Starting phenix.real_space_refine on Fri Aug 7 08:09:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thd_41254/08_2026/8thd_41254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thd_41254/08_2026/8thd_41254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thd_41254/08_2026/8thd_41254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thd_41254/08_2026/8thd_41254.map" model { file = "/net/cci-nas-00/data/ceres_data/8thd_41254/08_2026/8thd_41254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thd_41254/08_2026/8thd_41254.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 3 5.21 5 S 98 5.16 5 C 12905 2.51 5 N 3437 2.21 5 O 3939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20396 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3863 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 4 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2495 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2571 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2629 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2675 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain breaks: 1 Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "G" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2011 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2003 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, '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: 2.92, per 1000 atoms: 0.14 Number of scatterers: 20396 At special positions: 0 Unit cell: (115.92, 119.232, 150.696, 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 98 16.00 P 14 15.00 Mg 3 11.99 O 3939 8.00 N 3437 7.00 C 12905 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: 1.43 Conformation dependent library (CDL) restraints added in 634.3 milliseconds 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4898 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 16 sheets defined 50.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 256 through 276 removed outlier: 3.586A pdb=" N LYS A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 373 through 387 removed outlier: 6.616A pdb=" N ASP A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.514A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.521A pdb=" N VAL A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 Processing helix chain 'A' and resid 499 through 511 Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.660A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.518A pdb=" N PHE A 592 " --> pdb=" O MET A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 629 removed outlier: 3.786A pdb=" N HIS A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 628 " --> pdb=" O GLN A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.996A pdb=" N ARG A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 661 Processing helix chain 'A' and resid 700 through 708 removed outlier: 4.138A pdb=" N LEU A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 716 Processing helix chain 'A' and resid 716 through 735 Processing helix chain 'A' and resid 773 through 781 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.052A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 4.027A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.742A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.786A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.671A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 88 through 102 removed outlier: 3.871A pdb=" N VAL C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.735A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 153' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.525A pdb=" N HIS C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.923A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.574A pdb=" N ILE C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.651A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 313 Processing helix chain 'C' and resid 315 through 334 removed outlier: 3.578A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 4.124A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 84 through 92 removed outlier: 4.344A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.519A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.844A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.563A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.589A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.897A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 105 removed outlier: 7.971A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN E 104 " --> pdb=" O MET E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 119 removed outlier: 4.044A pdb=" N MET E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.517A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.720A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 245 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.092A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.257A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.624A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 166 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 3.812A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.507A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 221 Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.633A pdb=" N LYS H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 219 No H-bonds generated for 'chain 'H' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 removed outlier: 3.749A pdb=" N VAL A 227 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.664A pdb=" N CYS A 438 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 335 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A 461 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N HIS A 337 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 600 through 601 removed outlier: 6.411A pdb=" N LEU A 600 " --> pdb=" O VAL E 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.033A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.281A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 