Starting phenix.real_space_refine on Fri Jun 5 07:36:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tao_55753/06_2026/9tao_55753.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tao_55753/06_2026/9tao_55753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tao_55753/06_2026/9tao_55753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tao_55753/06_2026/9tao_55753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tao_55753/06_2026/9tao_55753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tao_55753/06_2026/9tao_55753.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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: 5 Type Number sf(0) Gaussians P 19 5.49 5 S 115 5.16 5 C 12566 2.51 5 N 2803 2.21 5 O 3261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18764 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2421 Classifications: {'peptide': 309} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "L" Number of atoms: 4685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4685 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 18, 'TRANS': 594} Chain: "A" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'TRANS': 106} Chain breaks: 1 Chain: "J" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1237 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 482} Chain: "N" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3673 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 463} Chain: "H" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'3PE': 2, '7PH': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 151 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'3PE': 1, '7PH': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'3PE': 1, '7PH': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 310 Unusual residues: {'3PE': 4, 'UQ8': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "L" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "N" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Time building chain proxies: 4.06, per 1000 atoms: 0.22 Number of scatterers: 18764 At special positions: 0 Unit cell: (87.45, 160.05, 176.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 115 16.00 P 19 15.00 O 3261 8.00 N 2803 7.00 C 12566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 804.5 milliseconds 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 4 sheets defined 79.4% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 5 through 39 Processing helix chain 'H' and resid 55 through 69 removed outlier: 4.302A pdb=" N VAL H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 97 removed outlier: 3.693A pdb=" N LEU H 85 " --> pdb=" O VAL H 81 " (cutoff:3.500A) Proline residue: H 87 - end of helix removed outlier: 4.859A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU H 95 " --> pdb=" O PHE H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 101 Processing helix chain 'H' and resid 115 through 137 removed outlier: 3.969A pdb=" N PHE H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA H 133 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP H 135 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 157 Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.999A pdb=" N LEU H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 172 Processing helix chain 'H' and resid 175 through 183 removed outlier: 3.546A pdb=" N GLN H 183 " --> pdb=" O ILE H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 207 Processing helix chain 'H' and resid 231 through 257 removed outlier: 3.550A pdb=" N PHE H 237 " --> pdb=" O LYS H 233 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR H 242 " --> pdb=" O PHE H 238 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE H 245 " --> pdb=" O GLU H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 289 Processing helix chain 'H' and resid 293 through 304 removed outlier: 3.562A pdb=" N ILE H 304 " --> pdb=" O PHE H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 325 Processing helix chain 'K' and resid 3 through 25 removed outlier: 3.620A pdb=" N GLY K 7 " --> pdb=" O PRO K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 54 Processing helix chain 'K' and resid 56 through 88 removed outlier: 3.662A pdb=" N ARG K 86 " --> pdb=" O GLN K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 removed outlier: 3.587A pdb=" N VAL K 95 " --> pdb=" O ILE K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 20 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 26 through 56 removed outlier: 3.529A pdb=" N ILE L 32 " --> pdb=" O ASN L 28 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER L 37 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 107 removed outlier: 3.714A pdb=" N VAL L 91 " --> pdb=" O THR L 87 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 133 Processing helix chain 'L' and resid 135 through 155 removed outlier: 3.621A pdb=" N GLY L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY L 147 " --> pdb=" O TRP L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 193 Processing helix chain 'L' and resid 203 through 208 Processing helix chain 'L' and resid 214 through 229 removed outlier: 3.762A pdb=" N GLY L 224 " --> pdb=" O LEU L 220 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY L 225 " --> pdb=" O MET L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 242 removed outlier: 4.290A pdb=" N ALA L 240 " --> pdb=" O GLN L 236 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA L 242 " --> pdb=" O TRP L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 254 Processing helix chain 'L' and resid 260 through 268 Processing helix chain 'L' and resid 269 through 275 Processing helix chain 'L' and resid 276 through 299 removed outlier: 4.121A pdb=" N LEU L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS L 281 " --> pdb=" O PRO L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 317 removed outlier: 3.782A pdb=" N GLY L 317 " --> pdb=" O MET L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 325 removed outlier: 5.293A pdb=" N LEU L 323 " --> pdb=" O MET L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 337 Processing helix chain 'L' and resid 339 through 356 Processing helix chain 'L' and resid 361 through 365 Processing helix chain 'L' and resid 367 through 371 removed outlier: 3.701A pdb=" N LYS L 370 " --> pdb=" O GLY L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 388 Processing helix chain 'L' and resid 395 through 410 removed outlier: 4.245A pdb=" N GLU L 401 " --> pdb=" O PHE L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 429 removed outlier: 3.936A pdb=" N VAL L 416 " --> pdb=" O ILE L 412 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA L 417 " --> pdb=" O ASN L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 437 Processing helix chain 'L' and resid 453 through 464 Processing helix chain 'L' and resid 466 through 471 Processing helix chain 'L' and resid 486 through 513 removed outlier: 4.371A pdb=" N GLY L 498 " --> pdb=" O GLU L 494 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL L 499 " --> pdb=" O ILE L 495 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 537 removed outlier: 3.844A pdb=" N ASN L 537 " --> pdb=" O THR L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 549 removed outlier: 3.617A pdb=" N LEU L 544 " --> pdb=" O GLY L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 549 through 561 Processing helix chain 