Starting phenix.real_space_refine on Tue May 20 19:47:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thd_41254/05_2025/8thd_41254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thd_41254/05_2025/8thd_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_41254/05_2025/8thd_41254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thd_41254/05_2025/8thd_41254.map" model { file = "/net/cci-nas-00/data/ceres_data/8thd_41254/05_2025/8thd_41254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thd_41254/05_2025/8thd_41254.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.03, per 1000 atoms: 0.64 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: 5.39 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.37 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: 7.72 Time building geometry restraints manager: 6.26 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=" C PRO D 132 " pdb=" O PRO D 132 " ideal model delta sigma weight residual 1.246 1.213 0.033 8.50e-03 1.38e+04 1.47e+01 bond pdb=" CA PRO D 132 " pdb=" C PRO D 132 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.23e+01 bond pdb=" N ARG D 101 " pdb=" CA ARG D 101 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.21e-02 6.83e+03 8.55e+00 bond pdb=" N GLY C 110 " pdb=" CA GLY C 110 " ideal model delta sigma weight residual 1.450 1.476 -0.026 9.10e-03 1.21e+04 8.11e+00 bond pdb=" N ILE E 96 " pdb=" CA ILE E 96 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 8.05e+00 ... (remaining 20718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 27441 1.96 - 3.92: 503 3.92 - 5.88: 76 5.88 - 7.83: 13 7.83 - 9.79: 5 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=" C GLN E 32 " pdb=" CA GLN E 32 " pdb=" CB GLN E 32 " ideal model delta sigma weight residual 110.33 113.95 -3.62 1.02e+00 9.61e-01 1.26e+01 ... (remaining 28033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 11840 25.07 - 50.14: 812 50.14 - 75.21: 133 75.21 - 100.28: 8 100.28 - 125.35: 1 Dihedral angle restraints: 12794 sinusoidal: 5292 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=" CA LEU D 58 " pdb=" C LEU D 58 " pdb=" N PRO D 59 " pdb=" CA PRO D 59 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE C 331 " pdb=" C PHE C 331 " pdb=" N GLU C 332 " pdb=" CA GLU C 332 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 12791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2729 0.054 - 0.107: 477 0.107 - 0.161: 77 0.161 - 0.215: 7 0.215 - 0.268: 1 Chirality restraints: 3291 Sorted by residual: 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=" CA ILE E 96 " pdb=" N ILE E 96 " pdb=" C ILE E 96 " pdb=" CB ILE E 96 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE C 106 " pdb=" N ILE C 106 " pdb=" C ILE C 106 " pdb=" CB ILE C 106 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3288 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 48.620 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 20723 Z= 0.185 Angle : 0.652 9.794 28038 Z= 0.370 Chirality : 0.042 0.268 3291 Planarity : 0.005 0.090 3551 Dihedral : 16.149 125.349 7896 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP A 488 HIS 0.004 0.001 HIS D 124 PHE 0.025 0.001 PHE A 509 TYR 0.016 0.001 TYR D 64 ARG 0.010 0.001 ARG G 149 Details of bonding type rmsd hydrogen bonds : bond 0.17325 ( 1047) hydrogen bonds : angle 6.77174 ( 3015) covalent geometry : bond 0.00312 (20723) covalent geometry : angle 0.65205 (28038) *********************** 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 : 2.333 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: 0.6581 (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: 0.8101 (mm-40) cc_final: 0.7671 (mm-40) REVERT: C 109 LYS cc_start: 0.6744 (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: 0.6737 (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: 0.5839 (ttpt) outliers start: 10 outliers final: 2 residues processed: 660 average time/residue: 0.3387 time to fit residues: 329.4677 Evaluate side-chains 365 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 361 time to evaluate : 2.421 ------------------------------------------------------------------------------- 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 211 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 128 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.188653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126368 restraints weight = 28037.640| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.47 r_work: 0.3415 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20723 Z= 0.195 Angle : 0.656 10.707 28038 Z= 0.329 Chirality : 0.044 0.225 3291 Planarity : 0.005 0.054 3551 Dihedral : 7.558 115.719 2825 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.95 % Allowed : 17.98 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2527 helix: 1.39 (0.15), residues: 1152 sheet: 0.07 (0.25), residues: 455 loop : -1.07 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 420 HIS 0.004 0.001 HIS G 190 PHE 0.027 0.002 PHE A 509 TYR 0.020 0.002 TYR D 160 ARG 0.012 0.001 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 1047) hydrogen bonds : angle 5.06847 ( 3015) covalent geometry : bond 0.00455 (20723) covalent geometry : angle 0.65595 (28038) *********************** 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 