83 removed outlier: 6.116A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 Processing sheet with id=AA8, first strand: chain 'D' and resid 135 through 140 removed outlier: 5.544A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.498A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 57 through 60 removed outlier: 3.597A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 3.751A pdb=" N MET F 70 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL F 26 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 250 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 136 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS F 196 " --> pdb=" O SER F 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 204 through 208 removed outlier: 3.759A pdb=" N LEU F 205 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA F 171 " --> pdb=" O GLY F 178 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY F 178 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER F 177 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER F 179 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU G 113 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 100 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 2 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.792A pdb=" N MET G 70 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL G 26 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 206 through 208 removed outlier: 6.028A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE G 181 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU H 88 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU H 59 " --> pdb=" O LYS H 5 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71 removed outlier: 5.936A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER H 230 " --> pdb=" O PRO H 234 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 139 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 177 through 182 removed outlier: 3.548A pdb=" N GLY H 178 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA H 171 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU H 205 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE H 162 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL H 203 " --> pdb=" O ILE H 162 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6749 1.36 - 1.51: 5016 1.51 - 1.65: 8806 1.65 - 1.80: 75 1.80 - 1.95: 77 Bond restraints: 20723 Sorted by residual: bond pdb=" O3B AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" O3B AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" O3B AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 1.673 1.588 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" O3A AGS C 401 " pdb=" PA AGS C 401 " ideal model delta sigma weight residual 1.664 1.587 0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 20718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 27454 2.13 - 4.26: 471 4.26 - 6.40: 74 6.40 - 8.53: 22 8.53 - 10.66: 17 Bond angle restraints: 28038 Sorted by residual: angle pdb=" CA ILE E 96 " pdb=" C ILE E 96 " pdb=" O ILE E 96 " ideal model delta sigma weight residual 121.64 117.90 3.74 9.80e-01 1.04e+00 1.46e+01 angle pdb=" N ILE F 128 " pdb=" CA ILE F 128 " pdb=" C ILE F 128 " ideal model delta sigma weight residual 111.91 108.62 3.29 8.90e-01 1.26e+00 1.37e+01 angle pdb=" N LYS G 20 " pdb=" CA LYS G 20 " pdb=" C LYS G 20 " ideal model delta sigma weight residual 111.02 115.53 -4.51 1.22e+00 6.72e-01 1.37e+01 angle pdb=" CA CYS H 81 " pdb=" C CYS H 81 " pdb=" O CYS H 81 " ideal model delta sigma weight residual 122.63 117.87 4.76 1.29e+00 6.01e-01 1.36e+01 angle pdb=" O3A AGS D 401 " pdb=" PB AGS D 401 " pdb=" O3B AGS D 401 " ideal model delta sigma weight residual 100.38 111.04 -10.66 3.00e+00 1.11e-01 1.26e+01 ... (remaining 28033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 12398 35.19 - 70.37: 426 70.37 - 105.56: 36 105.56 - 140.75: 1 140.75 - 175.94: 5 Dihedral angle restraints: 12866 sinusoidal: 5364 harmonic: 7502 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 174.65 125.35 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O1A AGS C 401 " pdb=" O3A AGS C 401 " pdb=" PA AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sinusoidal sigma weight residual 82.37 -93.57 175.94 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2B AGS C 401 " pdb=" O3B AGS C 401 " pdb=" PB AGS C 401 " pdb=" PG AGS C 401 " ideal model delta sinusoidal sigma weight residual 7.37 -178.90 -173.73 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2740 0.055 - 0.111: 470 0.111 - 0.166: 61 0.166 - 0.221: 7 0.221 - 0.276: 5 Chirality restraints: 3283 Sorted by residual: chirality pdb=" C3' AGS D 401 " pdb=" C2' AGS D 401 " pdb=" C4' AGS D 401 " pdb=" O3' AGS D 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB ILE F 162 " pdb=" CA ILE F 162 " pdb=" CG1 ILE F 162 " pdb=" CG2 ILE F 162 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3280 not shown) Planarity restraints: 3551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 66 " 0.060 5.00e-02 4.00e+02 9.03e-02 1.31e+01 pdb=" N PRO D 67 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 196 " -0.044 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 197 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 144 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C CYS C 144 " -0.042 2.00e-02 2.50e+03 pdb=" O CYS C 144 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL C 145 " 0.014 2.00e-02 2.50e+03 ... (remaining 3548 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 301 2.67 - 3.22: 19112 3.22 - 3.78: 31860 3.78 - 4.34: 43124 4.34 - 4.90: 71679 Nonbonded interactions: 166076 Sorted by model distance: nonbonded pdb=" O GLY D 70 " pdb=" OG1 THR D 74 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.142 2.170 nonbonded pdb=" OD2 ASP D 140 " pdb="MG MG D 402 " model vdw 2.210 2.170 nonbonded pdb=" O LYS F 31 " pdb=" OH TYR F 60 " model vdw 2.252 3.040 nonbonded pdb=" O2B AGS D 401 " pdb="MG MG D 402 " model vdw 2.255 2.170 ... (remaining 166071 