Starting phenix.real_space_refine on Wed Mar 4 16:09:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3f_29694/03_2026/8g3f_29694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3f_29694/03_2026/8g3f_29694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3f_29694/03_2026/8g3f_29694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3f_29694/03_2026/8g3f_29694.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3f_29694/03_2026/8g3f_29694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3f_29694/03_2026/8g3f_29694.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.01, per 1000 atoms: 0.21 Number of scatterers: 14442 At special positions: 0 Unit cell: (95.048, 113.36, 198.816, 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: 1.11 Conformation dependent library (CDL) restraints added in 506.8 milliseconds 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: 76 helices and 12 sheets defined 61.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.640A pdb=" N TYR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 47 removed outlier: 3.836A pdb=" N ASN A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.621A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 3.586A pdb=" N ILE A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 removed outlier: 3.839A pdb=" N ILE A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.560A pdb=" N LYS A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 176 removed outlier: 4.291A pdb=" N VAL A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 176 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 222 removed outlier: 4.371A pdb=" N GLY A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 253 removed outlier: 4.302A pdb=" N VAL A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 272 through 282 removed outlier: 3.614A pdb=" N SER A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.980A pdb=" N SER A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 292 through 325 removed outlier: 3.653A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 removed outlier: 3.902A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.776A pdb=" N GLN A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.601A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.772A 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 515 through 556 removed outlier: 4.031A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.544A pdb=" N LYS A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 602 removed outlier: 3.774A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 3.514A pdb=" N GLN A 602 " --> pdb=" O TYR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 removed outlier: 5.486A pdb=" N PHE A 606 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 607 " --> pdb=" O GLY A 604 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 608 " --> pdb=" O TRP A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 603 through 608' Processing helix chain 'A' and resid 614 through 633 removed outlier: 3.969A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.804A pdb=" N LYS A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 117 through 132 removed outlier: 3.745A pdb=" N GLU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 removed outlier: 4.120A pdb=" N ARG B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.603A pdb=" N ILE B 144 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 158 removed outlier: 3.604A pdb=" N LYS B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 203 through 209 removed outlier: 4.091A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) 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 removed outlier: 3.526A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.669A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.928A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 193 Processing helix chain 'C' and resid 203 through 209 removed outlier: 3.998A pdb=" N TYR C 209 " --> pdb=" O VAL C 205 " (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 9 through 29 removed outlier: 3.649A pdb=" N ILE D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 14 " --> pdb=" O ARG D 10 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 61 removed outlier: 3.569A pdb=" N VAL D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.612A pdb=" N GLU D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 139 removed outlier: 4.381A pdb=" N VAL D 90 " --> pdb=" O PHE D 86 " (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 176 removed outlier: 5.178A pdb=" N GLU D 173 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU D 176 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 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 271 Proline residue: D 269 - end of helix Processing helix chain 'D' and resid 281 through 285 removed outlier: 3.599A pdb=" N GLN D 285 " --> pdb=" O HIS D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 300 removed outlier: 4.007A pdb=" N ALA D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 removed outlier: 3.986A pdb=" N HIS D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 11 through 30 removed outlier: 3.563A pdb=" N ASP E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 37 removed outlier: 3.592A pdb=" N ASN E 37 " --> pdb=" O SER E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 34 through 37' Processing helix chain 'E' and resid 38 through 61 removed outlier: 4.090A pdb=" N ARG E 58 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS E 59 " --> pdb=" O PHE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 71 removed outlier: 4.075A pdb=" N LYS E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 79 removed outlier: 4.180A pdb=" N ILE E 79 " --> pdb=" O VAL E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 138 removed outlier: 3.654A pdb=" N ALA E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET E 89 " --> pdb=" O PRO E 85 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) 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 182 through 194 removed outlier: 4.278A pdb=" N LEU E 186 " --> pdb=" O GLN E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 218 through 235 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 281 through 287 removed outlier: 3.748A pdb=" N ALA E 286 " --> pdb=" O HIS E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 300 removed outlier: 4.551A pdb=" N TYR E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) 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: 3.602A pdb=" N LEU A 511 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 364 removed outlier: 8.822A pdb=" N VAL A 458 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA A 386 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 457 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 404 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA A 403 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY A 439 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 425 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30 removed outlier: 5.859A pdb=" N ALA B 6 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N HIS B 65 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS B 8 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR B 63 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS B 61 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=AA5, first strand: chain 'B' and resid 88 through 90 removed outlier: 7.457A pdb=" N GLY B 88 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE B 165 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 200 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ALA B 167 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET B 199 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE B 35 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE B 214 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER B 37 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 29 removed outlier: 4.024A pdb=" N GLU C 5 " --> pdb=" O HIS C 65 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS C 65 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.568A pdb=" N GLY C 88 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 198 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 179 through 182 Processing sheet with id=AB1, first strand: chain 'D' and resid 205 through 209 removed outlier: 3.611A pdb=" N ILE D 243 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D 245 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 179 through 181 removed outlier: 3.725A pdb=" N GLU E 179 " --> pdb=" O SER E 216 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 216 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.567A pdb=" N GLN E 208 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER E 245 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 320 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS E 305 " --> pdb=" O THR E 321 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2268 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: 2.24 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2343 1.32 - 1.44: 3765 1.44 - 1.57: 8465 1.57 - 1.69: 22 1.69 - 1.82: 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 1.469 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C16 6OU A 702 " pdb=" O18 6OU A 702 " ideal model delta sigma weight residual 1.327 1.464 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.462 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C31 6OU A 703 " pdb=" O30 6OU A 703 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C14 6OU A 702 " pdb=" C15 6OU A 702 " ideal model delta sigma weight residual 1.521 1.609 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 14704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.96: 19721 4.96 - 9.93: 51 9.93 - 14.89: 0 14.89 - 19.85: 4 19.85 - 24.81: 2 Bond angle restraints: 19778 Sorted by residual: angle pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " pdb=" C42 6OU A 703 " ideal model delta sigma weight residual 127.56 152.37 -24.81 3.00e+00 1.11e-01 6.84e+01 angle pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " pdb=" C42 6OU A 702 " ideal model delta sigma weight residual 127.56 152.10 -24.54 3.00e+00 1.11e-01 6.69e+01 angle pdb=" O22 6OU A 702 " pdb=" P23 6OU A 702 " pdb=" O26 6OU A 702 " ideal model delta sigma weight residual 93.95 110.79 -16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C39 6OU A 702 " pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " ideal model delta sigma weight residual 127.60 111.61 15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O22 6OU A 703 " pdb=" P23 6OU A 703 " pdb=" O26 6OU A 703 " ideal model delta sigma weight residual 93.95 109.65 -15.70 3.00e+00 1.11e-01 2.74e+01 ... (remaining 19773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 8665 35.61 - 71.21: 215 71.21 - 106.82: 16 106.82 - 142.42: 1 142.42 - 178.03: 4 Dihedral angle restraints: 8901 sinusoidal: 3689 