Starting phenix.real_space_refine on Sun Nov 17 22:10:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/11_2024/8g3l_29701.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/11_2024/8g3l_29701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/11_2024/8g3l_29701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/11_2024/8g3l_29701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/11_2024/8g3l_29701.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/11_2024/8g3l_29701.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 2 5.49 5 S 62 5.16 5 C 9385 2.51 5 N 2374 2.21 5 O 2619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14442 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'6OU': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.03, per 1000 atoms: 0.63 Number of scatterers: 14442 At special positions: 0 Unit cell: (93.304, 117.72, 197.072, 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 62 16.00 P 2 15.00 O 2619 8.00 N 2374 7.00 C 9385 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: 3.93 Conformation dependent library (CDL) restraints added in 1.9 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 12 sheets defined 60.6% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 4.049A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.665A pdb=" N TYR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.741A pdb=" N VAL A 47 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.974A pdb=" N THR A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.626A pdb=" N GLY A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.632A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.944A pdb=" N LEU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 removed outlier: 4.031A pdb=" N GLY A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 272 through 286 removed outlier: 3.566A pdb=" N VAL A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 316 removed outlier: 3.783A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.538A pdb=" N VAL A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 3.905A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.616A pdb=" N MET A 369 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.585A pdb=" N GLN A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.835A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 518 through 557 removed outlier: 3.622A pdb=" N LYS A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 570 through 602 removed outlier: 3.856A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 614 through 633 removed outlier: 3.960A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 644 removed outlier: 4.234A pdb=" N TYR A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.533A pdb=" N SER B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 109 through 112 removed outlier: 3.894A pdb=" N ILE B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.931A pdb=" N ARG B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 145 through 158 removed outlier: 3.644A pdb=" N LYS B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 101 through 108 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.527A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.673A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 193 removed outlier: 3.609A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.794A pdb=" N ALA C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 11 through 30 removed outlier: 3.695A pdb=" N ALA D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 27 " --> pdb=" O MET D 23 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 61 removed outlier: 3.869A pdb=" N VAL D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 50 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'D' and resid 84 through 139 removed outlier: 4.065A pdb=" N MET D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL D 90 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 142 through 169 Processing helix chain 'D' and resid 170 through 175 removed outlier: 5.630A pdb=" N GLU D 173 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 194 removed outlier: 4.202A pdb=" N LEU D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 217 through 235 Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 281 through 285 Processing helix chain 'D' and resid 289 through 300 removed outlier: 4.331A pdb=" N TYR D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 327 Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 11 through 30 removed outlier: 3.546A pdb=" N PHE E 16 " --> pdb=" O TRP E 12 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU E 17 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLN E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 61 removed outlier: 3.951A pdb=" N ARG E 58 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS E 59 " --> pdb=" O PHE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 84 through 138 Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 143 through 170 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 217 through 235 removed outlier: 3.919A pdb=" N LEU E 221 " --> pdb=" O ASP E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 289 through 303 removed outlier: 4.064A pdb=" N TYR E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA E 300 " --> pdb=" O LYS E 296 " (cutoff:3.500A) Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 324 through 327 Processing helix chain 'E' and resid 328 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.640A pdb=" N LEU A 511 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354 removed outlier: 4.002A pdb=" N LYS A 354 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 485 " --> pdb=" O LYS A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.640A pdb=" N LYS A 425 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N VAL A 458 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA A 386 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 457 