477 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 386 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6835 (tp40) REVERT: A 359 ASN cc_start: 0.7604 (p0) cc_final: 0.7223 (t0) REVERT: A 361 TYR cc_start: 0.8966 (p90) cc_final: 0.8527 (p90) REVERT: A 505 MET cc_start: 0.9022 (tpp) cc_final: 0.8454 (mmt) REVERT: A 588 MET cc_start: 0.7487 (mmp) cc_final: 0.6743 (mtm) REVERT: B 115 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8120 (mt-10) REVERT: C 109 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.5835 (mptt) REVERT: C 139 LYS cc_start: 0.8904 (tppt) cc_final: 0.8586 (mptt) REVERT: C 140 ASN cc_start: 0.7985 (t0) cc_final: 0.7707 (t0) REVERT: C 316 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7762 (t0) REVERT: D 132 PRO cc_start: 0.8047 (Cg_exo) cc_final: 0.7814 (Cg_endo) REVERT: D 157 MET cc_start: 0.7164 (ptt) cc_final: 0.6610 (ptt) REVERT: D 249 LYS cc_start: 0.8537 (mttt) cc_final: 0.8049 (mtpt) REVERT: E 8 TYR cc_start: 0.8278 (m-80) cc_final: 0.7728 (m-10) REVERT: E 217 ASP cc_start: 0.8016 (t0) cc_final: 0.7749 (t0) REVERT: F 70 MET cc_start: 0.1986 (mtp) cc_final: 0.1469 (mtp) REVERT: F 174 ASP cc_start: 0.6559 (p0) cc_final: 0.6274 (m-30) REVERT: F 196 LYS cc_start: 0.4270 (mmtt) cc_final: 0.3824 (tptp) REVERT: F 249 PHE cc_start: 0.5534 (m-80) cc_final: 0.3924 (m-80) REVERT: G 1 MET cc_start: 0.3249 (mtt) cc_final: 0.2963 (mtt) REVERT: G 8 GLU cc_start: 0.5822 (tp30) cc_final: 0.5202 (tm-30) REVERT: G 63 ASP cc_start: 0.5342 (p0) cc_final: 0.5029 (p0) REVERT: G 190 HIS cc_start: 0.4851 (p90) cc_final: 0.4570 (p-80) REVERT: H 7 GLU cc_start: 0.7413 (mp0) cc_final: 0.6795 (tt0) REVERT: H 24 GLN cc_start: 0.8075 (tt0) cc_final: 0.7769 (mt0) REVERT: H 58 GLN cc_start: 0.8019 (tt0) cc_final: 0.7583 (mt0) REVERT: H 146 LYS cc_start: 0.8090 (tptm) cc_final: 0.7854 (tptm) REVERT: H 196 LYS cc_start: 0.5372 (mmtm) cc_final: 0.4830 (ttmm) REVERT: H 245 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6929 (p90) outliers start: 91 outliers final: 42 residues processed: 451 average time/residue: 0.3127 time to fit residues: 217.2567 Evaluate side-chains 365 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 319 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 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 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 171 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 133 optimal weight: 0.4980 chunk 156 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 190 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 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** A 711 GLN B 41 ASN C 140 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 ASN E 18 HIS E 317 ASN H 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.189487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127904 restraints weight = 27782.410| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.42 r_work: 0.3439 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3380 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= 0.128 Angle : 0.568 9.595 28038 Z= 0.284 Chirality : 0.041 0.202 3291 Planarity : 0.004 0.042 3551 Dihedral : 7.335 115.396 2821 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.30 % Allowed : 19.28 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2527 helix: 1.58 (0.15), residues: 1158 sheet: 0.11 (0.24), residues: 458 loop : -0.94 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 11 HIS 0.003 0.001 HIS A 506 PHE 0.021 0.001 PHE A 509 TYR 0.018 0.001 TYR E 8 ARG 0.005 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 1047) hydrogen bonds : angle 4.75003 ( 3015) covalent geometry : bond 0.00295 (20723) covalent geometry : angle 0.56785 (28038) *********************** 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 426 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 350 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ASN cc_start: 0.7580 (p0) cc_final: 0.7229 (t0) REVERT: A 361 TYR cc_start: 0.8932 (p90) cc_final: 0.8628 (p90) REVERT: A 505 MET cc_start: 0.8908 (tpp) cc_final: 0.8327 (mmt) REVERT: A 528 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6181 (tp) REVERT: A 588 MET cc_start: 0.7493 (mmp) cc_final: 0.6758 (mtm) REVERT: B 115 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8073 (mt-10) REVERT: B 199 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7268 (mm-30) REVERT: C 99 ASP cc_start: 0.8619 (m-30) cc_final: 0.8364 (m-30) REVERT: C 109 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.5791 (mptt) REVERT: C 139 LYS cc_start: 0.8781 (tppt) cc_final: 0.8539 (mptt) REVERT: C 316 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7613 (t0) REVERT: D 61 MET cc_start: 0.7298 (pmm) cc_final: 0.6973 (ptt) REVERT: D 131 CYS cc_start: 0.8179 (p) cc_final: 0.6844 (t) REVERT: D 188 ARG cc_start: 0.6788 (ttt-90) cc_final: 0.6415 (ttt-90) REVERT: E 67 ARG cc_start: 0.8164 (mtp-110) cc_final: 0.7837 (mtt90) REVERT: E 100 ASP cc_start: 0.7611 (t0) cc_final: 0.7387 (t0) REVERT: F 126 LEU cc_start: 0.2999 (mt) cc_final: 0.2622 (tp) REVERT: F 174 ASP cc_start: 0.6598 (p0) cc_final: 0.6343 (m-30) REVERT: F 196 LYS cc_start: 0.4306 (mmtt) cc_final: 0.3839 (tptp) REVERT: F 249 PHE cc_start: 0.5415 (m-80) cc_final: 