'L' and resid 563 through 569 Processing helix chain 'L' and resid 570 through 584 Processing helix chain 'L' and resid 585 through 587 No H-bonds generated for 'chain 'L' and resid 585 through 587' Processing helix chain 'L' and resid 590 through 613 Processing helix chain 'A' and resid 7 through 37 Processing helix chain 'A' and resid 66 through 90 removed outlier: 3.549A pdb=" N LEU A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 120 removed outlier: 6.320A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 24 through 47 Processing helix chain 'J' and resid 48 through 58 removed outlier: 3.709A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 73 Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 79 through 85 Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 89 through 113 removed outlier: 5.588A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.823A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 134 Processing helix chain 'J' and resid 137 through 159 removed outlier: 3.561A pdb=" N SER J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 6 Processing helix chain 'M' and resid 7 through 18 Processing helix chain 'M' and resid 20 through 24 Processing helix chain 'M' and resid 26 through 51 removed outlier: 3.867A pdb=" N GLY M 51 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 55 Processing helix chain 'M' and resid 84 through 105 Processing helix chain 'M' and resid 112 through 133 removed outlier: 4.067A pdb=" N PHE M 116 " --> pdb=" O TYR M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 146 removed outlier: 3.851A pdb=" N MET M 146 " --> pdb=" O PHE M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 156 Processing helix chain 'M' and resid 163 through 201 removed outlier: 3.761A pdb=" N ARG M 167 " --> pdb=" O ASP M 163 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER M 181 " --> pdb=" O TYR M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 234 removed outlier: 3.838A pdb=" N ALA M 230 " --> pdb=" O GLY M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 250 removed outlier: 3.857A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 275 removed outlier: 3.940A pdb=" N TYR M 269 " --> pdb=" O LYS M 265 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 310 through 331 removed outlier: 3.619A pdb=" N SER M 319 " --> pdb=" O ILE M 315 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER M 321 " --> pdb=" O TYR M 317 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL M 326 " --> pdb=" O HIS M 322 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 367 removed outlier: 3.561A pdb=" N ILE M 343 " --> pdb=" O GLN M 339 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY M 360 " --> pdb=" O PHE M 356 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR M 363 " --> pdb=" O CYS M 359 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG M 365 " --> pdb=" O GLN M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 396 removed outlier: 3.714A pdb=" N LEU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 403 through 416 removed outlier: 6.548A pdb=" N MET M 409 " --> pdb=" O VAL M 405 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE M 410 " --> pdb=" O GLY M 406 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN M 416 " --> pdb=" O PHE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 444 removed outlier: 3.527A pdb=" N THR M 422 " --> pdb=" O VAL M 418 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE M 427 " --> pdb=" O VAL M 423 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY M 428 " --> pdb=" O ILE M 424 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU M 429 " --> pdb=" O SER M 425 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL M 430 " --> pdb=" O THR M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 481 Processing helix chain 'M' and resid 482 through 489 removed outlier: 3.535A pdb=" N THR M 488 " --> pdb=" O PRO M 484 " (cutoff:3.500A) Processing helix chain 'M' and resid 489 through 502 Processing helix chain 'N' and resid 8 through 10 No H-bonds generated for 'chain 'N' and resid 8 through 10' Processing helix chain 'N' and resid 11 through 31 Processing helix chain 'N' and resid 33 through 51 Processing helix chain 'N' and resid 51 through 59 Processing helix chain 'N' and resid 70 through 97 Proline residue: N 93 - end of helix removed outlier: 4.282A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 122 Processing helix chain 'N' and resid 124 through 144 Proline residue: N 138 - end of helix removed outlier: 3.894A pdb=" N GLY N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 182 Processing helix chain 'N' and resid 185 through 193 removed outlier: 3.604A pdb=" N LEU N 189 " --> pdb=" O PHE N 186 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLY N 190 " --> pdb=" O VAL N 187 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS N 191 " --> pdb=" O ALA N 188 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN N 192 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU N 193 " --> pdb=" O GLY N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 218 removed outlier: 3.670A pdb=" N GLY N 213 " --> pdb=" O LEU N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 234 Processing helix chain 'N' and resid 235 through 261 removed outlier: 4.190A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 266 through 288 removed outlier: 3.872A pdb=" N ASN N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 315 removed outlier: 3.675A pdb=" N ILE N 303 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER N 304 " --> pdb=" O TYR N 300 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA N 312 " --> pdb=" O TYR N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 348 removed outlier: 3.671A pdb=" N VAL N 344 " --> pdb=" O ALA N 340 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 357 removed outlier: 4.080A pdb=" N ASP N 357 " --> pdb=" O PRO N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 368 Processing helix chain 'N' and resid 369 through 384 Processing helix chain 'N' and resid 389 through 405 removed outlier: 3.564A pdb=" N ILE N 393 " --> pdb=" O THR N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 431 removed outlier: 4.079A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) Processing helix chain 'N' and resid 432 through 434 No H-bonds generated for 'chain 'N' and resid 432 through 434' Processing helix chain 'N' and resid 447 through 470 Processing helix chain 'N' and resid 471 through 481 Processing sheet with id=AA1, first strand: chain 'L' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'L' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'M' and resid 66 through 72 removed outlier: 3.647A pdb=" N TRP M 71 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 61 through 63 removed outlier: 3.571A pdb=" N MET N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) 1278 hydrogen bonds defined for protein. 