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 404 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE A 405 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 440 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 90 removed outlier: 7.515A pdb=" N GLY B 88 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASP B 168 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 90 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE B 165 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL B 200 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA B 167 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE B 35 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 214 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER B 37 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.809A pdb=" N GLY C 88 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 198 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 167 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 199 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AA9, first strand: chain 'D' and resid 205 through 209 removed outlier: 3.564A pdb=" N LYS D 248 " --> pdb=" O GLN D 251 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 251 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 305 through 311 Processing sheet with id=AB2, first strand: chain 'E' and resid 179 through 182 removed outlier: 4.006A pdb=" N GLU E 179 " --> pdb=" O SER E 216 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER E 216 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 214 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 205 through 209 removed outlier: 5.819A pdb=" N ASP E 206 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N SER E 245 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN E 208 " --> pdb=" O SER E 245 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLN E 247 " --> pdb=" O GLN E 208 " (cutoff:3.500A) 773 hydrogen bonds defined for protein. 2229 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: 4.63 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2344 1.31 - 1.44: 3764 1.44 - 1.56: 8465 1.56 - 1.69: 22 1.69 - 1.81: 114 Bond restraints: 14709 Sorted by residual: bond pdb=" C10 OLA E 401 " pdb=" C9 OLA E 401 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C16 6OU A 702 " pdb=" O18 6OU A 702 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C14 6OU A 702 " pdb=" C15 6OU A 702 " ideal model delta sigma weight residual 1.521 1.607 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C31 6OU A 703 " pdb=" O30 6OU A 703 " ideal model delta sigma weight residual 1.331 1.417 -0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 14704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 19726 5.18 - 10.36: 45 10.36 - 15.54: 3 15.54 - 20.72: 2 20.72 - 25.90: 2 Bond angle restraints: 19778 Sorted by residual: angle pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " pdb=" C42 6OU A 702 " ideal model delta sigma weight residual 127.56 153.46 -25.90 3.00e+00 1.11e-01 7.45e+01 angle pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " pdb=" C42 6OU A 703 " ideal model delta sigma weight residual 127.56 151.55 -23.99 3.00e+00 1.11e-01 6.40e+01 angle pdb=" O22 6OU A 702 " pdb=" P23 6OU A 702 " pdb=" O26 6OU A 702 " ideal model delta sigma weight residual 93.95 110.61 -16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" C39 6OU A 703 " pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " ideal model delta sigma weight residual 127.60 111.71 15.89 3.00e+00 1.11e-01 2.81e+01 angle pdb=" O22 6OU A 703 " pdb=" P23 6OU A 703 " pdb=" O26 6OU A 703 " ideal model delta sigma weight residual 93.95 108.87 -14.92 3.00e+00 1.11e-01 2.47e+01 ... (remaining 19773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 8672 35.85 - 71.70: 202 71.70 - 107.55: 21 107.55 - 143.40: 4 143.40 - 179.25: 2 Dihedral angle restraints: 8901 sinusoidal: 3689 harmonic: 5212 Sorted by residual: dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" O30 6OU A 703 " pdb=" C31 6OU A 703 " ideal model delta sinusoidal sigma weight residual 212.33 33.08 179.25 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" O30 6OU A 703 " pdb=" C31 6OU A 703 " ideal model delta sinusoidal sigma weight residual 85.49 -88.88 174.37 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" C21 6OU A 703 " pdb=" O22 6OU A 703 " ideal model delta sinusoidal sigma weight residual 301.00 158.85 142.15 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 8898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1880 0.060 - 0.120: 335 0.120 - 0.180: 28 0.180 - 0.240: 2 0.240 - 0.300: 1 Chirality restraints: 2246 Sorted by residual: chirality pdb=" C20 6OU A 702 " pdb=" C19 6OU A 702 " pdb=" C21 6OU A 702 " pdb=" O30 6OU A 702 " both_signs ideal model delta sigma weight residual False 2.35 2.65 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE C 198 " pdb=" CA ILE C 198 " pdb=" CG1 ILE C 198 " pdb=" CG2 ILE C 198 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE A 563 " pdb=" N ILE A 563 " pdb=" C ILE A 563 " pdb=" CB ILE A 563 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 2243 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " 0.287 2.00e-02 2.50e+03 2.20e-01 4.82e+02 pdb=" C11 OLA E 401 " -0.112 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " 0.116 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " -0.291 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 153 " 0.031 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP D 153 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP D 153 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 153 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 153 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 153 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 153 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 153 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 153 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 153 