0.3902 (m-80) REVERT: G 1 MET cc_start: 0.3261 (mtt) cc_final: 0.3047 (mtt) REVERT: G 63 ASP cc_start: 0.5306 (p0) cc_final: 0.5071 (p0) REVERT: G 190 HIS cc_start: 0.4951 (p90) cc_final: 0.4665 (p-80) REVERT: H 7 GLU cc_start: 0.7391 (mp0) cc_final: 0.6820 (tt0) REVERT: H 24 GLN cc_start: 0.8149 (tt0) cc_final: 0.7843 (mt0) REVERT: H 44 ARG cc_start: 0.8307 (mtt90) cc_final: 0.7989 (mtt180) REVERT: H 58 GLN cc_start: 0.8006 (tt0) cc_final: 0.7691 (mt0) REVERT: H 196 LYS cc_start: 0.5244 (mmtm) cc_final: 0.4870 (ttmm) REVERT: H 245 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6858 (p90) outliers start: 76 outliers final: 46 residues processed: 403 average time/residue: 0.3113 time to fit residues: 194.2772 Evaluate side-chains 360 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 310 time to evaluate : 2.445 ------------------------------------------------------------------------------- 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 239 LEU Chi-restraints excluded: chain A residue 250 LEU 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 479 SER 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 81 GLU 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 316 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 ILE 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 203 VAL 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 181 ILE Chi-restraints excluded: chain G residue 206 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 43 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 167 optimal weight: 0.0770 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 60 optimal weight: 0.0870 chunk 74 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN A 622 GLN A 711 GLN B 250 GLN D 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.184279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136545 restraints weight = 28138.968| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.75 r_work: 0.3323 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20723 Z= 0.129 Angle : 0.552 9.947 28038 Z= 0.275 Chirality : 0.041 0.199 3291 Planarity : 0.004 0.039 3551 Dihedral : 7.205 114.760 2818 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.65 % Allowed : 19.84 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2527 helix: 1.63 (0.15), residues: 1160 sheet: 0.14 (0.24), residues: 459 loop : -0.87 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 780 HIS 0.003 0.001 HIS A 506 PHE 0.019 0.001 PHE A 509 TYR 0.016 0.001 TYR D 244 ARG 0.008 0.000 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 1047) hydrogen bonds : angle 4.53470 ( 3015) covalent geometry : bond 0.00299 (20723) covalent geometry : angle 0.55187 (28038) *********************** 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 420 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 336 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 ASP cc_start: 0.8018 (m-30) cc_final: 0.7794 (m-30) REVERT: A 505 MET cc_start: 0.8746 (tpp) cc_final: 0.8186 (mmt) REVERT: A 588 MET cc_start: 0.7610 (mmp) cc_final: 0.6850 (mtm) REVERT: B 94 LYS cc_start: 0.9014 (ttpp) cc_final: 0.8811 (ttpp) REVERT: B 204 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8437 (tp-100) REVERT: C 99 ASP cc_start: 0.8513 (m-30) cc_final: 0.8309 (m-30) REVERT: C 109 LYS cc_start: 0.6591 (OUTLIER) cc_final: 0.5776 (mptt) REVERT: C 316 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7611 (t0) REVERT: D 81 GLU cc_start: 0.7650 (tt0) cc_final: 0.7308 (mt-10) REVERT: D 131 CYS cc_start: 0.8260 (p) cc_final: 0.7059 (t) REVERT: D 188 ARG cc_start: 0.6858 (ttt-90) cc_final: 0.6617 (ttt-90) REVERT: E 224 GLN cc_start: 0.8790 (tt0) cc_final: 0.8429 (mt0) REVERT: E 249 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7165 (mmmt) REVERT: F 50 LEU cc_start: 0.8036 (pp) cc_final: 0.7540 (mt) REVERT: F 126 LEU cc_start: 0.3121 (mt) cc_final: 0.2703 (tp) REVERT: F 174 ASP cc_start: 0.6590 (p0) cc_final: 0.6320 (m-30) REVERT: F 196 LYS cc_start: 0.4300 (mmtt) cc_final: 0.3797 (tptp) REVERT: F 246 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.6902 (tt) REVERT: F 249 PHE cc_start: 0.5340 (m-80) cc_final: 0.3776 (m-80) REVERT: G 8 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6681 (tm-30) REVERT: G 63 ASP cc_start: 0.5406 (p0) cc_final: 0.5200 (p0) REVERT: G 190 HIS cc_start: 0.5014 (p90) cc_final: 0.4681 (p-80) REVERT: H 7 GLU cc_start: 0.7339 (mp0) cc_final: 0.6842 (tt0) REVERT: H 24 GLN cc_start: 0.8173 (tt0) cc_final: 0.7933 (mt0) REVERT: H 44 ARG cc_start: 0.8334 (mtt90) cc_final: 0.8123 (mtt180) REVERT: H 58 GLN cc_start: 0.7903 (tt0) cc_final: 0.7693 (mt0) REVERT: H 80 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7447 (mtm110) REVERT: H 124 ASP cc_start: 0.6623 (t70) cc_final: 0.5362 (p0) REVERT: H 196 LYS cc_start: 0.5602 (mmtm) cc_final: 0.5022 (ttmm) REVERT: H 245 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7136 (p90) outliers start: 84 outliers final: 53 residues processed: 397 average time/residue: 0.3188 time to fit residues: 195.1573 Evaluate side-chains 363 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 306 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 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 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 