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 254) selection = (chain 'H' and resid 1 through 254) } 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 14.060 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 0.099 20723 Z= 0.218 Angle : 0.724 10.661 28038 Z= 0.384 Chirality : 0.043 0.276 3283 Planarity : 0.005 0.090 3551 Dihedral : 17.508 175.937 7968 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.43 % Allowed : 18.06 % Favored : 81.50 % 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: 0.17 (0.16), residues: 2527 helix: 1.22 (0.15), residues: 1144 sheet: 0.11 (0.25), residues: 471 loop : -1.28 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 149 TYR 0.016 0.001 TYR D 64 PHE 0.025 0.001 PHE A 509 TRP 0.009 0.001 TRP A 488 HIS 0.004 0.001 HIS D 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.22 (20723) covalent geometry : angle 0.72389 / 0.38 (28038) hydrogen bonds : bond 0.17325 / 11.55 ( 1047) hydrogen bonds : angle 6.77174 / 4.76 ( 3015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 653 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6582 (tp40) REVERT: A 359 ASN cc_start: 0.7637 (p0) cc_final: 0.7185 (t0) REVERT: A 361 TYR cc_start: 0.8663 (p90) cc_final: 0.8170 (p90) REVERT: A 505 MET cc_start: 0.8954 (tpp) cc_final: 0.8424 (mmt) REVERT: A 588 MET cc_start: 0.7567 (mmp) cc_final: 0.6882 (mtm) REVERT: C 15 TRP cc_start: 0.8650 (m-10) cc_final: 0.8228 (m-10) REVERT: C 30 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7671 (mm-40) REVERT: C 109 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6031 (mptt) REVERT: D 49 LEU cc_start: 0.8525 (mt) cc_final: 0.8256 (mt) REVERT: D 83 TYR cc_start: 0.5684 (m-10) cc_final: 0.5181 (m-10) REVERT: D 132 PRO cc_start: 0.7948 (Cg_exo) cc_final: 0.7743 (Cg_endo) REVERT: D 134 TYR cc_start: 0.5532 (p90) cc_final: 0.5141 (p90) REVERT: D 343 LEU cc_start: 0.8749 (tp) cc_final: 0.8323 (tp) REVERT: F 70 MET cc_start: 0.1808 (mtp) cc_final: 0.1353 (mtp) REVERT: F 137 LEU cc_start: 0.1989 (pp) cc_final: 0.1704 (pp) REVERT: F 180 VAL cc_start: 0.2749 (t) cc_final: 0.2439 (m) REVERT: F 196 LYS cc_start: 0.3868 (mmtt) cc_final: 0.3565 (tptp) REVERT: G 8 GLU cc_start: 0.5159 (tp30) cc_final: 0.4905 (tm-30) REVERT: G 36 ILE cc_start: 0.6974 (pt) cc_final: 0.6738 (mt) REVERT: G 63 ASP cc_start: 0.4360 (p0) cc_final: 0.4106 (p0) REVERT: H 7 GLU cc_start: 0.6904 (mp0) cc_final: 0.6518 (tt0) REVERT: H 58 GLN cc_start: 0.7925 (tt0) cc_final: 0.7479 (mt0) REVERT: H 124 ASP cc_start: 0.6315 (t70) cc_final: 0.4742 (p0) REVERT: H 196 LYS cc_start: 0.6118 (mmtm) cc_final: 0.5737 (ttpp) outliers start: 10 outliers final: 2 residues processed: 660 average time/residue: 0.1289 time to fit residues: 128.1233 Evaluate side-chains 364 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 360 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 GLN A 406 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS B 220 ASN D 42 GLN D 313 ASN E 32 GLN G 94 ASN G 153 GLN H 29 GLN H 153 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.188686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126466 restraints weight = 28108.721| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.43 r_work: 0.3393 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20723 Z= 0.195 Angle : 0.666 11.428 28038 Z= 0.331 Chirality : 0.044 0.260 3283 Planarity : 0.005 0.053 3551 Dihedral : 11.934 169.477 2897 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.82 % Allowed : 18.02 % Favored : 78.16 % 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: 0.41 (0.16), residues: 2527 helix: 1.41 (0.15), residues: 1154 sheet: 0.09 (0.25), residues: 455 loop : -1.06 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 80 TYR 0.019 0.002 TYR E 8 PHE 0.031 0.002 PHE D 63 TRP 0.008 0.001 TRP A 420 HIS 0.006 0.001 HIS G 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (20723) covalent geometry : angle 0.66647 / 0.33 (28038) hydrogen bonds : bond 0.04348 / 2.97 ( 1047) hydrogen bonds : angle 5.04881 / 3.55 ( 3015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 383 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6841 (tp40) REVERT: A 359 ASN cc_start: 0.7627 (p0) cc_final: 0.7227 (t0) REVERT: A 361 TYR cc_start: 0.8971 (p90) cc_final: 0.8532 (p90) REVERT: A 379 ASP cc_start: 0.7798 (m-30) cc_final: 0.7512 (m-30) REVERT: A 505 MET cc_start: 0.9014 (tpp) cc_final: 0.8449 (mmt) REVERT: A 588 MET cc_start: 0.7501 (mmp) cc_final: 0.6753 (mtm) REVERT: B 115 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8129 (mt-10) REVERT: C 109 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.5839 (mptt) REVERT: C 139 LYS cc_start: 0.8893 (tppt) cc_final: 0.8568 (mptt) REVERT: C 140 ASN cc_start: 0.7996 (t0) cc_final: 0.7715 (t0) REVERT: C 316 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7755 (t0) REVERT: D 132 PRO cc_start: 0.8052 (Cg_exo) cc_final: 0.7435 (Cg_endo) REVERT: D 154 ARG cc_start: 0.6924 (tpt90) cc_final: 0.6723 (tpt90) REVERT: D 157 MET cc_start: 0.7152 (ptt) cc_final: 0.6605 (ptt) REVERT: D 249 LYS cc_start: 0.8522 (mttt) cc_final: 0.8024 (mtpt) REVERT: E 8 TYR cc_start: 0.8270 (m-80) cc_final: 0.7724 (m-10) REVERT: E 20 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7278 (tm-30) REVERT: E 217 ASP cc_start: 0.8015 (t0) cc_final: 0.7748 (t0) REVERT: F 70 MET cc_start: 0.1942 (mtp) cc_final: 0.1454 (mtp) REVERT: F 174 ASP cc_start: 0.6563 (p0) cc_final: 0.6283 (m-30) REVERT: F 196 LYS cc_start: 0.4279 (mmtt) cc_final: 0.3833 (tptp) REVERT: F 249 PHE cc_start: 0.5556 (m-80) cc_final: 0.3974 (m-80) REVERT: G 1 MET cc_start: 0.3404 (mtt) cc_final: 0.3147 (mtt) REVERT: G 8 GLU cc_start: 0.5855 (tp30) cc_final: 0.5218 (tm-30) REVERT: G 63 ASP cc_start: 0.5389 (p0) cc_final: 0.5077 (p0) REVERT: G 149 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7355 (mtm-85) REVERT: G 190 HIS cc_start: 0.4817 (p90) cc_final: 0.4573 (p-80) REVERT: H 7 GLU cc_start: 0.7411 (mp0) cc_final: 0.6798 (tt0) REVERT: H 24 GLN cc_start: 0.8084 (tt0) cc_final: 0.7776 (mt0) REVERT: H 58 GLN