3786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2960 1.33 - 1.45: 5025 1.45 - 1.58: 10796 1.58 - 1.70: 28 1.70 - 1.83: 222 Bond restraints: 19031 Sorted by residual: bond pdb=" O11 7PH H 403 " pdb=" P 7PH H 403 " ideal model delta sigma weight residual 1.611 1.828 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O11 7PH J 203 " pdb=" P 7PH J 203 " ideal model delta sigma weight residual 1.611 1.827 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" O11 7PH J 202 " pdb=" P 7PH J 202 " ideal model delta sigma weight residual 1.611 1.827 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" O11 7PH M 603 " pdb=" P 7PH M 603 " ideal model delta sigma weight residual 1.611 1.826 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" O11 7PH M 602 " pdb=" P 7PH M 602 " ideal model delta sigma weight residual 1.611 1.826 -0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 19026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.53: 25670 12.53 - 25.06: 10 25.06 - 37.60: 0 37.60 - 50.13: 0 50.13 - 62.66: 5 Bond angle restraints: 25685 Sorted by residual: angle pdb=" O13 7PH M 602 " pdb=" P 7PH M 602 " pdb=" O14 7PH M 602 " ideal model delta sigma weight residual 54.30 116.96 -62.66 3.00e+00 1.11e-01 4.36e+02 angle pdb=" O13 7PH J 202 " pdb=" P 7PH J 202 " pdb=" O14 7PH J 202 " ideal model delta sigma weight residual 54.30 116.92 -62.62 3.00e+00 1.11e-01 4.36e+02 angle pdb=" O13 7PH M 603 " pdb=" P 7PH M 603 " pdb=" O14 7PH M 603 " ideal model delta sigma weight residual 54.30 116.91 -62.61 3.00e+00 1.11e-01 4.36e+02 angle pdb=" O13 7PH H 403 " pdb=" P 7PH H 403 " pdb=" O14 7PH H 403 " ideal model delta sigma weight residual 54.30 116.85 -62.55 3.00e+00 1.11e-01 4.35e+02 angle pdb=" O13 7PH J 203 " pdb=" P 7PH J 203 " pdb=" O14 7PH J 203 " ideal model delta sigma weight residual 54.30 116.84 -62.54 3.00e+00 1.11e-01 4.35e+02 ... (remaining 25680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 10741 35.02 - 70.04: 453 70.04 - 105.06: 29 105.06 - 140.07: 4 140.07 - 175.09: 3 Dihedral angle restraints: 11230 sinusoidal: 4736 harmonic: 6494 Sorted by residual: dihedral pdb=" C20 UQ8 N 505 " pdb=" C19 UQ8 N 505 " pdb=" C21 UQ8 N 505 " pdb=" C22 UQ8 N 505 " ideal model delta sinusoidal sigma weight residual 289.14 114.05 175.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C41 UQ8 N 505 " pdb=" C42 UQ8 N 505 " pdb=" C43 UQ8 N 505 " pdb=" C44 UQ8 N 505 " ideal model delta sinusoidal sigma weight residual 114.10 -96.89 -149.01 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" C41 UQ8 N 506 " pdb=" C42 UQ8 N 506 " pdb=" C43 UQ8 N 506 " pdb=" C44 UQ8 N 506 " ideal model delta sinusoidal sigma weight residual 114.10 -98.20 -147.70 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 11227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2356 0.051 - 0.101: 477 0.101 - 0.152: 58 0.152 - 0.203: 14 0.203 - 0.253: 12 Chirality restraints: 2917 Sorted by residual: chirality pdb=" CA VAL L 95 " pdb=" N VAL L 95 " pdb=" C VAL L 95 " pdb=" CB VAL L 95 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA GLU N 438 " pdb=" N GLU N 438 " pdb=" C GLU N 438 " pdb=" CB GLU N 438 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA LEU L 222 " pdb=" N LEU L 222 " pdb=" C LEU L 222 " pdb=" CB LEU L 222 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2914 not shown) Planarity restraints: 3033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 95 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C VAL L 95 " -0.061 2.00e-02 2.50e+03 pdb=" O VAL L 95 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY L 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 493 " -0.014 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C LEU L 493 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU L 493 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU L 494 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 31 " 0.261 9.50e-02 1.11e+02 1.17e-01 8.36e+00 pdb=" NE ARG N 31 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG N 31 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG N 31 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG N 31 " 0.009 2.00e-02 2.50e+03 ... (remaining 3030 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3251 2.76 - 3.30: 18223 3.30 - 3.83: 33570 3.83 - 4.37: 38864 4.37 - 4.90: 66767 Nonbonded interactions: 160675 Sorted by model distance: nonbonded pdb=" O GLY N 385 " pdb=" O HOH N 601 " model vdw 2.230 3.040 nonbonded pdb=" O MET H 88 " pdb=" OG1 THR H 92 " model vdw 2.255 3.040 nonbonded pdb=" O LYS N 217 " pdb=" O HOH N 602 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASP L 563 " pdb=" OH TYR M 300 " model vdw 2.274 3.040 nonbonded pdb=" O LEU M 264 " pdb=" O HOH M 701 " model vdw 2.275 3.040 ... (remaining 160670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 32.040 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.160 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 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 : 0.007 0.217 19031 Z= 0.368 Angle : 1.183 62.662 25685 Z= 0.503 Chirality : 0.042 0.253 2917 Planarity : 0.005 0.117 3033 Dihedral : 18.252 175.093 7082 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 3.94 % Allowed : 21.16 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.18), residues: 2263 helix: 2.05 (0.13), residues: 1673 sheet: -1.82 (1.80), residues: 10 loop : -1.33 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 529 TYR 0.017 0.001 TYR L 428 PHE 0.031 0.001 PHE H 268 TRP 0.015 0.001 TRP H 73 HIS 0.005 0.001 HIS N 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.37 (19031) covalent geometry : angle 1.18287 / 0.50 (25685) hydrogen bonds : bond 0.12515 / 8.31 ( 1278) hydrogen bonds : angle 4.96017 / 3.56 ( 3786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 398 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: H 63 ASP cc_start: 0.7795 (m-30) cc_final: 0.7502 (m-30) REVERT: L 222 LEU cc_start: 0.4987 (OUTLIER) cc_final: 0.4779 (tt) REVERT: L 521 SER cc_start: 0.4391 (p) cc_final: 0.3976 (t) REVERT: M 303 TRP cc_start: 0.7482 (OUTLIER) cc_final: 0.7011 (m-10) REVERT: N 1 MET cc_start: 0.5872 (mtt) cc_final: 0.5217 (ptp) REVERT: N 317 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6493 (mm110) outliers start: 72 outliers final: 25 residues processed: 452 average time/residue: 0.5297 time to fit residues: 273.3280 Evaluate side-chains 331 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 495 ILE Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain N residue 462 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 453 HIS A 79 ASN M 119 ASN M 348 HIS M 361 GLN M 403 ASN N 124 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.130735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108160 restraints weight = 32084.206| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.36 r_work: 0.3423 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19031 Z= 0.163 Angle : 0.605 11.480 25685 Z= 0.297 Chirality : 0.040 0.157 2917 Planarity : 0.004 0.062 3033 Dihedral : 13.888 165.505 3378 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 6.18 % Allowed : 22.85 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.18), residues: 2263 helix: 2.14 (0.13), residues: 1679 sheet: -1.90 (1.86), residues: 10 loop : -1.15 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 427 TYR 0.029 0.002 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.018 0.001 TRP L 25 HIS 0.008 0.001 HIS L 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (19031) covalent geometry : angle 0.60515 / 0.30 (25685) hydrogen bonds : bond 0.04491 / 2.97 ( 1278) hydrogen bonds : angle 4.14612 / 2.95 ( 3786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 316 time to evaluate : 0.712 Fit side-chains REVERT: H 36 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: H 63 