224 SER Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 275 VAL 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 E residue 333 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 36 ILE 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 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 30 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 99 optimal weight: 0.9980 chunk 208 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.184214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136564 restraints weight = 27886.732| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.68 r_work: 0.3346 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20723 Z= 0.116 Angle : 0.528 11.382 28038 Z= 0.263 Chirality : 0.040 0.203 3291 Planarity : 0.003 0.033 3551 Dihedral : 7.081 114.530 2818 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.39 % Allowed : 20.36 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2527 helix: 1.74 (0.15), residues: 1158 sheet: 0.16 (0.24), residues: 464 loop : -0.79 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 266 HIS 0.003 0.001 HIS A 506 PHE 0.031 0.001 PHE G 19 TYR 0.024 0.001 TYR H 211 ARG 0.007 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 1047) hydrogen bonds : angle 4.38226 ( 3015) covalent geometry : bond 0.00267 (20723) covalent geometry : angle 0.52759 (28038) *********************** 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 416 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 338 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.8677 (tpp) cc_final: 0.8123 (mmt) REVERT: A 528 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6181 (tp) REVERT: A 588 MET cc_start: 0.7536 (mmp) cc_final: 0.6788 (mtm) REVERT: C 99 ASP cc_start: 0.8441 (m-30) cc_final: 0.8236 (m-30) REVERT: C 109 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.5754 (mptt) REVERT: C 316 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7498 (t0) REVERT: D 81 GLU cc_start: 0.7595 (tt0) cc_final: 0.7156 (mt-10) REVERT: D 134 TYR cc_start: 0.5240 (p90) cc_final: 0.5010 (p90) REVERT: D 188 ARG cc_start: 0.6944 (ttt-90) cc_final: 0.6721 (ttt-90) REVERT: E 8 TYR cc_start: 0.8222 (m-80) cc_final: 0.7732 (m-10) REVERT: E 224 GLN cc_start: 0.8705 (tt0) cc_final: 0.8418 (mt0) REVERT: E 249 LYS cc_start: 0.7721 (mtpp) cc_final: 0.7146 (mmmt) REVERT: F 126 LEU cc_start: 0.3089 (mt) cc_final: 0.2683 (tp) REVERT: F 174 ASP cc_start: 0.6595 (p0) cc_final: 0.6294 (m-30) REVERT: F 196 LYS cc_start: 0.4376 (mmtt) cc_final: 0.3875 (tptp) REVERT: F 246 LEU cc_start: 0.7584 (tt) cc_final: 0.7271 (tt) REVERT: F 249 PHE cc_start: 0.5322 (m-80) cc_final: 0.3800 (m-80) REVERT: G 190 HIS cc_start: 0.5032 (p90) cc_final: 0.4828 (p90) REVERT: H 7 GLU cc_start: 0.7318 (mp0) cc_final: 0.6437 (pm20) REVERT: H 24 GLN cc_start: 0.8151 (tt0) cc_final: 0.7920 (mt0) REVERT: H 58 GLN cc_start: 0.7874 (tt0) cc_final: 0.7665 (mt0) REVERT: H 80 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7414 (mtm110) REVERT: H 122 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6983 (p0) REVERT: H 124 ASP cc_start: 0.6657 (t70) cc_final: 0.5345 (p0) REVERT: H 196 LYS cc_start: 0.5585 (mmtm) cc_final: 0.5029 (ttmm) REVERT: H 245 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7052 (p90) outliers start: 78 outliers final: 48 residues processed: 394 average time/residue: 0.3252 time to fit residues: 196.9276 Evaluate side-chains 365 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 2.527 ------------------------------------------------------------------------------- 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 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 528 LEU Chi-restraints excluded: chain B residue 45 MET 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 90 ILE 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 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 28 VAL Chi-restraints excluded: chain D residue 58 LEU 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 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 F residue 28 PHE Chi-restraints excluded: chain F residue 188 MET 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 165 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN ** D 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.184712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126656 restraints weight = 28345.547| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.86 r_work: 0.3326 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20723 Z= 0.209 Angle : 0.607 10.252 28038 Z= 0.300 Chirality : 0.043 0.206 3291 Planarity : 0.004 0.037 3551 Dihedral : 7.245 116.304 2818 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.26 % Allowed : 20.76 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2527 helix: 1.59 (0.15), residues: 1160 sheet: 0.05 (0.24), residues: 467 loop : -0.74 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 510 HIS 0.004 0.001 HIS B 44 PHE 0.044 0.002 PHE G 19 TYR 0.023 0.002 TYR H 211 ARG 0.007 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 1047) hydrogen bonds : angle 4.47175 ( 3015) covalent geometry : bond 0.00508 (20723) covalent geometry : angle 0.60742 (28038) *********************** 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 