cc_start: 0.8035 (tt0) cc_final: 0.7594 (mt0) REVERT: H 146 LYS cc_start: 0.8075 (tptm) cc_final: 0.7846 (tptm) REVERT: H 196 LYS cc_start: 0.5370 (mmtm) cc_final: 0.4831 (ttmm) REVERT: H 245 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6938 (p90) outliers start: 88 outliers final: 41 residues processed: 445 average time/residue: 0.1180 time to fit residues: 82.1637 Evaluate side-chains 361 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 146 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 224 optimal weight: 7.9990 chunk 225 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN A 622 GLN A 711 GLN B 41 ASN C 140 ASN D 42 GLN D 313 ASN E 18 HIS E 317 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.184192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136564 restraints weight = 28169.867| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.95 r_work: 0.3295 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20723 Z= 0.151 Angle : 0.583 10.000 28038 Z= 0.289 Chirality : 0.042 0.206 3283 Planarity : 0.004 0.039 3551 Dihedral : 10.857 161.557 2893 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.69 % Allowed : 19.02 % Favored : 77.29 % 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: 0.60 (0.17), residues: 2527 helix: 1.56 (0.15), residues: 1158 sheet: 0.10 (0.24), residues: 458 loop : -0.93 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 91 TYR 0.015 0.002 TYR D 134 PHE 0.022 0.001 PHE A 509 TRP 0.007 0.001 TRP B 11 HIS 0.004 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (20723) covalent geometry : angle 0.58328 / 0.29 (28038) hydrogen bonds : bond 0.03936 / 2.65 ( 1047) hydrogen bonds : angle 4.73212 / 3.34 ( 3015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 345 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 SER cc_start: 0.8360 (m) cc_final: 0.8154 (p) REVERT: A 361 TYR cc_start: 0.8974 (p90) cc_final: 0.8679 (p90) REVERT: A 383 ASP cc_start: 0.8085 (m-30) cc_final: 0.7883 (m-30) REVERT: A 505 MET cc_start: 0.8842 (tpp) cc_final: 0.8305 (mmt) REVERT: A 528 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6186 (tp) REVERT: A 550 ASP cc_start: 0.8849 (t70) cc_final: 0.8632 (t0) REVERT: A 588 MET cc_start: 0.7609 (mmp) cc_final: 0.6863 (mtm) REVERT: B 94 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8810 (tttp) REVERT: C 99 ASP cc_start: 0.8478 (m-30) cc_final: 0.8257 (m-30) REVERT: C 109 LYS cc_start: 0.6617 (OUTLIER) cc_final: 0.5773 (mptt) REVERT: C 139 LYS cc_start: 0.8780 (tppt) cc_final: 0.8531 (mptt) REVERT: C 316 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7681 (t0) REVERT: D 157 MET cc_start: 0.6976 (ptt) cc_final: 0.6662 (ptt) REVERT: E 249 LYS cc_start: 0.7750 (mtpp) cc_final: 0.7161 (mmmt) REVERT: F 126 LEU cc_start: 0.3061 (mt) cc_final: 0.2659 (tp) REVERT: F 131 LEU cc_start: 0.1281 (mm) cc_final: 0.0979 (pt) REVERT: F 174 ASP cc_start: 0.6588 (p0) cc_final: 0.6326 (m-30) REVERT: F 196 LYS cc_start: 0.4322 (mmtt) cc_final: 0.3820 (tptp) REVERT: F 249 PHE cc_start: 0.5398 (m-80) cc_final: 0.3814 (m-80) REVERT: G 63 ASP cc_start: 0.5386 (p0) cc_final: 0.5174 (p0) REVERT: G 161 MET cc_start: 0.7286 (ttm) cc_final: 0.7061 (mtp) REVERT: G 190 HIS cc_start: 0.4976 (p90) cc_final: 0.4659 (p-80) REVERT: H 7 GLU cc_start: 0.7386 (mp0) cc_final: 0.6868 (tt0) REVERT: H 24 GLN cc_start: 0.8210 (tt0) cc_final: 0.7941 (mt0) REVERT: H 44 ARG cc_start: 0.8308 (mtt90) cc_final: 0.8105 (mtt180) REVERT: H 58 GLN cc_start: 0.7962 (tt0) cc_final: 0.7634 (mt0) REVERT: H 196 LYS cc_start: 0.5422 (mmtm) cc_final: 0.5010 (ttmm) REVERT: H 245 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7208 (p90) outliers start: 85 outliers final: 49 residues processed: 408 average time/residue: 0.1240 time to fit residues: 79.1950 Evaluate side-chains 374 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 94 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 36 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.4536 > 50:) chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 250 GLN D 25 GLN D 42 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.182709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134737 restraints weight = 28122.176| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.73 r_work: 0.3288 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20723 Z= 0.156 Angle : 0.566 10.081 28038 Z= 0.281 Chirality : 0.042 0.204 3283 Planarity : 0.004 0.034 3551 Dihedral : 10.307 160.459 2890 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.65 % Allowed : 20.02 % Favored : 76.34 % 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: 0.68 (0.17), residues: 2527 helix: 1.63 (0.15), residues: 1155 sheet: 0.11 (0.24), residues: 459 loop : -0.87 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 80 TYR 0.014 0.001 TYR D 286 PHE 0.021 0.002 PHE A 509 TRP 0.009 0.001 TRP A 780 HIS 0.006 0.001 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (20723) covalent geometry : angle 0.56578 / 0.28 (28038) hydrogen bonds : bond 0.03755 / 2.55 ( 1047) hydrogen bonds : angle 4.55365 / 3.23 ( 3015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 339 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 SER cc_start: 0.8210 (m) cc_final: 0.7999 (p) REVERT: A 361 TYR cc_start: 0.8978 (p90) cc_final: 0.8771 (p90) REVERT: A 383 ASP cc_start: 0.8100 (m-30) cc_final: 0.7863 (m-30) REVERT: A 505 MET cc_start: 0.8789 (tpp) cc_final: 0.8231 (mmt) REVERT: A 588 MET cc_start: 0.7655 (mmp) cc_final: 0.6912 (mtm) REVERT: B 94 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8828 (tttp) REVERT: B 204 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8536 (tp-100) REVERT: C 99 ASP cc_start: 0.8476 (m-30) cc_final: 0.8272 (m-30) REVERT: C 109 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.5760 (mptt) REVERT: C 139 LYS cc_start: 0.8825 (tppt) cc_final: 0.8576 (mptt) REVERT: C 316 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7629 (t0) REVERT: D 134 TYR cc_start: 0.5352 (p90) cc_final: 0.4829 (p90) REVERT: E 224 GLN cc_start: 0.8743 (tt0) cc_final: 