REVERT: H 153 HIS cc_start: 0.7754 (m90) cc_final: 0.7512 (m-70) REVERT: H 232 ASP cc_start: 0.7201 (p0) cc_final: 0.6876 (m-30) REVERT: H 248 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7126 (tttm) outliers start: 83 outliers final: 33 residues processed: 382 average time/residue: 0.6417 time to fit residues: 278.5457 Evaluate side-chains 369 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 321 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 248 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 65 optimal weight: 6.9990 chunk 85 optimal weight: 0.3980 chunk 188 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 504 GLN B 332 ASN C 37 HIS C 91 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 194 HIS E 213 HIS E 320 HIS ** G 246 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 = 0.3993 r_free = 0.3993 target = 0.171226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.129648 restraints weight = 24964.739| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.75 r_work: 0.3315 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22309 Z= 0.198 Angle : 0.597 9.067 30398 Z= 0.307 Chirality : 0.043 0.178 3528 Planarity : 0.005 0.071 3723 Dihedral : 15.937 178.932 3533 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.42 % Allowed : 18.70 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.16), residues: 2623 helix: 1.25 (0.15), residues: 1274 sheet: -0.39 (0.21), residues: 524 loop : -0.09 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 301 TYR 0.015 0.002 TYR E 318 PHE 0.015 0.002 PHE F 215 TRP 0.008 0.001 TRP E 251 HIS 0.023 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (22309) covalent geometry : angle 0.59699 / 0.31 (30398) hydrogen bonds : bond 0.03803 / 2.54 ( 1143) hydrogen bonds : angle 4.08693 / 2.91 ( 3258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 315 time to evaluate : 0.876 Fit side-chains REVERT: A 507 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8550 (tt) REVERT: A 630 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8245 (mm-40) REVERT: A 807 ARG cc_start: 0.6582 (tpm170) cc_final: 0.6165 (tpm170) REVERT: A 830 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7613 (mm) REVERT: B 66 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8181 (mt-10) REVERT: B 72 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8341 (pt) REVERT: B 99 LYS cc_start: 0.8846 (mttt) cc_final: 0.8309 (mmtt) REVERT: B 307 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 51 ASP cc_start: 0.7649 (t0) cc_final: 0.7280 (t0) REVERT: C 133 ASP cc_start: 0.7969 (m-30) cc_final: 0.7731 (m-30) REVERT: D 56 GLU cc_start: 0.8215 (mp0) cc_final: 0.7906 (mp0) REVERT: D 107 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: D 209 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: D 275 ASP cc_start: 0.7984 (m-30) cc_final: 0.7766 (m-30) REVERT: D 294 LYS cc_start: 0.8336 (mttt) cc_final: 0.7913 (tttp) REVERT: E 9 ARG cc_start: 0.8685 (ttp-170) cc_final: 0.8290 (ttt180) REVERT: E 31 GLN cc_start: 0.7427 (mt0) cc_final: 0.7025 (pt0) REVERT: E 122 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: E 205 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8309 (mt) REVERT: E 218 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8428 (tttt) REVERT: E 310 GLU cc_start: 0.7822 (tp30) cc_final: 0.7605 (tp30) REVERT: F 68 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8016 (mpp) REVERT: F 248 LYS cc_start: 0.8167 (mttt) cc_final: 0.7492 (mptt) REVERT: G 23 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8147 (mm) REVERT: G 244 MET cc_start: 0.7586 (mpt) cc_final: 0.7320 (mmt) REVERT: H 88 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.6971 (mm) REVERT: H 153 HIS cc_start: 0.7820 (m90) cc_final: 0.7579 (m-70) REVERT: H 232 ASP cc_start: 0.7207 (p0) cc_final: 0.6885 (m-30) REVERT: H 248 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7100 (tttm) outliers start: 79 outliers final: 39 residues processed: 370 average time/residue: 0.6634 time to fit residues: 279.3137 Evaluate side-chains 355 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 248 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 155 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 504 GLN B 332 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 194 HIS E 213 HIS ** G 246 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 = 0.4006 r_free = 0.4006 target = 0.172391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.129662 restraints weight = 24994.966| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.84 r_work: 0.3306 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22309 Z= 0.144 Angle : 0.565 10.904 30398 Z= 0.292 Chirality : 0.041 0.198 3528 Planarity : 0.004 0.069 3723 Dihedral : 15.869 178.930 3533 