421 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 323 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8096 (mmt-90) cc_final: 0.7705 (mmp80) REVERT: A 383 ASP cc_start: 0.8026 (m-30) cc_final: 0.7824 (m-30) REVERT: A 505 MET cc_start: 0.8877 (tpp) cc_final: 0.8284 (mmt) REVERT: A 528 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6056 (tp) REVERT: A 588 MET cc_start: 0.7648 (mmp) cc_final: 0.6940 (mtm) REVERT: B 188 ASN cc_start: 0.8067 (m-40) cc_final: 0.7858 (m-40) REVERT: C 109 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.5904 (mptt) REVERT: C 205 MET cc_start: 0.8622 (mmm) cc_final: 0.8391 (mmt) REVERT: C 316 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7674 (t0) REVERT: D 81 GLU cc_start: 0.7515 (tt0) cc_final: 0.6999 (mt-10) REVERT: D 131 CYS cc_start: 0.8444 (p) cc_final: 0.7280 (t) REVERT: D 134 TYR cc_start: 0.5319 (p90) cc_final: 0.5040 (p90) REVERT: D 188 ARG cc_start: 0.7087 (ttt-90) cc_final: 0.6843 (ttt-90) REVERT: E 8 TYR cc_start: 0.8267 (m-80) cc_final: 0.7706 (m-10) REVERT: E 224 GLN cc_start: 0.8667 (tt0) cc_final: 0.8367 (mt0) REVERT: E 249 LYS cc_start: 0.7724 (mtpp) cc_final: 0.7149 (mmmt) REVERT: F 126 LEU cc_start: 0.3099 (mt) cc_final: 0.2730 (tp) REVERT: F 174 ASP cc_start: 0.6736 (p0) cc_final: 0.6484 (m-30) REVERT: F 196 LYS cc_start: 0.4341 (mmtt) cc_final: 0.3911 (tptp) REVERT: F 246 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7319 (tt) REVERT: F 249 PHE cc_start: 0.5365 (m-80) cc_final: 0.3820 (m-80) REVERT: G 125 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5891 (t80) REVERT: G 190 HIS cc_start: 0.5027 (p90) cc_final: 0.4618 (p-80) REVERT: H 7 GLU cc_start: 0.7657 (mp0) cc_final: 0.6746 (pm20) REVERT: H 24 GLN cc_start: 0.8251 (tt0) cc_final: 0.7936 (mt0) REVERT: H 58 GLN cc_start: 0.8143 (tt0) cc_final: 0.7699 (mt0) REVERT: H 122 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6998 (p0) REVERT: H 124 ASP cc_start: 0.6832 (t70) cc_final: 0.5539 (p0) REVERT: H 196 LYS cc_start: 0.5484 (mmtm) cc_final: 0.4988 (ttmm) REVERT: H 245 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.7113 (p90) outliers start: 98 outliers final: 70 residues processed: 395 average time/residue: 0.3052 time to fit residues: 185.9438 Evaluate side-chains 377 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 300 time to evaluate : 2.172 ------------------------------------------------------------------------------- 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 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 485 CYS 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 596 ILE Chi-restraints excluded: chain A residue 600 LEU 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 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 321 ASN 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 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 58 LEU 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 353 LEU Chi-restraints excluded: chain F residue 21 ASP 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 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 125 PHE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 21 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 176 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN B 250 GLN ** D 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.182262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126281 restraints weight = 28207.510| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.69 r_work: 0.3294 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20723 Z= 0.229 Angle : 0.634 10.758 28038 Z= 0.317 Chirality : 0.044 0.247 3291 Planarity : 0.004 0.038 3551 Dihedral : 7.417 116.008 2818 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.30 % Allowed : 21.28 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2527 helix: 1.48 (0.15), residues: 1158 sheet: -0.07 (0.24), residues: 473 loop : -0.74 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 510 HIS 0.004 0.001 HIS G 64 PHE 0.019 0.002 PHE A 509 TYR 0.022 0.002 TYR H 211 ARG 0.009 0.001 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1047) hydrogen bonds : angle 4.56793 ( 3015) covalent geometry : bond 0.00553 (20723) covalent geometry : angle 0.63423 (28038) *********************** 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 400 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 301 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7021 (mttt) REVERT: A 505 MET cc_start: 0.8831 (tpp) cc_final: 0.8347 (mmt) REVERT: A 528 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6206 (tp) REVERT: A 588 MET cc_start: 0.7713 (mmp) cc_final: 0.7128 (mtm) REVERT: C 109 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.5956 (mptt) REVERT: C 316 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7665 (t0) REVERT: D 61 MET cc_start: 0.7665 (pmm) cc_final: 0.7046 (ptp) REVERT: D 81 GLU cc_start: 0.7546 (tt0) cc_final: 0.7096 (mt-10) REVERT: D 145 MET cc_start: 0.1778 (mmm) cc_final: 0.1569 (mmt) REVERT: D 188 ARG cc_start: 0.7144 (ttt-90) cc_final: 0.6912 (ttt-90) REVERT: E 135 TYR cc_start: 0.8741 (p90) cc_final: 0.8428 (p90) REVERT: E 224 GLN cc_start: 0.8725 (tt0) cc_final: 0.8403 (mt0) REVERT: E 249 LYS cc_start: 0.7774 (mtpp) cc_final: 