0.8375 (mt0) REVERT: E 249 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7172 (mmmt) REVERT: F 126 LEU cc_start: 0.3117 (mt) cc_final: 0.2721 (tp) REVERT: F 174 ASP cc_start: 0.6632 (p0) cc_final: 0.6371 (m-30) REVERT: F 196 LYS cc_start: 0.4412 (mmtt) cc_final: 0.3917 (tptp) REVERT: F 246 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7236 (tt) REVERT: F 249 PHE cc_start: 0.5356 (m-80) cc_final: 0.3780 (m-80) REVERT: G 8 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6805 (tm-30) REVERT: G 63 ASP cc_start: 0.5352 (p0) cc_final: 0.5113 (p0) REVERT: G 190 HIS cc_start: 0.5135 (p90) cc_final: 0.4783 (p-80) REVERT: H 7 GLU cc_start: 0.7499 (mp0) cc_final: 0.6557 (pm20) REVERT: H 24 GLN cc_start: 0.8196 (tt0) cc_final: 0.7950 (mt0) REVERT: H 44 ARG cc_start: 0.8410 (mtt90) cc_final: 0.8200 (mtt180) REVERT: H 58 GLN cc_start: 0.7998 (tt0) cc_final: 0.7654 (mt0) REVERT: H 80 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7418 (mtm110) REVERT: H 124 ASP cc_start: 0.6746 (t70) cc_final: 0.5403 (p0) REVERT: H 196 LYS cc_start: 0.5579 (mmtm) cc_final: 0.5048 (ttmm) REVERT: H 245 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7220 (p90) outliers start: 84 outliers final: 56 residues processed: 400 average time/residue: 0.1209 time to fit residues: 75.4553 Evaluate side-chains 372 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 312 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 241 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 242 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 250 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.185567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122353 restraints weight = 28269.655| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.52 r_work: 0.3364 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20723 Z= 0.178 Angle : 0.577 11.164 28038 Z= 0.286 Chirality : 0.042 0.211 3283 Planarity : 0.004 0.037 3551 Dihedral : 10.178 178.568 2890 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.65 % Allowed : 19.89 % Favored : 75.47 % 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: 0.72 (0.17), residues: 2527 helix: 1.65 (0.15), residues: 1155 sheet: 0.01 (0.24), residues: 465 loop : -0.75 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 67 TYR 0.027 0.002 TYR H 211 PHE 0.024 0.002 PHE G 19 TRP 0.009 0.001 TRP A 266 HIS 0.004 0.001 HIS E 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (20723) covalent geometry : angle 0.57713 / 0.29 (28038) hydrogen bonds : bond 0.03831 / 2.60 ( 1047) hydrogen bonds : angle 4.52732 / 3.21 ( 3015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 322 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7905 (mmt-90) REVERT: A 270 SER cc_start: 0.8149 (m) cc_final: 0.7930 (p) REVERT: A 361 TYR cc_start: 0.9002 (p90) cc_final: 0.8670 (p90) REVERT: A 383 ASP cc_start: 0.8058 (m-30) cc_final: 0.7816 (m-30) REVERT: A 505 MET cc_start: 0.8888 (tpp) cc_final: 0.8310 (mmt) REVERT: A 528 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6018 (tp) REVERT: A 575 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8735 (tppt) REVERT: A 588 MET cc_start: 0.7576 (mmp) cc_final: 0.6875 (mtm) REVERT: B 94 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8824 (tttp) REVERT: B 204 GLN cc_start: 0.8863 (tp-100) cc_final: 0.8518 (tp-100) REVERT: C 109 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.5924 (mptt) REVERT: C 139 LYS cc_start: 0.8848 (tppt) cc_final: 0.8604 (mptt) REVERT: C 316 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7586 (t0) REVERT: D 134 TYR cc_start: 0.5334 (p90) cc_final: 0.5060 (p90) REVERT: D 188 ARG cc_start: 0.7055 (ttt-90) cc_final: 0.6803 (ttt-90) REVERT: E 224 GLN cc_start: 0.8701 (tt0) cc_final: 0.8336 (mt0) REVERT: E 249 LYS cc_start: 0.7711 (mtpp) cc_final: 0.7128 (mmmt) REVERT: F 126 LEU cc_start: 0.3156 (mt) cc_final: 0.2762 (tp) REVERT: F 174 ASP cc_start: 0.6662 (p0) cc_final: 0.6389 (m-30) REVERT: F 196 LYS cc_start: 0.4273 (mmtt) cc_final: 0.3831 (tptp) REVERT: F 217 LYS cc_start: 0.6757 (tptp) cc_final: 0.6553 (tptp) REVERT: F 246 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7288 (tt) REVERT: F 249 PHE cc_start: 0.5357 (m-80) cc_final: 0.3770 (m-80) REVERT: H 7 GLU cc_start: 0.7670 (mp0) cc_final: 0.6722 (pm20) REVERT: H 24 GLN cc_start: 0.8215 (tt0) cc_final: 0.7882 (mt0) REVERT: H 44 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8202 (mtt180) REVERT: H 58 GLN cc_start: 0.8150 (tt0) cc_final: 0.7717 (mt0) REVERT: H 80 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7574 (mtm110) REVERT: H 122 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.7000 (p0) REVERT: H 124 ASP cc_start: 0.6859 (t70) cc_final: 0.5480 (p0) REVERT: H 196 LYS cc_start: 0.5413 (mmtm) cc_final: 0.4896 (ttmm) REVERT: H 245 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.7027 (p90) outliers start: 107 outliers final: 77 residues processed: 402 average time/residue: 0.1242 time to fit residues: 78.4616 Evaluate side-chains 381 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 297 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 608 GLN C 210 ASN D 25 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.183313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.132710 restraints weight = 28057.063| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.85 r_work: 0.3284 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20723 Z= 0.200 Angle : 0.599 10.269 28038 Z= 0.298 Chirality : 0.042 0.229 3283 Planarity : 0.004 0.037 3551 Dihedral : 10.040 162.562 2890 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.43 % Allowed : 20.97 % Favored : 74.60 % 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: 0.68 (0.17), residues: 2527 helix: 1.59 (0.15), residues: 1159 sheet: -0.04 (0.24), residues: 470 loop : -0.72 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 129 TYR 0.025 0.002 TYR H 211 PHE 0.041 0.002 PHE G 19 TRP 0.008 0.001 TRP A 420 HIS 0.004 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (20723) covalent geometry : angle 0.59941 / 0.30 (28038) hydrogen bonds : bond 0.03976 / 2.71 ( 1047) hydrogen bonds : angle 4.52865 / 3.22 ( 3015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 305 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 SER cc_start: 0.8215 (m) cc_final: 0.7975 (p) REVERT: A 379 ASP cc_start: 0.7968 (m-30) cc_final: 0.7666 (m-30) REVERT: A 383 ASP cc_start: 0.8112 (m-30) cc_final: 0.7900 (m-30) REVERT: A 462 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6934 (mttt) REVERT: A 505 MET cc_start: 0.8837 (tpp) cc_final: 0.8323 (mmt) REVERT: A 528 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6176 (tp) REVERT: A 575 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8765 (tppt) REVERT: A 588 MET cc_start: 0.7678 (mmp) cc_final: 0.7072 (mtm) REVERT: C 109 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.5943 (mptt) REVERT: C 139 LYS cc_start: 0.8780 (tppt) cc_final: 0.8539 (mptt) REVERT: C 205 MET cc_start: 0.8689 (mmm) cc_final: 0.8344 (mmt) REVERT: C 316 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7645 (t0) REVERT: D 132 PRO cc_start: 0.7996 (Cg_exo) cc_final: 0.7789 (Cg_endo) REVERT: D 188 ARG cc_start: 0.7124 (ttt-90) cc_final: 0.6848 (ttt-90) REVERT: E 224 GLN cc_start: 0.8702 (tt0) cc_final: 0.8353 (mt0) REVERT: E 249 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7175 (mmmt) REVERT: F 126 LEU cc_start: 0.3196 (mt) cc_final: 0.2788 (tp) REVERT: F 174 ASP cc_start: 0.6731 (p0) cc_final: 0.6480 (m-30) REVERT: F 196 LYS cc_start: 0.4311 (mmtt) cc_final: 0.3829 (tptp) REVERT: F 246 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7193 (tt) REVERT: F 249 PHE cc_start: 0.5337 (m-80) cc_final: 0.3685 (m-80) REVERT: G 190 HIS cc_start: 0.5759 (p-80) cc_final: 0.5555 (p90) REVERT: H 7 GLU cc_start: 0.7671 (mp0) cc_final: 0.6848 (pm20) REVERT: H 24 GLN cc_start: 0.8292 (tt0) cc_final: 0.8003 (mt0) REVERT: H 55 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: H 58 GLN cc_start: 0.8144 (tt0) cc_final: 0.7592 (mt0) REVERT: H 80 ARG cc_start: 0.7943 (ttp-110) cc_final: 0.7530 (mtm110) REVERT: H 122 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6945 (p0) REVERT: H 124 ASP cc_start: 0.6965 (t70) cc_final: 0.5643 (p0) REVERT: H 196 LYS cc_start: 0.5693 (mmtm) cc_final: 0.5047 (ttmm) REVERT: H 245 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7463 (p90) outliers start: 102 outliers final: 75 residues processed: 383 average time/residue: 0.1292 time to fit residues: 76.8302 Evaluate side-chains 358 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 274 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 7 optimal weight: 0.7980 chunk 250 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 195 optimal weight: 0.0000 chunk 66 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 185 optimal weight: 20.0000 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN B 220 ASN D 25 GLN D 321 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.186623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125656 restraints weight = 28218.805| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.40 r_work: 0.3392 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20723 Z= 0.111 Angle : 0.553 9.714 28038 Z= 0.273 Chirality : 0.040 0.249 3283 Planarity : 0.004 0.034 3551 Dihedral : 9.883 159.499 2890 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.39 % Allowed : 22.32 % Favored : 74.29 % 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: 0.87 (0.17), residues: 2527 helix: 1.80 (0.15), residues: 1157 sheet: 0.01 (0.24), residues: 476 loop : -0.68 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 68 TYR 0.018 0.001 TYR E 161 PHE 0.021 0.001 PHE A 509 TRP 0.010 0.001 TRP A 266 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (20723) covalent geometry : angle 0.55316 / 0.27 (28038) hydrogen bonds : bond 0.03368 / 2.28 ( 1047) hydrogen bonds : angle 4.36657 / 3.10 ( 3015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 302 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 ASP cc_start: 0.7903 (m-30) cc_final: 0.7589 (m-30) REVERT: A 383 ASP cc_start: 0.7990 (m-30) cc_final: 0.7771 (m-30) REVERT: A 462 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6846 (mttt) REVERT: A 505 MET cc_start: 0.8711 (tpp) cc_final: 0.8228 (mmt) REVERT: A 528 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6080 (tp) REVERT: A 575 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8695 (tppt) REVERT: A 588 MET cc_start: 0.7577 (mmp) cc_final: 0.6977 (mtm) REVERT: C 109 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.5930 (mptt) REVERT: C 139 LYS cc_start: 0.8787 (tppt) cc_final: 0.8531 (mptt) REVERT: C 205 MET cc_start: 0.8482 (mmm) cc_final: 0.8115 (mmt) REVERT: C 316 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7415 (t0) REVERT: D 61 MET cc_start: 0.7445 (pmm) cc_final: 0.6926 (ptp) REVERT: E 8 TYR cc_start: 0.8219 (m-80) cc_final: 0.7720 (m-10) REVERT: E 224 GLN cc_start: 0.8704 (tt0) cc_final: 0.8377 (mt0) REVERT: F 126 LEU cc_start: 0.3235 (mt) cc_final: 0.2815 (tp) REVERT: F 174 ASP cc_start: 0.6727 (p0) cc_final: 0.6473 (m-30) REVERT: F 196 LYS cc_start: 0.4249 (mmtt) cc_final: 0.3821 (tptp) REVERT: F 246 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7157 (tt) REVERT: F 249 PHE cc_start: 0.5208 (m-80) cc_final: 0.3604 (m-80) REVERT: G 8 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6933 (mp0) REVERT: G 19 PHE cc_start: 0.7009 (t80) cc_final: 0.6577 (t80) REVERT: H 7 GLU cc_start: 0.7587 (mp0) cc_final: 0.6823 (pm20) REVERT: H 24 GLN cc_start: 0.8190 (tt0) cc_final: 0.7907 (mt0) REVERT: H 55 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: H 58 GLN cc_start: 0.8017 (tt0) cc_final: 0.7574 (mt0) REVERT: H 80 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7515 (mtm110) REVERT: H 122 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6959 (p0) REVERT: H 124 ASP cc_start: 0.6910 (t70) cc_final: 0.5561 (p0) REVERT: H 196 LYS cc_start: 0.5657 (mmtm) cc_final: 0.5035 (ttmm) REVERT: H 245 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7273 (p90) outliers