ASP cc_start: 0.8046 (m-30) cc_final: 0.7536 (m-30) REVERT: H 80 ARG cc_start: 0.7881 (ptt180) cc_final: 0.7285 (ptm-80) REVERT: H 139 ASN cc_start: 0.7826 (t0) cc_final: 0.7604 (t0) REVERT: H 214 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7857 (mp10) REVERT: H 219 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7797 (mm-40) REVERT: H 221 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6874 (tt) REVERT: H 241 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: H 281 MET cc_start: 0.8060 (mmm) cc_final: 0.7655 (mpm) REVERT: H 293 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7577 (mtp-110) REVERT: L 3 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5481 (ttm) REVERT: L 99 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7240 (pp) REVERT: L 110 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6194 (mt-10) REVERT: L 140 TYR cc_start: 0.7984 (t80) cc_final: 0.7767 (t80) REVERT: L 328 TRP cc_start: 0.6345 (OUTLIER) cc_final: 0.6081 (m-90) REVERT: L 365 MET cc_start: 0.6179 (tmt) cc_final: 0.5716 (pp-130) REVERT: L 368 LEU cc_start: 0.7892 (mt) cc_final: 0.7657 (mm) REVERT: L 466 PHE cc_start: 0.2709 (OUTLIER) cc_final: 0.2030 (p90) REVERT: L 518 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5675 (tm) REVERT: L 521 SER cc_start: 0.7053 (p) cc_final: 0.6703 (t) REVERT: A 8 GLU cc_start: 0.7969 (tp30) cc_final: 0.7259 (tp30) REVERT: J 86 GLN cc_start: 0.7774 (mt0) cc_final: 0.7510 (mt0) REVERT: M 23 PHE cc_start: 0.7297 (m-80) cc_final: 0.6665 (t80) REVERT: M 64 GLN cc_start: 0.7797 (mp10) cc_final: 0.7208 (tm130) REVERT: M 177 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: M 303 TRP cc_start: 0.7318 (OUTLIER) cc_final: 0.6660 (m-10) REVERT: M 403 ASN cc_start: 0.6380 (m-40) cc_final: 0.6180 (m110) REVERT: N 1 MET cc_start: 0.6114 (mtt) cc_final: 0.4308 (ptp) outliers start: 113 outliers final: 39 residues processed: 394 average time/residue: 0.5494 time to fit residues: 247.5107 Evaluate side-chains 338 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 288 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 214 GLN Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 250 SER Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 466 PHE Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 84 ASP Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 481 TYR Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 324 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 211 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 177 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 210 HIS L 78 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 ASN M 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.127069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.104901 restraints weight = 32268.463| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.33 r_work: 0.3401 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19031 Z= 0.167 Angle : 0.612 11.377 25685 Z= 0.298 Chirality : 0.040 0.193 2917 Planarity : 0.004 0.060 3033 Dihedral : 13.538 160.161 3355 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 6.45 % Allowed : 22.80 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.18), residues: 2263 helix: 2.01 (0.12), residues: 1694 sheet: -1.38 (2.04), residues: 10 loop : -1.18 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 427 TYR 0.027 0.002 TYR M 435 PHE 0.028 0.002 PHE L 341 TRP 0.015 0.001 TRP M 378 HIS 0.007 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (19031) covalent geometry : angle 0.61214 / 0.30 (25685) hydrogen bonds : bond 0.04382 / 2.91 ( 1278) hydrogen bonds : angle 4.08962 / 2.92 ( 3786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 321 time to evaluate : 0.530 Fit side-chains REVERT: H 80 ARG cc_start: 0.7980 (ptt180) cc_final: 0.7309 (ptt-90) REVERT: H 139 ASN cc_start: 0.8009 (t0) cc_final: 0.7752 (t0) REVERT: H 219 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7798 (mm-40) REVERT: H 221 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6954 (tt) REVERT: H 241 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: H 281 MET cc_start: 0.8089 (mmm) cc_final: 0.7586 (mpm) REVERT: H 293 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7574 (mtp-110) REVERT: L 22 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.4681 (tpt-90) REVERT: L 91 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6286 (p) REVERT: L 140 TYR cc_start: 0.8017 (t80) cc_final: 0.7815 (t80) REVERT: L 199 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: L 328 TRP cc_start: 0.6330 (OUTLIER) cc_final: 0.6098 (m-90) REVERT: L 336 MET cc_start: 0.3796 (tpt) cc_final: 0.3406 (tpt) REVERT: L 365 MET cc_start: 0.6103 (tmt) cc_final: 0.5644 (pp-130) REVERT: L 419 LEU cc_start: 0.7696 (mt) cc_final: 0.7211 (tt) REVERT: L 463 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6548 (tp) REVERT: L 466 PHE cc_start: 0.2885 (OUTLIER) cc_final: 0.2323 (p90) REVERT: L 515 LYS cc_start: 0.8287 (pptt) cc_final: 0.7959 (mptt) REVERT: L 518 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.5791 (tm) REVERT: L 521 SER cc_start: 0.7115 (p) cc_final: 0.6887 (t) REVERT: L 545 TYR cc_start: 0.7683 (m-80) cc_final: 0.7452 (m-80) REVERT: A 8 GLU cc_start: 0.8026 (tp30) cc_final: 0.7345 (tp30) REVERT: A 94 GLU cc_start: 0.8925 (mp0) cc_final: 0.8612 (mp0) REVERT: J 86 GLN cc_start: 0.7709 (mt0) cc_final: 0.7411 (mt0) REVERT: J 120 ASP cc_start: 0.8696 (p0) cc_final: 0.8440 (p0) REVERT: J 162 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6660 (tm-30) REVERT: M 20 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7775 (t) REVERT: M 21 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7592 (mm-30) REVERT: M 23 PHE cc_start: 0.7349 (m-80) cc_final: 0.6978 (m-10) REVERT: M 64 GLN cc_start: 0.7887 (mp10) cc_final: 0.7138 (tm130) REVERT: M 69 MET cc_start: 0.7263 (ttp) cc_final: 0.7005 (ttp) REVERT: M 177 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: M 381 MET cc_start: 0.8128 (mtt) cc_final: 0.7438 (mtt) REVERT: M 384 LEU cc_start: 0.6581 (tt) cc_final: 0.5779 (tp) REVERT: N 1 MET cc_start: 0.6086 (mtt) cc_final: 0.4270 (ptp) REVERT: N 404 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7671 (tt0) outliers start: 118 outliers final: 53 residues processed: 403 average time/residue: 0.5436 time to fit residues: 250.8910 Evaluate side-chains 362 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 297 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 22 ARG Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 345 LEU Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 466 PHE Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 543 TRP Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 368 THR Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 476 VAL Chi-restraints excluded: chain M residue 481 TYR Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 324 GLU Chi-restraints excluded: chain N residue 404 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 36 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 78 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN M 119 ASN M 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.127072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104890 restraints weight = 32403.543| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.34 r_work: 0.3369 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19031 