0.7233 (mmmt) REVERT: F 126 LEU cc_start: 0.3147 (mt) cc_final: 0.2751 (tp) REVERT: F 196 LYS cc_start: 0.4233 (mmtt) cc_final: 0.3813 (tptp) REVERT: F 249 PHE cc_start: 0.5329 (m-80) cc_final: 0.3623 (m-80) REVERT: G 19 PHE cc_start: 0.7121 (t80) cc_final: 0.6898 (t80) REVERT: G 125 PHE cc_start: 0.6268 (OUTLIER) cc_final: 0.5930 (t80) REVERT: G 232 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6382 (tm-30) REVERT: H 7 GLU cc_start: 0.7692 (mp0) cc_final: 0.6857 (pm20) REVERT: H 24 GLN cc_start: 0.8207 (tt0) cc_final: 0.7956 (mt0) REVERT: H 55 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: H 58 GLN cc_start: 0.8186 (tt0) cc_final: 0.7624 (mt0) REVERT: H 80 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7434 (mtm110) REVERT: H 122 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6987 (p0) REVERT: H 124 ASP cc_start: 0.7003 (t70) cc_final: 0.5614 (p0) REVERT: H 196 LYS cc_start: 0.5815 (mmtm) cc_final: 0.5196 (ttmm) REVERT: H 224 ARG cc_start: 0.6942 (mtp85) cc_final: 0.6597 (mtp85) REVERT: H 245 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7534 (p90) outliers start: 99 outliers final: 68 residues processed: 374 average time/residue: 0.3243 time to fit residues: 188.3604 Evaluate side-chains 353 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 277 time to evaluate : 2.498 ------------------------------------------------------------------------------- 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 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 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 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 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 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 353 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 67 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 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 151 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 215 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 213 optimal weight: 30.0000 chunk 238 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.181920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124768 restraints weight = 28459.413| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.97 r_work: 0.3283 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20723 Z= 0.228 Angle : 0.634 9.579 28038 Z= 0.315 Chirality : 0.044 0.232 3291 Planarity : 0.004 0.045 3551 Dihedral : 7.499 115.737 2818 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.73 % Allowed : 22.15 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2527 helix: 1.45 (0.15), residues: 1157 sheet: -0.07 (0.24), residues: 476 loop : -0.76 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 510 HIS 0.005 0.001 HIS G 64 PHE 0.020 0.002 PHE C 331 TYR 0.021 0.002 TYR H 211 ARG 0.011 0.001 ARG D 165 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 1047) hydrogen bonds : angle 4.55038 ( 3015) covalent geometry : bond 0.00552 (20723) covalent geometry : angle 0.63439 (28038) *********************** 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 368 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 282 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6956 (mttt) REVERT: A 505 MET cc_start: 0.8882 (tpp) cc_final: 0.8401 (mmt) REVERT: A 528 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.5961 (tp) REVERT: A 588 MET cc_start: 0.7771 (mmp) cc_final: 0.7148 (mtm) REVERT: C 109 LYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6061 (mptt) REVERT: C 316 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7666 (t0) REVERT: D 61 MET cc_start: 0.7615 (pmm) cc_final: 0.6961 (ptp) REVERT: D 81 GLU cc_start: 0.7583 (tt0) cc_final: 0.7040 (mt-10) REVERT: D 131 CYS cc_start: 0.8659 (p) cc_final: 0.7461 (t) REVERT: D 132 PRO cc_start: 0.8272 (Cg_exo) cc_final: 0.8051 (Cg_endo) REVERT: D 188 ARG cc_start: 0.7254 (ttt-90) cc_final: 0.7010 (ttt-90) REVERT: E 224 GLN cc_start: 0.8750 (tt0) cc_final: 0.8396 (mt0) REVERT: F 126 LEU cc_start: 0.3206 (mt) cc_final: 0.2820 (tp) REVERT: F 196 LYS cc_start: 0.4331 (mmtt) cc_final: 0.3895 (tptp) REVERT: F 249 PHE cc_start: 0.5369 (m-80) cc_final: 0.3704 (m-80) REVERT: G 125 PHE cc_start: 0.6330 (OUTLIER) cc_final: 0.5970 (t80) REVERT: G 232 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6165 (tm-30) REVERT: H 7 GLU cc_start: 0.7896 (mp0) cc_final: 0.6987 (pm20) REVERT: H 24 GLN cc_start: 0.8257 (tt0) cc_final: 0.7755 (mt0) REVERT: H 55 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: H 58 GLN cc_start: 0.8291 (tt0) cc_final: 0.7639 (mt0) REVERT: H 80 ARG cc_start: 0.8014 (ttp-110) cc_final: 0.7619 (mtm110) REVERT: H 122 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6962 (p0) REVERT: H 124 ASP cc_start: 0.7089 (t70) cc_final: 0.5527 (p0) REVERT: H 161 MET cc_start: 0.6094 (ttt) cc_final: 0.5816 (ttt) REVERT: H 196 LYS cc_start: 0.5624 (mmtm) cc_final: 0.5002 (ttmm) REVERT: H 245 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7449 (p90) outliers start: 86 outliers final: 69 residues processed: 348 average time/residue: 0.3139 time to fit residues: 169.2342 Evaluate side-chains 353 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 276 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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 