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.94 % Allowed : 19.70 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2623 helix: 1.35 (0.15), residues: 1273 sheet: -0.50 (0.21), residues: 536 loop : -0.01 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 301 TYR 0.014 0.001 TYR D 229 PHE 0.016 0.001 PHE G 214 TRP 0.007 0.001 TRP G 28 HIS 0.021 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (22309) covalent geometry : angle 0.56528 / 0.29 (30398) hydrogen bonds : bond 0.03400 / 2.27 ( 1143) hydrogen bonds : angle 4.05344 / 2.89 ( 3258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 316 time to evaluate : 0.897 Fit side-chains REVERT: A 387 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 414 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7483 (mm-30) REVERT: A 507 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8545 (tt) REVERT: A 630 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8267 (mm-40) REVERT: A 674 ASP cc_start: 0.8297 (t0) cc_final: 0.7999 (m-30) REVERT: A 807 ARG cc_start: 0.6593 (tpm170) cc_final: 0.6249 (tpp-160) REVERT: A 830 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7568 (mm) REVERT: B 66 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8190 (mt-10) REVERT: B 72 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8445 (pt) REVERT: B 99 LYS cc_start: 0.8872 (mttt) cc_final: 0.8330 (mmtt) REVERT: B 277 GLU cc_start: 0.8348 (mp0) cc_final: 0.7866 (mp0) REVERT: B 307 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7588 (tm-30) REVERT: C 51 ASP cc_start: 0.7711 (t0) cc_final: 0.7341 (t0) REVERT: C 133 ASP cc_start: 0.8040 (m-30) cc_final: 0.7804 (m-30) REVERT: C 320 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8507 (mm) REVERT: D 56 GLU cc_start: 0.8213 (mp0) cc_final: 0.7914 (mp0) REVERT: D 107 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: D 121 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: D 209 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: D 275 ASP cc_start: 0.8003 (m-30) cc_final: 0.7787 (m-30) REVERT: D 294 LYS cc_start: 0.8336 (mttt) cc_final: 0.7927 (tttp) REVERT: D 299 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: E 9 ARG cc_start: 0.8677 (ttp-170) cc_final: 0.8290 (ttt180) REVERT: E 31 GLN cc_start: 0.7455 (mt0) cc_final: 0.7055 (pt0) REVERT: E 122 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6596 (tm-30) REVERT: E 205 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8353 (mt) REVERT: E 218 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8450 (tttt) REVERT: E 310 GLU cc_start: 0.7834 (tp30) cc_final: 0.7629 (tp30) REVERT: F 58 ASP cc_start: 0.7668 (t0) cc_final: 0.7303 (t0) REVERT: F 68 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8122 (mpp) REVERT: F 211 TYR cc_start: 0.8272 (m-80) cc_final: 0.7895 (m-80) REVERT: F 248 LYS cc_start: 0.8222 (mttt) cc_final: 0.7539 (mptt) REVERT: G 23 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8176 (mm) REVERT: G 244 MET cc_start: 0.7670 (mpt) cc_final: 0.7319 (mmt) REVERT: H 1 MET cc_start: 0.3902 (tpp) cc_final: 0.3594 (ppp) REVERT: H 88 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.6962 (mm) REVERT: H 153 HIS cc_start: 0.7850 (m90) cc_final: 0.7592 (m-70) REVERT: H 232 ASP cc_start: 0.7201 (p0) cc_final: 0.6871 (m-30) REVERT: H 248 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7054 (tttm) outliers start: 68 outliers final: 37 residues processed: 362 average time/residue: 0.6524 time to fit residues: 268.7085 Evaluate side-chains 360 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 306 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 248 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 241 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 504 GLN B 332 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 194 HIS F 38 GLN ** G 246 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 = 0.4005 r_free = 0.4005 target = 0.172297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130025 restraints weight = 25022.647| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.01 r_work: 0.3283 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22309 Z= 0.148 Angle : 0.571 11.510 30398 Z= 0.294 Chirality : 0.041 0.249 3528 Planarity : 0.004 0.070 3723 Dihedral : 15.864 178.659 3533 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.55 % Allowed : 20.48 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2623 helix: 1.36 (0.15), residues: 1273 sheet: -0.45 (0.21), residues: 532 loop : -0.02 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 301 TYR 0.014 0.001 TYR D 229 PHE 0.020 0.001 PHE G 214 TRP 0.007 0.001 TRP E 251 HIS 0.020 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (22309) covalent geometry : angle 0.57092 / 0.29 (30398) hydrogen bonds : bond 0.03401 / 2.28 ( 1143) hydrogen bonds : angle 4.05003 / 2.89 ( 3258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 0.747 Fit side-chains REVERT: A 507 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8560 (tt) REVERT: A 630 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8243 (mm-40) REVERT: A 674 ASP cc_start: 0.8342 (t0) cc_final: 0.8075 (m-30) REVERT: A 807 ARG cc_start: 0.6656 (tpm170) cc_final: 0.6282 (tpp-160) REVERT: A 830 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7557 (mm) REVERT: B 66 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8212 (mt-10) REVERT: B 72 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8428 (pt) REVERT: B 99 LYS cc_start: 0.8920 (mttt) cc_final: 0.8346 (mmtt) REVERT: B 277 GLU cc_start: 0.8391 (mp0) cc_final: 0.7853 (mp0) REVERT: B 307 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7560 (tm-30) REVERT: C 51 ASP cc_start: 0.7745 (t0) cc_final: 0.7367 (t0) REVERT: C 133 ASP cc_start: 0.8075 (m-30) cc_final: 0.7841 (m-30) REVERT: C 320 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8527 (mm) REVERT: D 56 GLU cc_start: 0.8260 (mp0) cc_final: 0.7946 (mp0) REVERT: D 107 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: D 121 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: D 209 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: D 275 ASP cc_start: 0.8030 (m-30) cc_final: 0.7813 (m-30) REVERT: D 294 LYS cc_start: 0.8337 (mttt) cc_final: 0.7895 (tttp) REVERT: D 299 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: E 9 ARG cc_start: 0.8674 (ttp-170) cc_final: 0.8283 (ttt180) REVERT: E 31 GLN cc_start: 0.7435 (mt0) cc_final: 0.7005 (pt0) REVERT: E 122 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6593 (tm-30) REVERT: E 205 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8347 (mt) REVERT: E 218 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8435 (tttt) REVERT: E 310 GLU cc_start: 0.7868 (tp30) cc_final: 0.7645 (tp30) REVERT: F 5 ARG cc_start: 0.7954 (ttt180) cc_final: 0.7675 (ttt-90) REVERT: F 58 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7176 (t0) REVERT: F 68 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8165 (mpp) REVERT: F 203 VAL cc_start: 0.7766 (p) cc_final: 0.7376 (m) REVERT: F 211 TYR cc_start: 0.8235 (m-80) cc_final: 0.7748 (m-80) REVERT: F 215 PHE cc_start: 0.8369 (m-10) cc_final: 0.8035 (m-80) REVERT: F 248 LYS cc_start: 0.8208 (mttt) cc_final: 0.7501 (mptt) REVERT: G 23 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8089 (mm) REVERT: G 244 MET cc_start: 0.7755 (mpt) cc_final: 0.7338 (mmt) REVERT: H 1 MET cc_start: 0.4003 (tpp) cc_final: 0.3634 (ppp) REVERT: H 71 ASN cc_start: 0.7671 (p0) cc_final: 0.7356 (p0) REVERT: H 88 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.6959 (mm) REVERT: H 153 HIS cc_start: 0.7889 (m90) cc_final: 0.7595 (m-70) REVERT: H 232 ASP cc_start: 0.7231 (p0) cc_final: 0.6880 (m-30) REVERT: H 248 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7064 (tttm) outliers start: 59 outliers final: 34 residues processed: 353 average time/residue: 0.6368 time to fit residues: 255.2510 Evaluate side-chains 360 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 309 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 796 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 248 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 257 optimal weight: 0.0970 chunk 11 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 190 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN A 504 GLN B 332 ASN C 317 ASN D 308 ASN E 22 GLN E 102 ASN E 194 HIS E 213 HIS F 38 GLN ** G 246 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 = 0.4025 r_free = 0.4025 target = 0.174208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132049 restraints weight = 24987.001| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.98 r_work: 0.3310 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22309 Z= 0.111 Angle : 0.541 9.956 30398 Z= 0.281 Chirality : 0.040 0.280 3528 Planarity : 0.004 0.068 3723 Dihedral : 15.759 174.599 3532 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.47 % Allowed : 20.52 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.17), residues: 2623 helix: 1.48 (0.15), residues: 1280 sheet: -0.42 (0.21), residues: 536 loop : 0.08 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 301 TYR 0.011 0.001 TYR D 229 PHE 0.023 0.001 PHE G 214 TRP 0.007 0.001 TRP G 28 HIS 0.020 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (22309) covalent geometry : angle 0.54066 / 0.28 (30398) hydrogen bonds : bond 0.03051 / 2.05 ( 1143) hydrogen bonds : angle 3.98260 / 2.84 ( 3258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8663.55 seconds wall clock time: 148 minutes 10.50 seconds (8890.50 seconds total)