Z= 0.144 Angle : 0.595 11.273 25685 Z= 0.290 Chirality : 0.040 0.219 2917 Planarity : 0.004 0.061 3033 Dihedral : 13.389 160.962 3355 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 6.45 % Allowed : 23.02 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.18), residues: 2263 helix: 2.01 (0.12), residues: 1704 sheet: -1.37 (1.95), residues: 10 loop : -1.23 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 22 TYR 0.034 0.002 TYR M 435 PHE 0.025 0.001 PHE L 341 TRP 0.017 0.001 TRP M 378 HIS 0.007 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (19031) covalent geometry : angle 0.59536 / 0.29 (25685) hydrogen bonds : bond 0.04151 / 2.75 ( 1278) hydrogen bonds : angle 4.02639 / 2.87 ( 3786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 322 time to evaluate : 0.683 Fit side-chains REVERT: H 60 LEU cc_start: 0.8920 (tp) cc_final: 0.8558 (tt) REVERT: H 80 ARG cc_start: 0.7967 (ptt180) cc_final: 0.7183 (ptt-90) REVERT: H 139 ASN cc_start: 0.8043 (t0) cc_final: 0.7840 (t0) REVERT: H 219 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7786 (mm-40) REVERT: H 221 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6982 (tt) REVERT: H 241 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: H 281 MET cc_start: 0.8100 (mmm) cc_final: 0.7829 (mmm) REVERT: K 46 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8452 (t80) REVERT: L 22 ARG cc_start: 0.5882 (mtm180) cc_final: 0.4629 (tpp80) REVERT: L 91 VAL cc_start: 0.6879 (OUTLIER) cc_final: 0.6365 (p) REVERT: L 110 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6228 (mt-10) REVERT: L 199 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: L 336 MET cc_start: 0.3706 (tpt) cc_final: 0.3347 (tpt) REVERT: L 419 LEU cc_start: 0.7714 (mt) cc_final: 0.7223 (tt) REVERT: L 463 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6504 (mp) REVERT: L 466 PHE cc_start: 0.3130 (OUTLIER) cc_final: 0.2589 (p90) REVERT: L 521 SER cc_start: 0.7217 (p) cc_final: 0.6861 (t) REVERT: L 545 TYR cc_start: 0.7670 (m-80) cc_final: 0.7458 (m-80) REVERT: L 568 MET cc_start: 0.6880 (ttm) cc_final: 0.6581 (ttm) REVERT: A 8 GLU cc_start: 0.7990 (tp30) cc_final: 0.7592 (tp30) REVERT: A 94 GLU cc_start: 0.8936 (mp0) cc_final: 0.8629 (mp0) REVERT: J 2 GLU cc_start: 0.7887 (mp0) cc_final: 0.7670 (mp0) REVERT: J 86 GLN cc_start: 0.7685 (mt0) cc_final: 0.7403 (mt0) REVERT: J 120 ASP cc_start: 0.8621 (p0) cc_final: 0.8300 (p0) REVERT: M 1 MET cc_start: 0.6795 (tmt) cc_final: 0.6571 (tmt) REVERT: M 20 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7951 (t) REVERT: M 21 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7810 (mm-30) REVERT: M 23 PHE cc_start: 0.7361 (m-80) cc_final: 0.6971 (m-10) REVERT: M 64 GLN cc_start: 0.7975 (mp10) cc_final: 0.7069 (tm130) REVERT: M 69 MET cc_start: 0.7352 (ttp) cc_final: 0.6994 (ttp) REVERT: M 177 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: M 235 MET cc_start: 0.7575 (tmm) cc_final: 0.7360 (tmm) REVERT: M 381 MET cc_start: 0.8150 (mtt) cc_final: 0.7514 (mtt) REVERT: M 384 LEU cc_start: 0.6393 (tt) cc_final: 0.5649 (tp) REVERT: N 1 MET cc_start: 0.6105 (mtt) cc_final: 0.4284 (ptp) REVERT: N 323 MET cc_start: 0.8413 (mtp) cc_final: 0.8209 (mmm) REVERT: N 404 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7691 (tt0) outliers start: 118 outliers final: 55 residues processed: 409 average time/residue: 0.5201 time to fit residues: 243.9405 Evaluate side-chains 364 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 299 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 466 PHE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 517 THR Chi-restraints excluded: chain L residue 543 TRP Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 481 TYR Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 404 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 78 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 83 optimal weight: 0.0030 chunk 76 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 78 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 ASN L 411 HIS J 115 ASN M 119 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 455 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.127373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104969 restraints weight = 32091.785| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.35 r_work: 0.3377 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19031 Z= 0.128 Angle : 0.596 11.229 25685 Z= 0.287 Chirality : 0.039 0.204 2917 Planarity : 0.004 0.061 3033 Dihedral : 13.188 159.747 3354 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 5.36 % Allowed : 24.93 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.18), residues: 2263 helix: 2.10 (0.13), residues: 1690 sheet: -1.62 (1.92), residues: 10 loop : -1.19 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 286 TYR 0.031 0.002 TYR M 435 PHE 0.026 0.001 PHE L 341 TRP 0.015 0.001 TRP M 383 HIS 0.006 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (19031) covalent geometry : angle 0.59569 / 0.29 (25685) hydrogen bonds : bond 0.03986 / 2.64 ( 1278) hydrogen bonds : angle 3.97175 / 2.84 ( 3786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 315 time to evaluate : 0.642 Fit side-chains REVERT: H 80 ARG cc_start: 0.7866 (ptt180) cc_final: 0.7082 (ptt-90) REVERT: H 139 ASN cc_start: 0.8140 (t0) cc_final: 0.7896 (t0) REVERT: H 221 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6987 (tt) REVERT: H 241 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: H 281 MET cc_start: 0.8068 (mmm) cc_final: 0.7798 (mmm) REVERT: H 289 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9078 (tt) REVERT: H 293 ARG cc_start: 0.7930 (mtp180) cc_final: 0.7549 (mtp-110) REVERT: L 22 ARG cc_start: 0.5699 (OUTLIER) cc_final: 0.4257 (mmm-85) REVERT: L 101 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6568 (tpp) REVERT: L 319 MET cc_start: 0.7813 (mpp) cc_final: 0.7094 (mpp) REVERT: L 336 MET cc_start: 0.3630 (tpt) cc_final: 0.3400 (tpt) REVERT: L 419 LEU cc_start: 0.7694 (mt) cc_final: 0.7216 (tt) REVERT: L 463 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6457 (mp) REVERT: L 466 PHE cc_start: 0.3188 (OUTLIER) cc_final: 0.2763 (p90) REVERT: L 521 SER cc_start: 0.7118 (p) cc_final: 0.6739 (t) REVERT: L 562 ARG cc_start: 0.7488 (tpp-160) cc_final: 0.7014 (mmm160) REVERT: L 568 MET cc_start: 0.6845 (ttm) cc_final: 0.6543 (ttm) REVERT: A 8 GLU cc_start: 0.7970 (tp30) cc_final: 0.7546 (tp30) REVERT: A 94 GLU cc_start: 0.8916 (mp0) cc_final: 0.8599 (mp0) REVERT: J 2 GLU cc_start: 0.7887 (mp0) cc_final: 0.7669 (mp0) REVERT: J 86 GLN cc_start: 0.7668 (mt0) cc_final: 0.7379 (mt0) REVERT: J 120 ASP cc_start: 0.8568 (p0) cc_final: 0.8194 (p0) REVERT: M 1 MET cc_start: 0.6844 (tmt) cc_final: 0.6581 (tmt) REVERT: M 20 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7971 (t) REVERT: M 21 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7544 (mm-30) REVERT: M 23 PHE cc_start: 0.7391 (m-80) cc_final: 0.6983 (m-10) REVERT: M 64 GLN cc_start: 0.7939 (mp10) cc_final: 0.7535 (mp10) REVERT: M 69 MET cc_start: 0.7351 (ttp) cc_final: 0.7030 (ttp) REVERT: M 110 GLU cc_start: 0.6555 (pm20) cc_final: 0.6319 (pm20) REVERT: M 177 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: M 235 MET cc_start: 0.7504 (tmm) cc_final: 0.7299 (tmm) REVERT: N 1 MET cc_start: 0.6156 (mtt) cc_final: 0.4300 (ptp) REVERT: N 404 