start: 78 outliers final: 51 residues processed: 362 average time/residue: 0.1276 time to fit residues: 72.5334 Evaluate side-chains 348 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 288 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 51 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.186087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128394 restraints weight = 28155.397| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.77 r_work: 0.3379 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20723 Z= 0.131 Angle : 0.557 8.976 28038 Z= 0.274 Chirality : 0.041 0.270 3283 Planarity : 0.004 0.034 3551 Dihedral : 9.801 156.278 2890 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.34 % Allowed : 22.28 % Favored : 74.38 % 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: 0.90 (0.17), residues: 2527 helix: 1.82 (0.15), residues: 1157 sheet: 0.03 (0.24), residues: 476 loop : -0.67 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 67 TYR 0.016 0.001 TYR H 211 PHE 0.018 0.001 PHE A 509 TRP 0.010 0.001 TRP A 266 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (20723) covalent geometry : angle 0.55733 / 0.27 (28038) hydrogen bonds : bond 0.03426 / 2.32 ( 1047) hydrogen bonds : angle 4.34192 / 3.08 ( 3015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 295 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 ASP cc_start: 0.7997 (m-30) cc_final: 0.7697 (m-30) REVERT: A 383 ASP cc_start: 0.8043 (m-30) cc_final: 0.7838 (m-30) REVERT: A 462 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6921 (mttt) REVERT: A 486 ASP cc_start: 0.7435 (m-30) cc_final: 0.7113 (t0) REVERT: A 505 MET cc_start: 0.8769 (tpp) cc_final: 0.8248 (mmt) REVERT: A 528 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6047 (tp) REVERT: A 575 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8695 (tppt) REVERT: A 588 MET cc_start: 0.7628 (mmp) cc_final: 0.7010 (mtm) REVERT: B 321 ASN cc_start: 0.7534 (m-40) cc_final: 0.7296 (m110) REVERT: C 109 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.5979 (mptt) REVERT: C 139 LYS cc_start: 0.8800 (tppt) cc_final: 0.8544 (mptt) REVERT: C 205 MET cc_start: 0.8518 (mmm) cc_final: 0.8138 (mmt) REVERT: C 316 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7477 (t0) REVERT: E 8 TYR cc_start: 0.8252 (m-80) cc_final: 0.7721 (m-10) REVERT: E 224 GLN cc_start: 0.8716 (tt0) cc_final: 0.8391 (mt0) REVERT: F 126 LEU cc_start: 0.3152 (mt) cc_final: 0.2744 (tp) REVERT: F 196 LYS cc_start: 0.4294 (mmtt) cc_final: 0.3864 (tptp) REVERT: F 239 PHE cc_start: 0.3729 (m-80) cc_final: 0.3470 (t80) REVERT: F 249 PHE cc_start: 0.5276 (m-80) cc_final: 0.3723 (m-80) REVERT: G 8 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7079 (mp0) REVERT: G 19 PHE cc_start: 0.6919 (t80) cc_final: 0.6474 (t80) REVERT: G 125 PHE cc_start: 0.6334 (OUTLIER) cc_final: 0.6010 (t80) REVERT: H 7 GLU cc_start: 0.7661 (mp0) cc_final: 0.6770 (pm20) REVERT: H 24 GLN cc_start: 0.8194 (tt0) cc_final: 0.7890 (mt0) REVERT: H 55 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: H 58 GLN cc_start: 0.8114 (tt0) cc_final: 0.7675 (mt0) REVERT: H 122 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6959 (p0) REVERT: H 124 ASP cc_start: 0.6999 (t70) cc_final: 0.5613 (p0) REVERT: H 196 LYS cc_start: 0.5683 (mmtm) cc_final: 0.5046 (ttmm) REVERT: H 245 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7297 (p90) outliers start: 77 outliers final: 60 residues processed: 354 average time/residue: 0.1248 time to fit residues: 69.1707 Evaluate side-chains 352 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 283 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 125 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.186092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.128030 restraints weight = 28101.467| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.81 r_work: 0.3360 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20723 Z= 0.132 Angle : 0.561 9.284 28038 Z= 0.276 Chirality : 0.041 0.281 3283 Planarity : 0.004 0.039 3551 Dihedral : 9.762 155.531 2890 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.47 % Allowed : 22.49 % Favored : 74.03 % 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: 0.92 (0.17), residues: 2527 helix: 1.83 (0.15), residues: 1157 sheet: 0.04 (0.24), residues: 475 loop : -0.64 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 154 TYR 0.025 0.001 TYR D 83 PHE 0.022 0.001 PHE A 722 TRP 0.012 0.001 TRP A 266 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (20723) covalent geometry : angle 0.56117 / 0.28 (28038) hydrogen bonds : bond 0.03395 / 2.31 ( 1047) hydrogen bonds : angle 4.32376 / 3.07 ( 3015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 291 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 ASP cc_start: 0.8072 (m-30) cc_final: 0.7734 (m-30) REVERT: A 383 ASP cc_start: 0.8070 (m-30) cc_final: 0.7845 (m-30) REVERT: A 486 ASP cc_start: 0.7472 (m-30) cc_final: 0.7188 (t0) REVERT: A 505 MET cc_start: 0.8796 (tpp) cc_final: 0.8267 (mmt) REVERT: A 528 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.5911 (tp) REVERT: A 575 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8634 (tppt) REVERT: A 588 MET cc_start: 0.7669 (mmp) cc_final: 0.7018 (mtm) REVERT: C 109 LYS cc_start: 0.6780 (OUTLIER) cc_final: 0.6071 (mptt) REVERT: C 139 LYS cc_start: 0.8823 (tppt) cc_final: 0.8564 (mptt) REVERT: C 316 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7502 (t0) REVERT: D 131 CYS cc_start: 0.8517 (p) cc_final: 0.7917 (p) REVERT: D 132 PRO cc_start: 0.8085 (Cg_exo) cc_final: 0.7852 (Cg_endo) REVERT: D 188 ARG cc_start: 0.7072 (ttt-90) cc_final: 0.6659 (ttp80) REVERT: E 8 TYR cc_start: 0.8257 (m-80) cc_final: 0.7691 (m-10) REVERT: E 224 GLN cc_start: 0.8682 (tt0) cc_final: 0.8339 (mt0) REVERT: F 126 LEU cc_start: 0.3203 (mt) cc_final: 0.2788 (tp) REVERT: F 196 LYS cc_start: 0.4259 (mmtt) cc_final: 0.3815 (tptp) REVERT: F 239 PHE cc_start: 0.3720 (m-80) cc_final: 0.3419 (t80) REVERT: F 249 PHE cc_start: 0.5278 (m-80) cc_final: 0.3705 (m-80) REVERT: G 19 PHE cc_start: 0.6942 (t80) cc_final: 0.6501 (t80) REVERT: G 48 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7496 (p) REVERT: G 125 PHE cc_start: 0.6285 (OUTLIER) cc_final: 0.5954 (t80) REVERT: H 7 GLU cc_start: 0.7714 (mp0) cc_final: 0.6793 (pm20) REVERT: H 24 GLN cc_start: 0.8198 (tt0) cc_final: 0.7857 (mt0) REVERT: H 55 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: H 58 GLN cc_start: 0.8096 (tt0) cc_final: 0.7602 (mt0) REVERT: H 80 ARG cc_start: 0.7882 (ttp-110) cc_final: 0.7457 (mtm110) REVERT: H 122 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6954 (p0) REVERT: H 124 ASP cc_start: 0.6999 (t70) cc_final: 0.5565 (p0) REVERT: H 196 LYS cc_start: 0.5604 (mmtm) cc_final: 0.4970 (ttmm) outliers start: 80 outliers final: 63 residues processed: 349 average time/residue: 0.1202 time to fit residues: 65.6303 Evaluate side-chains 351 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 280 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 29 optimal weight: 0.0020 chunk 215 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 158 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 GLN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.187187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127689 restraints weight = 28312.782| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.15 r_work: 0.3339 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20723 Z= 0.114 Angle : 0.557 9.302 28038 Z= 0.275 Chirality : 0.041 0.285 3283 Planarity : 0.004 0.045 3551 Dihedral : 9.720 154.804 2890 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.17 % Allowed : 22.84 % Favored : 73.99 % 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: 0.97 (0.17), residues: 2527 helix: 1.86 (0.15), residues: 1158 sheet: 0.05 (0.24), residues: 476 loop : -0.60 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 154 TYR 0.015 0.001 TYR D 83 PHE 0.020 0.001 PHE A 722 TRP 0.012 0.001 TRP A 266 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (20723) covalent geometry : angle 0.55743 / 0.27 (28038) hydrogen bonds : bond 0.03265 / 2.20 ( 1047) hydrogen bonds : angle 4.29713 / 3.05 ( 3015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 294 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8124 (mmt-90) cc_final: 0.7640 (mmp80) REVERT: A 379 ASP cc_start: 0.8108 (m-30) cc_final: 0.7772 (m-30) REVERT: A 383 ASP cc_start: 0.8080 (m-30) cc_final: 0.7855 (m-30) REVERT: A 486 ASP cc_start: 0.7480 (m-30) cc_final: 0.7197 (t0) REVERT: A 505 MET cc_start: 0.8786 (tpp) cc_final: 0.8267 (mmt) REVERT: A 528 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5767 (tp) REVERT: A 575 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8615 (tppt) REVERT: A 588 MET cc_start: 0.7673 (mmp) cc_final: 0.6982 (mtm) REVERT: C 109 LYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6047 (mptt) REVERT: C 209 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8673 (mm) REVERT: C 316 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7468 (t0) REVERT: D 131 CYS cc_start: 0.8507 (p) cc_final: 0.7951 (p) REVERT: D 132 PRO cc_start: 0.8046 (Cg_exo) cc_final: 0.7709 (Cg_endo) REVERT: D 157 MET cc_start: 0.6784 (ptt) cc_final: 0.5959 (tpp) REVERT: D 160 TYR cc_start: 0.6864 (m-80) cc_final: 0.6632 (m-80) REVERT: D 188 ARG cc_start: 0.7089 (ttt-90) cc_final: 0.6678 (ttp80) REVERT: E 8 TYR cc_start: 0.8254 (m-80) cc_final: 0.7679 (m-10) REVERT: E 224 GLN cc_start: 0.8673 (tt0) cc_final: 0.8327 (mt0) REVERT: F 126 LEU cc_start: 0.3285 (mt) cc_final: 0.2863 (tp) REVERT: F 196 LYS cc_start: 0.4243 (mmtt) cc_final: 0.3796 (tptp) REVERT: F 239 PHE cc_start: 0.3682 (m-80) cc_final: 0.3396 (t80) REVERT: F 249 PHE cc_start: 0.5211 (m-80) cc_final: 0.3635 (m-80) REVERT: G 19 PHE cc_start: 0.6993 (t80) cc_final: 0.6550 (t80) REVERT: G 48 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7570 (p) REVERT: G 125 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5946 (t80) REVERT: G 165 GLU cc_start: 0.5679 (tp30) cc_final: 0.5169 (tm-30) REVERT: H 7 GLU cc_start: 0.7730 (mp0) cc_final: 0.6783 (pm20) REVERT: H 24 GLN cc_start: 0.8262 (tt0) cc_final: 0.7886 (mt0) REVERT: H 58 GLN cc_start: 0.8098 (tt0) cc_final: 0.7693 (mt0) REVERT: H 80 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7498 (mtm110) REVERT: H 122 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6980 (p0) REVERT: H 124 ASP cc_start: 0.7004 (t70) cc_final: 0.5599 (p0) REVERT: H 196 LYS cc_start: 0.5603 (mmtm) cc_final: 0.4972 (ttmm) REVERT: H 245 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7180 (p90) outliers start: 73 outliers final: 59 residues processed: 352 average time/residue: 0.1143 time to fit residues: 63.4541 Evaluate side-chains 348 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 280 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 180 optimal weight: 20.0000 chunk 96 optimal weight: 0.0010 chunk 154 optimal weight: 3.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.187007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128421 restraints weight = 28317.635| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.14 r_work: 0.3332 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 20723 Z= 0.135 Angle : 0.714 59.199 28038 Z= 0.383 Chirality : 0.041 0.232 3283 Planarity : 0.004 0.045 3551 Dihedral : 9.720 154.887 2890 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.08 % Allowed : 23.23 % Favored : 73.69 % 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: 0.95 (0.17), residues: 2527 helix: 1.85 (0.15), residues: 1158 sheet: 0.04 (0.24), residues: 476 loop : -0.60 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 154 TYR 0.018 0.001 TYR D 83 PHE 0.018 0.001 PHE A 722 TRP 0.010 0.001 TRP A 266 HIS 0.006 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (20723) covalent geometry : angle 0.71406 / 0.38 (28038) hydrogen bonds : bond 0.03272 / 2.21 ( 1047) hydrogen bonds : angle 4.29618 / 3.05 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4457.42 seconds wall clock time: 77 minutes 3.51 seconds (4623.51 seconds total)