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 197 " -0.008 2.00e-02 2.50e+03 1.56e-02 6.06e+00 pdb=" CG TRP D 197 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP D 197 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 197 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 197 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP D 197 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 197 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 197 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 197 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 197 " 0.001 2.00e-02 2.50e+03 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 982 2.73 - 3.27: 14476 3.27 - 3.82: 22689 3.82 - 4.36: 25463 4.36 - 4.90: 44529 Nonbonded interactions: 108139 Sorted by model distance: nonbonded pdb=" ND2 ASN A 362 " pdb=" OD1 ASN A 382 " model vdw 2.191 3.120 nonbonded pdb=" NH2 ARG D 9 " pdb=" OE2 GLU D 60 " model vdw 2.226 3.120 nonbonded pdb=" OG SER C 145 " pdb=" OE1 GLN C 148 " model vdw 2.227 3.040 nonbonded pdb=" OG SER A 406 " pdb=" O ALA A 457 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.268 3.040 ... (remaining 108134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 334) } 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 group one per residue 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.680 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 14709 Z= 0.395 Angle : 0.805 25.896 19778 Z= 0.387 Chirality : 0.045 0.300 2246 Planarity : 0.006 0.220 2468 Dihedral : 16.626 179.254 5527 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1779 helix: 0.99 (0.17), residues: 1003 sheet: -1.02 (0.45), residues: 169 loop : -1.60 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP D 153 HIS 0.008 0.001 HIS A 596 PHE 0.026 0.002 PHE A 529 TYR 0.023 0.002 TYR A 315 ARG 0.010 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 57 TYR cc_start: 0.8347 (t80) cc_final: 0.8086 (t80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2736 time to fit residues: 66.7931 Evaluate side-chains 144 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.5980 chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14709 Z= 0.212 Angle : 0.584 11.643 19778 Z= 0.298 Chirality : 0.043 0.259 2246 Planarity : 0.003 0.039 2468 Dihedral : 11.996 165.934 2018 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 95.00 % Rotamer: Outliers : 0.51 % Allowed : 7.42 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1779 helix: 1.20 (0.17), residues: 1006 sheet: -0.96 (0.45), residues: 165 loop : -1.55 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 153 HIS 0.008 0.001 HIS D 134 PHE 0.022 0.001 PHE A 529 TYR 0.033 0.002 TYR E 151 ARG 0.005 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.5547 (mtt) cc_final: 0.5264 (mtm) REVERT: D 41 MET cc_start: 0.5591 (mmp) cc_final: 0.5377 (mmp) outliers start: 8 outliers final: 8 residues processed: 149 average time/residue: 0.2895 time to fit residues: 64.1573 Evaluate side-chains 144 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 133 optimal weight: 8.9990 chunk 109 optimal weight: 0.1980 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 0.2980 chunk 173 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 129 optimal weight: 50.0000 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14709 Z= 0.289 Angle : 0.603 13.201 19778 Z= 0.306 Chirality : 0.043 0.251 2246 Planarity : 0.003 0.040 2468 Dihedral : 11.434 170.814 2018 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 0.96 % Allowed : 11.07 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1779 helix: 1.13 (0.17), residues: 1006 sheet: -1.04 (0.43), residues: 167 loop : -1.56 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 122 HIS 0.006 0.001 HIS A 596 PHE 0.028 0.002 PHE A 529 TYR 0.028 0.002 TYR E 151 ARG 0.006 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7489 (ttm170) outliers start: 15 outliers final: 12 residues processed: 149 average time/residue: 0.2917 time to fit residues: 64.2286 Evaluate side-chains 148 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 161 optimal weight: 0.0060 chunk 171 optimal weight: 50.0000 chunk 84 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 0.0010 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 14709 Z= 0.156 Angle : 0.534 11.757 19778 Z= 0.267 Chirality : 0.040 0.235 2246 Planarity : 0.003 0.037 2468 Dihedral : 10.716 170.596 2018 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.11 % Rotamer: Outliers : 1.22 % Allowed : 12.28 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1779 helix: 1.47 (0.17), residues: 1010 sheet: -1.04 (0.41), residues: 176 loop : -1.49 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 122 HIS 0.005 0.001 HIS D 124 PHE 0.019 0.001 PHE A 529 TYR 0.024 0.001 TYR E 151 ARG 0.004 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7432 (ttm170) outliers start: 19 outliers final: 14 residues processed: 162 average time/residue: 0.2869 time to fit residues: 68.6804 Evaluate side-chains 153 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 30.0000 chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 127 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14709 Z= 0.278 Angle : 0.591 10.322 19778 Z= 0.298 Chirality : 0.043 0.214 2246 Planarity : 0.003 0.039 2468 Dihedral : 10.805 170.265 2018 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.60 % Allowed : 13.44 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1779 helix: 1.33 (0.17), residues: 1006 sheet: -1.01 (0.41), residues: 163 loop : -1.53 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 122 HIS 0.005 0.001 HIS A 596 PHE 0.029 0.002 PHE A 529 TYR 0.022 0.002 TYR E 151 ARG 0.006 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6421 (m-10) cc_final: 0.6037 (m-80) REVERT: B 83 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7791 (ttm170) outliers start: 25 outliers final: 17 residues processed: 158 average time/residue: 0.2670 time to fit residues: 63.1468 