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7688 (tt0) outliers start: 98 outliers final: 50 residues processed: 385 average time/residue: 0.5251 time to fit residues: 232.5675 Evaluate side-chains 351 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 291 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 ARG Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 466 PHE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 543 TRP Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 132 LEU Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 481 TYR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 324 GLU Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 404 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 186 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 162 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN M 119 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105418 restraints weight = 32084.227| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.33 r_work: 0.3374 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19031 Z= 0.126 Angle : 0.600 11.558 25685 Z= 0.286 Chirality : 0.039 0.239 2917 Planarity : 0.004 0.061 3033 Dihedral : 13.002 158.406 3352 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 5.19 % Allowed : 25.04 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.18), residues: 2263 helix: 2.07 (0.12), residues: 1701 sheet: -1.76 (1.90), residues: 10 loop : -1.26 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 268 TYR 0.029 0.002 TYR M 435 PHE 0.025 0.001 PHE L 341 TRP 0.012 0.001 TRP M 383 HIS 0.006 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (19031) covalent geometry : angle 0.59981 / 0.29 (25685) hydrogen bonds : bond 0.03916 / 2.60 ( 1278) hydrogen bonds : angle 3.93756 / 2.81 ( 3786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 309 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: H 32 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8165 (ttm) REVERT: H 80 ARG cc_start: 0.7942 (ptt180) cc_final: 0.7187 (ptt-90) REVERT: H 139 ASN cc_start: 0.8191 (t0) cc_final: 0.7895 (t0) REVERT: H 214 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: H 241 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: H 281 MET cc_start: 0.8134 (mmm) cc_final: 0.7809 (mmm) REVERT: H 293 ARG cc_start: 0.7901 (mtp180) cc_final: 0.7516 (mtp-110) REVERT: L 22 ARG cc_start: 0.5841 (mtm180) cc_final: 0.4545 (mmm-85) REVERT: L 101 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6586 (tpp) REVERT: L 158 TYR cc_start: 0.7707 (p90) cc_final: 0.7372 (p90) REVERT: L 199 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: L 419 LEU cc_start: 0.7685 (mt) cc_final: 0.7213 (tt) REVERT: L 463 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6481 (mp) REVERT: L 466 PHE cc_start: 0.3222 (OUTLIER) cc_final: 0.2841 (p90) REVERT: L 562 ARG cc_start: 0.7458 (tpp-160) cc_final: 0.6347 (mtm110) REVERT: L 568 MET cc_start: 0.6825 (ttm) cc_final: 0.6527 (ttm) REVERT: A 8 GLU cc_start: 0.7987 (tp30) cc_final: 0.7579 (tp30) REVERT: A 94 GLU cc_start: 0.8916 (mp0) cc_final: 0.8609 (mp0) REVERT: J 2 GLU cc_start: 0.7921 (mp0) cc_final: 0.7691 (mp0) REVERT: J 86 GLN cc_start: 0.7680 (mt0) cc_final: 0.7470 (mt0) REVERT: J 94 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7971 (mt) REVERT: J 120 ASP cc_start: 0.8558 (p0) cc_final: 0.8165 (p0) REVERT: M 1 MET cc_start: 0.6802 (tmt) cc_final: 0.6534 (tmt) REVERT: M 20 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8030 (t) REVERT: M 21 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7560 (mm-30) REVERT: M 23 PHE cc_start: 0.7425 (m-80) cc_final: 0.7050 (m-10) REVERT: M 64 GLN cc_start: 0.7944 (mp10) cc_final: 0.7532 (mp10) REVERT: M 69 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6990 (ttp) REVERT: M 110 GLU cc_start: 0.6625 (pm20) cc_final: 0.6377 (pm20) REVERT: M 177 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7333 (m-80) REVERT: M 235 MET cc_start: 0.7356 (tmm) cc_final: 0.7131 (tmm) REVERT: M 381 MET cc_start: 0.8099 (mtt) cc_final: 0.7581 (mtt) REVERT: N 1 MET cc_start: 0.6155 (mtt) cc_final: 0.4327 (ptp) REVERT: N 404 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7696 (tt0) outliers start: 95 outliers final: 51 residues processed: 376 average time/residue: 0.5440 time to fit residues: 234.8321 Evaluate side-chains 355 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 214 GLN Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 466 PHE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 522 ILE Chi-restraints excluded: chain L residue 543 TRP Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 177 TYR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 481 TYR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 324 GLU Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 404 GLN Chi-restraints excluded: chain N residue 458 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 143 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 63 optimal weight: 0.0670 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN M 119 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104824 restraints weight = 32387.527| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.35 r_work: 0.3409 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19031 Z= 0.132 Angle : 0.607 11.676 25685 Z= 0.287 Chirality : 0.039 0.203 2917 Planarity : 0.004 0.064 3033 Dihedral : 12.932 157.314 3352 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 5.08 % Allowed : 25.42 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.18), residues: 2263 helix: 2.07 (0.12), residues: 1695 sheet: -1.84 (1.87), residues: 10 loop : -1.18 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 286 TYR 0.028 0.002 TYR M 435 PHE 0.026 0.001 PHE L 341 TRP 0.012 0.001 TRP L 543 HIS 0.007 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (19031) covalent geometry : angle 0.60693 / 0.29 (25685) hydrogen bonds : bond 0.03967 / 2.64 ( 1278) hydrogen bonds : angle 3.93293 / 2.81 ( 3786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 307 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: H 64 MET cc_start: 0.8226 (mmt) cc_final: 0.8017 (mmp) REVERT: H 80 ARG cc_start: 0.7973 (ptt180) cc_final: 0.7411 (ptt-90) REVERT: H 139 ASN cc_start: 0.8125 (t0) cc_final: 0.7847 (t0) REVERT: H 241 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: H 293 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7689 (mtp-110) REVERT: K 4 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8635 (tp) REVERT: L 22 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.4640 (mmm-85) REVERT: L 88 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.6133 (ptt) REVERT: L 101 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6559 (tpp) REVERT: L 158 TYR cc_start: 0.7726 (p90) cc_final: 0.7375 (p90) REVERT: L 199 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: L 419 LEU cc_start: 0.7753 (mt) cc_final: 0.7253 (tt) REVERT: L 463 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6479 (mp) REVERT: L 466 PHE cc_start: 0.3224 (OUTLIER) cc_final: 0.2855 (p90) REVERT: L 562 ARG cc_start: 0.7445 (tpp-160) cc_final: 0.7045 (mmm160) REVERT: L 568 MET cc_start: 0.6875 (ttm) cc_final: 0.6571 (ttm) REVERT: A 8 GLU cc_start: 0.7998 (tp30) cc_final: 0.7605 (tp30) REVERT: A 94 GLU cc_start: 0.8908 (mp0) cc_final: 0.8605 (mp0) REVERT: J 2 GLU cc_start: 0.7969 (mp0) cc_final: 0.7749 (mp0) REVERT: J 86 GLN cc_start: 0.7782 (mt0) cc_final: 0.7420 (mt0) REVERT: J 94 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7997 (mt) REVERT: J 120 ASP cc_start: 0.8553 (p0) cc_final: 0.8138 (p0) REVERT: M 1 MET cc_start: 0.6876 (tmt) cc_final: 0.6658 (tmt) REVERT: M 21 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7551 (mm-30) REVERT: M 23 PHE cc_start: 0.7469 (m-80) cc_final: 0.7034 (m-10) REVERT: M 64 GLN cc_start: 0.7991 (mp10) cc_final: 0.7586 (mp10) REVERT: M 69 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7015 (ttp) REVERT: M 110 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6407 (pm20) REVERT: M 235 MET cc_start: 0.7384 (tmm) cc_final: 0.7026 (ppp) REVERT: N 1 MET cc_start: 0.6208 (mtt) cc_final: 0.4392 (ptp) REVERT: N 404 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7724 (tt0) outliers start: 93 outliers final: 53 residues processed: 377 average time/residue: 0.5457 time to fit residues: 235.3100 Evaluate side-chains 356 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 ARG Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 88 MET Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 466 PHE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 522 ILE Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 481 TYR Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 324 GLU Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 404 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 132 optimal weight: 0.8980 chunk 172 optimal weight: 0.0010 chunk 129 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 142 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 ASN J 115 ASN M 119 ASN M 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105388 restraints weight = 32030.641| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.33 r_work: 0.3420 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19031 Z= 0.123 Angle : 0.617 11.437 25685 Z= 0.290 Chirality : 0.039 0.239 2917 Planarity : 0.004 0.064 3033 Dihedral : 12.795 155.675 3352 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 4.65 % Allowed : 26.30 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.18), residues: 2263 helix: 2.05 (0.12), residues: 1712 sheet: -1.85 (1.86), residues: 10 loop : -1.20 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 286 TYR 0.029 0.002 TYR N 423 PHE 0.026 0.001 PHE L 341 TRP 0.015 0.001 TRP L 328 HIS 0.008 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (19031) covalent geometry : angle 0.61708 / 0.29 (25685) hydrogen bonds : bond 0.03858 / 2.56 ( 1278) hydrogen bonds : angle 3.91336 / 2.79 ( 3786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 300 time to evaluate : 0.820 Fit side-chains REVERT: H 80 ARG cc_start: 0.7986 (ptt180) cc_final: 0.7629 (ptt-90) REVERT: H 139 ASN cc_start: 0.8097 (t0) cc_final: 0.7874 (t0) REVERT: H 241 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: H 293 ARG cc_start: 0.7925 (mtp180) cc_final: 0.7509 (mtp-110) REVERT: K 4 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8632 (tp) REVERT: L 22 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.4586 (mmm-85) REVERT: L 101 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6536 (tpp) REVERT: L 158 TYR cc_start: 0.7718 (p90) cc_final: 0.7359 (p90) REVERT: L 419 LEU cc_start: 0.7730 (mt) cc_final: 0.7230 (tt) REVERT: L 466 PHE cc_start: 0.3485 (OUTLIER) cc_final: 0.3087 (p90) REVERT: L 562 ARG cc_start: 0.7422 (tpp-160) cc_final: 0.7049 (mmm160) REVERT: L 568 MET cc_start: 0.6856 (ttm) cc_final: 0.6550 (ttm) REVERT: A 8 GLU cc_start: 0.8002 (tp30) cc_final: 0.7611 (tp30) REVERT: A 94 GLU cc_start: 0.8898 (mp0) cc_final: 0.8595 (mp0) REVERT: J 2 GLU cc_start: 0.7993 (mp0) cc_final: 0.7754 (mp0) REVERT: J 79 SER cc_start: 0.7689 (OUTLIER) cc_final: 0.7334 (p) REVERT: J 83 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8286 (mp10) REVERT: J 86 GLN cc_start: 0.7705 (mt0) cc_final: 0.7414 (mt0) REVERT: J 94 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7982 (mt) REVERT: J 120 ASP cc_start: 0.8519 (p0) cc_final: 0.8104 (p0) REVERT: M 1 MET cc_start: 0.6562 (tmt) cc_final: 0.6361 (tmt) REVERT: M 21 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7543 (mm-30) REVERT: M 23 PHE cc_start: 0.7500 (m-80) cc_final: 0.7038 (m-10) REVERT: M 64 GLN cc_start: 0.7954 (mp10) cc_final: 0.7560 (mp10) REVERT: M 69 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7054 (ttp) REVERT: M 75 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.5644 (p90) REVERT: M 77 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7411 (mt) REVERT: M 110 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6416 (pm20) REVERT: M 235 MET cc_start: 0.7314 (tmm) cc_final: 0.6999 (ppp) REVERT: M 373 MET cc_start: 0.7939 (mmm) cc_final: 0.7426 (mtm) REVERT: N 1 MET cc_start: 0.6209 (mtt) cc_final: 0.4387 (ptp) REVERT: N 404 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7710 (tt0) outliers start: 85 outliers final: 50 residues processed: 363 average time/residue: 0.5505 time to fit residues: 229.0945 Evaluate side-chains 354 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 241 GLU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 22 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 425 THR Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 466 PHE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 522 ILE Chi-restraints excluded: chain L residue 543 TRP Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 405 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 481 TYR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 324 GLU Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 404 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 148 optimal weight: 0.2980 chunk 206 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 65 optimal weight: 0.0770 chunk 131 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 409 ASN L 411 HIS ** L 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.128328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106194 restraints weight = 31995.987| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.33 r_work: 0.3385 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19031 Z= 0.121 Angle : 0.615 11.809 25685 Z= 0.290 Chirality : 0.040 0.309 2917 Planarity : 0.004 0.064 3033 Dihedral : 12.682 154.161 3352 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 4.05 % Allowed : 27.12 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.18), residues: 2263 helix: 2.05 (0.12), residues: 1716 sheet: -1.73 (1.79), residues: 10 loop : -1.20 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 286 TYR 0.027 0.002 TYR N 423 PHE 0.025 0.001 PHE L 341 TRP 0.015 0.001 TRP L 238 HIS 0.008 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (19031) covalent geometry : angle 0.61469 / 0.29 (25685) hydrogen bonds : bond 0.03799 / 2.52 ( 1278) hydrogen bonds : angle 3.90639 / 2.79 ( 3786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 301 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: H 80 ARG cc_start: 0.8007 (ptt180) cc_final: 0.7424 (ptt-90) REVERT: H 139 ASN cc_start: 0.8056 (t0) cc_final: 0.7806 (t0) REVERT: H 293 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7509 (mtp-110) REVERT: L 22 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.4576 (mmm-85) REVERT: L 101 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6446 (tpp) REVERT: L 158 TYR cc_start: 0.7692 (p90) cc_final: 0.7331 (p90) REVERT: L 199 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: L 419 LEU cc_start: 0.7702 (mt) cc_final: 0.7201 (tt) REVERT: L 463 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6469 (mp) REVERT: L 562 ARG cc_start: 0.7386 (tpp-160) cc_final: 0.7027 (mmm160) REVERT: L 568 MET cc_start: 0.6785 (ttm) cc_final: 0.6475 (ttm) REVERT: A 8 GLU cc_start: 0.7981 (tp30) cc_final: 0.7583 (tp30) REVERT: A 94 GLU cc_start: 0.8905 (mp0) cc_final: 0.8598 (mp0) REVERT: J 2 GLU cc_start: 0.7952 (mp0) cc_final: 0.7717 (mp0) REVERT: J 86 GLN cc_start: 0.7678 (mt0) cc_final: 0.7432 (mt0) REVERT: J 94 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7960 (mt) REVERT: J 120 ASP cc_start: 0.8485 (p0) cc_final: 0.8065 (p0) REVERT: M 21 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7566 (mm-30) REVERT: M 23 PHE cc_start: 0.7458 (m-80) cc_final: 0.7056 (m-10) REVERT: M 64 GLN cc_start: 0.7961 (mp10) cc_final: 0.7575 (mp10) REVERT: M 69 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7040 (ttp) REVERT: M 75 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.5537 (p90) REVERT: M 77 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7430 (mt) REVERT: M 110 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6404 (pm20) REVERT: M 235 MET cc_start: 0.7288 (tmm) cc_final: 0.6978 (ppp) REVERT: M 373 MET cc_start: 0.7938 (mmm) cc_final: 0.7403 (mtm) REVERT: N 1 MET cc_start: 0.6244 (mtt) cc_final: 0.4388 (ptp) REVERT: N 376 MET cc_start: 0.8615 (mmm) cc_final: 0.8393 (tpt) REVERT: N 404 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7695 (tt0) outliers start: 74 outliers final: 51 residues processed: 359 average time/residue: 0.5500 time to fit residues: 226.1925 Evaluate side-chains 351 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 290 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 22 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 522 ILE Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 481 TYR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 324 GLU Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 154 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN L 190 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN M 119 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103666 restraints weight = 32041.929| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.32 r_work: 0.3381 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19031 Z= 0.157 Angle : 0.656 11.892 25685 Z= 0.310 Chirality : 0.041 0.267 2917 Planarity : 0.004 0.068 3033 Dihedral : 12.841 153.098 3351 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.02 % Favored : 95.93 % Rotamer: Outliers : 3.55 % Allowed : 27.50 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.18), residues: 2263 helix: 1.96 (0.12), residues: 1708 sheet: -1.57 (1.76), residues: 10 loop : -1.22 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 268 TYR 0.033 0.002 TYR N 423 PHE 0.027 0.002 PHE L 341 TRP 0.016 0.001 TRP L 238 HIS 0.007 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (19031) covalent geometry : angle 0.65593 / 0.31 (25685) hydrogen bonds : bond 0.04184 / 2.79 ( 1278) hydrogen bonds : angle 4.01113 / 2.86 ( 3786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 297 time to evaluate : 0.711 Fit side-chains REVERT: H 80 ARG cc_start: 0.8015 (ptt180) cc_final: 0.7436 (ptt-90) REVERT: H 139 ASN cc_start: 0.8088 (t0) cc_final: 0.7833 (t0) REVERT: H 293 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7522 (mtp-110) REVERT: L 22 ARG cc_start: 0.5991 (OUTLIER) cc_final: 0.4520 (mmm-85) REVERT: L 101 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6516 (tpp) REVERT: L 199 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: L 419 LEU cc_start: 0.7780 (mt) cc_final: 0.7294 (tt) REVERT: L 562 ARG cc_start: 0.7494 (tpp-160) cc_final: 0.7130 (mmm160) REVERT: L 568 MET cc_start: 0.6908 (ttm) cc_final: 0.6594 (ttm) REVERT: A 8 GLU cc_start: 0.7979 (tp30) cc_final: 0.7612 (tp30) REVERT: A 94 GLU cc_start: 0.8899 (mp0) cc_final: 0.8575 (mp0) REVERT: J 2 GLU cc_start: 0.8004 (mp0) cc_final: 0.7774 (mp0) REVERT: J 83 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8331 (mp10) REVERT: J 86 GLN cc_start: 0.7800 (mt0) cc_final: 0.7435 (mt0) REVERT: J 120 ASP cc_start: 0.8521 (p0) cc_final: 0.8103 (p0) REVERT: M 21 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7495 (mm-30) REVERT: M 23 PHE cc_start: 0.7519 (m-80) cc_final: 0.7082 (m-10) REVERT: M 64 GLN cc_start: 0.7972 (mp10) cc_final: 0.7572 (mp10) REVERT: M 69 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7068 (ttp) REVERT: M 75 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.5723 (p90) REVERT: M 77 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7517 (mt) REVERT: M 110 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6500 (pm20) REVERT: M 373 MET cc_start: 0.7972 (mmm) cc_final: 0.7450 (mtm) REVERT: N 1 MET cc_start: 0.6246 (mtt) cc_final: 0.4417 (ptp) REVERT: N 404 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7745 (tt0) outliers start: 65 outliers final: 49 residues processed: 350 average time/residue: 0.5551 time to fit residues: 221.6520 Evaluate side-chains 346 residues out of total 1829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 289 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain L residue 22 ARG Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 340 PHE Chi-restraints excluded: chain L residue 349 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 500 VAL Chi-restraints excluded: chain L residue 522 ILE Chi-restraints excluded: chain L residue 543 TRP Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 75 PHE Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 388 SER Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 433 SER Chi-restraints excluded: chain M residue 481 TYR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 301 SER Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 324 GLU Chi-restraints excluded: chain N residue 398 VAL Chi-restraints excluded: chain N residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 93 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 chunk 210 optimal weight: 0.5980 chunk 165 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN M 119 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104784 restraints weight = 32078.114| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.32 r_work: 0.3370 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19031 Z= 0.132 Angle : 0.648 13.546 25685 Z= 0.305 Chirality : 0.040 0.261 2917 Planarity : 0.004 0.067 3033 Dihedral : 12.753 150.904 3351 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 3.55 % Allowed : 27.77 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.18), residues: 2263 helix: 1.99 (0.12), residues: 1703 sheet: -1.58 (1.76), residues: 10 loop : -1.24 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 286 TYR 0.032 0.002 TYR N 423 PHE 0.025 0.001 PHE L 341 TRP 0.016 0.001 TRP L 238 HIS 0.007 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (19031) covalent geometry : angle 0.64791 / 0.30 (25685) hydrogen bonds : bond 0.03987 / 2.65 ( 1278) hydrogen bonds : angle 3.98432 / 2.84 ( 3786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7046.43 seconds wall clock time: 121 minutes 10.77 seconds (7270.77 seconds total)