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 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 596 ILE Chi-restraints excluded: chain A residue 600 LEU 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 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 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 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 266 ASP Chi-restraints excluded: chain D residue 330 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 1 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 154 LEU 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 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 203 VAL Chi-restraints excluded: chain H residue 225 VAL 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 2 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 135 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 224 optimal weight: 5.9990 chunk 147 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN A 406 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.184828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135475 restraints weight = 28148.123| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.86 r_work: 0.3353 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20723 Z= 0.126 Angle : 0.575 9.147 28038 Z= 0.284 Chirality : 0.041 0.197 3291 Planarity : 0.004 0.042 3551 Dihedral : 7.321 114.321 2818 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.21 % Allowed : 22.67 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2527 helix: 1.67 (0.15), residues: 1157 sheet: -0.01 (0.24), residues: 476 loop : -0.72 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 266 HIS 0.004 0.001 HIS E 18 PHE 0.022 0.001 PHE A 722 TYR 0.019 0.001 TYR E 161 ARG 0.010 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 1047) hydrogen bonds : angle 4.37971 ( 3015) covalent geometry : bond 0.00293 (20723) covalent geometry : angle 0.57515 (28038) *********************** 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 369 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 295 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8164 (mmt-90) cc_final: 0.7929 (mmp80) REVERT: A 362 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8759 (mm-40) REVERT: A 462 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7020 (mttt) REVERT: A 505 MET cc_start: 0.8669 (tpp) cc_final: 0.8198 (mmt) REVERT: A 528 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6192 (tp) REVERT: A 588 MET cc_start: 0.7658 (mmp) cc_final: 0.7115 (mtm) REVERT: C 109 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.5966 (mptt) REVERT: D 61 MET cc_start: 0.7479 (pmm) cc_final: 0.6858 (ptp) REVERT: D 81 GLU cc_start: 0.7476 (tt0) cc_final: 0.7008 (mt-10) REVERT: D 131 CYS cc_start: 0.8644 (p) cc_final: 0.7535 (t) REVERT: D 132 PRO cc_start: 0.8266 (Cg_exo) cc_final: 0.8053 (Cg_endo) REVERT: D 145 MET cc_start: 0.1761 (mmm) cc_final: 0.1542 (mmt) REVERT: D 157 MET cc_start: 0.6826 (ptt) cc_final: 0.6004 (tpp) REVERT: D 188 ARG cc_start: 0.7124 (ttt-90) cc_final: 0.6911 (ttt-90) REVERT: E 8 TYR cc_start: 0.8193 (m-80) cc_final: 0.7703 (m-10) REVERT: E 224 GLN cc_start: 0.8708 (tt0) cc_final: 0.8427 (mt0) REVERT: F 126 LEU cc_start: 0.3303 (mt) cc_final: 0.2856 (tp) REVERT: F 196 LYS cc_start: 0.4221 (mmtt) cc_final: 0.3818 (tptp) REVERT: F 239 PHE cc_start: 0.4070 (m-80) cc_final: 0.3743 (t80) REVERT: F 249 PHE cc_start: 0.5243 (m-80) cc_final: 0.3521 (m-80) REVERT: G 125 PHE cc_start: 0.6330 (OUTLIER) cc_final: 0.5980 (t80) REVERT: G 149 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.7694 (mtm-85) REVERT: G 232 GLU cc_start: 0.6655 (tm-30) cc_final: 0.5907 (tm-30) REVERT: H 7 GLU cc_start: 0.7639 (mp0) cc_final: 0.6884 (pm20) REVERT: H 24 GLN cc_start: 0.8219 (tt0) cc_final: 0.7799 (mt0) REVERT: H 55 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: H 58 GLN cc_start: 0.8110 (tt0) cc_final: 0.7725 (mt0) REVERT: H 80 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7488 (mtm110) REVERT: H 122 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.7062 (p0) REVERT: H 124 ASP cc_start: 0.7044 (t70) cc_final: 0.5531 (p0) REVERT: H 196 LYS cc_start: 0.5773 (mmtm) cc_final: 0.5163 (ttmm) REVERT: H 224 ARG cc_start: 0.6912 (mtp85) cc_final: 0.6478 (mtp85) outliers start: 74 outliers final: 55 residues processed: 350 average time/residue: 0.3271 time to fit residues: 177.4235 Evaluate side-chains 343 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 281 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 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 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 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 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 189 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE 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 275 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 12 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 21 ASP Chi-restraints excluded: chain F residue 188 MET 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 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 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 221 