Evaluate side-chains 154 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14709 Z= 0.280 Angle : 0.591 12.865 19778 Z= 0.298 Chirality : 0.043 0.206 2246 Planarity : 0.003 0.040 2468 Dihedral : 10.809 173.376 2018 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.34 % Favored : 94.60 % Rotamer: Outliers : 2.11 % Allowed : 14.20 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1779 helix: 1.29 (0.17), residues: 1007 sheet: -0.95 (0.41), residues: 158 loop : -1.52 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 122 HIS 0.005 0.001 HIS A 596 PHE 0.027 0.002 PHE A 529 TYR 0.019 0.002 TYR E 151 ARG 0.006 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7078 (mt0) REVERT: A 315 TYR cc_start: 0.6464 (m-10) cc_final: 0.6236 (m-80) REVERT: B 83 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7809 (ttp-170) outliers start: 33 outliers final: 19 residues processed: 160 average time/residue: 0.2701 time to fit residues: 64.9059 Evaluate side-chains 159 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 30.0000 chunk 19 optimal weight: 0.8980 chunk 97 optimal weight: 0.0070 chunk 125 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 170 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14709 Z= 0.161 Angle : 0.539 12.833 19778 Z= 0.270 Chirality : 0.041 0.227 2246 Planarity : 0.003 0.038 2468 Dihedral : 10.386 172.942 2018 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.34 % Allowed : 15.74 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1779 helix: 1.51 (0.17), residues: 1015 sheet: -0.93 (0.41), residues: 163 loop : -1.48 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 122 HIS 0.003 0.001 HIS E 134 PHE 0.020 0.001 PHE A 529 TYR 0.019 0.001 TYR E 151 ARG 0.006 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 MET cc_start: 0.3196 (ppp) cc_final: 0.2326 (ppp) REVERT: C 74 MET cc_start: -0.0592 (pmm) cc_final: -0.3258 (tmm) outliers start: 21 outliers final: 15 residues processed: 155 average time/residue: 0.2721 time to fit residues: 63.9581 Evaluate side-chains 152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14709 Z= 0.176 Angle : 0.552 13.119 19778 Z= 0.276 Chirality : 0.041 0.262 2246 Planarity : 0.003 0.037 2468 Dihedral : 10.213 168.349 2018 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.41 % Allowed : 16.25 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1779 helix: 1.49 (0.17), residues: 1022 sheet: -0.88 (0.41), residues: 167 loop : -1.44 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 122 HIS 0.004 0.001 HIS B 86 PHE 0.023 0.001 PHE A 529 TYR 0.017 0.001 TYR E 151 ARG 0.007 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7096 (mt0) outliers start: 22 outliers final: 18 residues processed: 151 average time/residue: 0.2728 time to fit residues: 62.3475 Evaluate side-chains 155 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 40.0000 chunk 149 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 0.0060 chunk 150 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 168 optimal weight: 20.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14709 Z= 0.202 Angle : 0.585 13.317 19778 Z= 0.291 Chirality : 0.042 0.258 2246 Planarity : 0.003 0.037 2468 Dihedral : 10.272 170.953 2018 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.34 % Allowed : 16.63 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1779 helix: 1.44 (0.17), residues: 1021 sheet: -0.80 (0.41), residues: 165 loop : -1.42 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 122 HIS 0.008 0.001 HIS A 510 PHE 0.025 0.001 PHE A 529 TYR 0.017 0.001 TYR E 151 ARG 0.006 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 MET cc_start: -0.0482 (pmm) cc_final: -0.3071 (tmm) outliers start: 21 outliers final: 19 residues processed: 152 average time/residue: 0.2592 time to fit residues: 59.8547 Evaluate side-chains 152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 162 optimal weight: 40.0000 chunk 140 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS D 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14709 Z= 0.331 Angle : 0.649 13.738 19778 Z= 0.326 Chirality : 0.044 0.304 2246 Planarity : 0.003 0.040 2468 Dihedral : 10.577 172.678 2018 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.66 % Allowed : 16.57 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1779 helix: 1.16 (0.17), residues: 1023 sheet: -0.79 (0.40), residues: 160 loop : -1.45 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 122 HIS 0.006 0.001 HIS A 510 PHE 0.029 0.002 PHE A 529 TYR 0.023 0.002 TYR A 311 ARG 0.006 0.001 ARG D 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 MET cc_start: -0.0452 (pmm) cc_final: -0.3052 (tmm) outliers start: 26 outliers final: 21 residues processed: 158 average time/residue: 0.2823 time to fit residues: 66.4337 Evaluate side-chains 157 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 23 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 140 optimal weight: 0.0370 chunk 58 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.228220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.191454 restraints weight = 18567.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.188133 restraints weight = 38240.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.184062 restraints weight = 34367.666| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 14709 Z= 0.171 Angle : 0.587 17.898 19778 Z= 0.291 Chirality : 0.042 0.300 2246 Planarity : 0.003 0.037 2468 Dihedral : 10.160 169.691 2018 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 1.47 % Allowed : 17.15 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1779 helix: 1.39 (0.17), residues: 1021 sheet: -0.69 (0.42), residues: 147 loop : -1.39 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 122 HIS 0.003 0.001 HIS D 134 PHE 0.019 0.001 PHE A 529 TYR 0.017 0.001 TYR E 151 ARG 0.008 0.000 ARG D 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2620.80 seconds wall clock time: 50 minutes 12.04 seconds (3012.04 seconds total)