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 0.0050 chunk 99 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN G 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.185591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136277 restraints weight = 28362.102| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.91 r_work: 0.3329 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5371 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= 0.129 Angle : 0.580 9.202 28038 Z= 0.286 Chirality : 0.041 0.205 3291 Planarity : 0.004 0.044 3551 Dihedral : 7.266 113.779 2818 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.91 % Allowed : 22.97 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2527 helix: 1.72 (0.15), residues: 1157 sheet: 0.02 (0.24), residues: 475 loop : -0.71 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 266 HIS 0.004 0.001 HIS A 460 PHE 0.030 0.001 PHE G 19 TYR 0.019 0.001 TYR E 161 ARG 0.009 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 1047) hydrogen bonds : angle 4.34580 ( 3015) covalent geometry : bond 0.00303 (20723) covalent geometry : angle 0.58003 (28038) ********************** 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 353 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 286 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 ASP cc_start: 0.7662 (m-30) cc_final: 0.7329 (t0) REVERT: A 505 MET cc_start: 0.8649 (tpp) cc_final: 0.8183 (mmt) REVERT: A 528 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6148 (tp) REVERT: A 588 MET cc_start: 0.7682 (mmp) cc_final: 0.7120 (mtm) REVERT: B 321 ASN cc_start: 0.7488 (m-40) cc_final: 0.7164 (m110) REVERT: C 109 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.6010 (mptt) REVERT: D 81 GLU cc_start: 0.7453 (tt0) cc_final: 0.6976 (mt-10) REVERT: D 131 CYS cc_start: 0.8636 (p) cc_final: 0.7643 (t) REVERT: D 132 PRO cc_start: 0.8279 (Cg_exo) cc_final: 0.7975 (Cg_endo) REVERT: D 157 MET cc_start: 0.6793 (ptt) cc_final: 0.6076 (tpp) REVERT: E 8 TYR cc_start: 0.8196 (m-80) cc_final: 0.7696 (m-10) REVERT: E 224 GLN cc_start: 0.8726 (tt0) cc_final: 0.8438 (mt0) REVERT: F 126 LEU cc_start: 0.3246 (mt) cc_final: 0.2837 (tp) REVERT: F 196 LYS cc_start: 0.4264 (mmtt) cc_final: 0.3845 (tptp) REVERT: F 239 PHE cc_start: 0.3891 (m-80) cc_final: 0.3578 (t80) REVERT: F 249 PHE cc_start: 0.5271 (m-80) cc_final: 0.3617 (m-80) REVERT: G 149 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.7663 (mtm-85) REVERT: G 165 GLU cc_start: 0.5703 (tp30) cc_final: 0.5278 (tm-30) REVERT: G 232 GLU cc_start: 0.6745 (tm-30) cc_final: 0.5849 (tm-30) REVERT: H 7 GLU cc_start: 0.7672 (mp0) cc_final: 0.6863 (pm20) REVERT: H 24 GLN cc_start: 0.8288 (tt0) cc_final: 0.7854 (mt0) REVERT: H 55 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: H 58 GLN cc_start: 0.8117 (tt0) cc_final: 0.7704 (mt0) REVERT: H 80 ARG cc_start: 0.7903 (ttp-110) cc_final: 0.7556 (mtm110) REVERT: H 122 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.7038 (p0) REVERT: H 124 ASP cc_start: 0.7074 (t70) cc_final: 0.5597 (p0) REVERT: H 196 LYS cc_start: 0.5725 (mmtm) cc_final: 0.5120 (ttmm) REVERT: H 224 ARG cc_start: 0.6954 (mtp85) cc_final: 0.6539 (mtp85) outliers start: 67 outliers final: 56 residues processed: 335 average time/residue: 0.3150 time to fit residues: 163.1838 Evaluate side-chains 342 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 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 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 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 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 189 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE 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 275 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 12 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 21 ASP Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 188 MET 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 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 95 THR 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 225 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 133 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN C 291 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.183668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.134155 restraints weight = 28313.710| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.82 r_work: 0.3304 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20723 Z= 0.170 Angle : 0.603 9.015 28038 Z= 0.298 Chirality : 0.042 0.267 3291 Planarity : 0.004 0.065 3551 Dihedral : 7.318 114.313 2818 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.08 % Allowed : 22.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.17), residues: 2527 helix: 1.64 (0.15), residues: 1155 sheet: 0.05 (0.24), residues: 470 loop : -0.75 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 266 HIS 0.006 0.001 HIS B 317 PHE 0.020 0.001 PHE A 722 TYR 0.020 0.002 TYR D 83 ARG 0.010 0.001 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 1047) hydrogen bonds : angle 4.38873 ( 3015) covalent geometry : bond 0.00409 (20723) covalent geometry : angle 0.60303 (28038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10927.69 seconds wall clock time: 189 minutes 51.68 seconds (11391.68 seconds total)