harmonic: 5212 Sorted by residual: dihedral pdb=" CA ILE A 282 " pdb=" C ILE A 282 " pdb=" N MET A 283 " pdb=" CA MET A 283 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ARG D 139 " pdb=" C ARG D 139 " pdb=" N MET D 140 " pdb=" CA MET D 140 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 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 -59.00 119.03 -178.03 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1731 0.048 - 0.097: 402 0.097 - 0.145: 97 0.145 - 0.193: 13 0.193 - 0.241: 3 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 2.59 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA PHE A 174 " pdb=" N PHE A 174 " pdb=" C PHE A 174 " pdb=" CB PHE A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE E 156 " pdb=" N ILE E 156 " pdb=" C ILE E 156 " pdb=" CB ILE E 156 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2243 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " -0.197 2.00e-02 2.50e+03 1.52e-01 2.32e+02 pdb=" C11 OLA E 401 " 0.088 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " -0.088 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 173 " 0.021 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C THR A 173 " -0.068 2.00e-02 2.50e+03 pdb=" O THR A 173 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE A 174 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 30 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO E 31 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 31 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 31 " 0.030 5.00e-02 4.00e+02 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 260 2.70 - 3.25: 14113 3.25 - 3.80: 21907 3.80 - 4.35: 26921 4.35 - 4.90: 44883 Nonbonded interactions: 108084 Sorted by model distance: nonbonded pdb=" OD1 ASP C 168 " pdb=" N GLU C 169 " model vdw 2.148 3.120 nonbonded pdb=" O PHE A 251 " pdb=" OG SER A 255 " model vdw 2.227 3.040 nonbonded pdb=" OG SER A 421 " pdb=" O TYR A 437 " model vdw 2.241 3.040 nonbonded pdb=" ND2 ASN C 7 " pdb=" OD1 ASP C 27 " model vdw 2.250 3.120 nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.259 3.040 ... (remaining 108079 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.890 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 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 : 0.005 0.137 14709 Z= 0.280 Angle : 0.791 24.814 19778 Z= 0.404 Chirality : 0.044 0.241 2246 Planarity : 0.005 0.152 2468 Dihedral : 16.236 178.030 5527 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.90 % Allowed : 0.83 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.21), residues: 1779 helix: 1.42 (0.17), residues: 998 sheet: -0.51 (0.43), residues: 159 loop : -1.81 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 212 TYR 0.022 0.001 TYR C 222 PHE 0.019 0.001 PHE A 124 TRP 0.028 0.002 TRP D 153 HIS 0.008 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00491 (14709) covalent geometry : angle 0.79097 (19778) hydrogen bonds : bond 0.15782 ( 793) hydrogen bonds : angle 5.62434 ( 2268) *********************** 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 245 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 THR cc_start: 0.7393 (m) cc_final: 0.7033 (p) REVERT: C 215 PHE cc_start: 0.7535 (m-80) cc_final: 0.7254 (m-80) REVERT: D 157 HIS cc_start: 0.5035 (t-90) cc_final: 0.4752 (t-90) REVERT: E 18 PHE cc_start: 0.6522 (m-80) cc_final: 0.6120 (t80) REVERT: E 23 MET cc_start: 0.7482 (tpp) cc_final: 0.7083 (tpp) REVERT: E 110 LEU cc_start: 0.8446 (tp) cc_final: 0.8176 (tt) REVERT: E 158 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7266 (tt) outliers start: 14 outliers final: 2 residues processed: 237 average time/residue: 0.1175 time to fit residues: 41.0390 Evaluate side-chains 186 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 183 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 159 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 GLN D 20 GLN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.203930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.160377 restraints weight = 23515.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.156445 restraints weight = 39273.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152127 restraints weight = 31478.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150455 restraints weight = 30239.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.149001 restraints weight = 24739.596| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1574 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= 0.174 Angle : 0.636 7.800 19778 Z= 0.330 Chirality : 0.043 0.167 2246 Planarity : 0.004 0.066 2468 Dihedral : 11.792 163.981 2023 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.92 % Allowed : 9.92 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1779 helix: 1.46 (0.17), residues: 993 sheet: -0.44 (0.44), residues: 156 loop : -1.67 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 226 TYR 0.027 0.002 TYR E 151 PHE 0.019 0.002 PHE A 529 TRP 0.033 0.002 TRP D 220 HIS 0.012 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00393 (14709) covalent geometry : angle 0.63641 (19778) hydrogen bonds : bond 0.06178 ( 793) hydrogen bonds : angle 4.77889 ( 2268) *********************** 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 225 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 THR cc_start: 0.7623 (m) cc_final: 0.7204 (p) REVERT: A 319 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7753 (mmtp) REVERT: A 344 LEU cc_start: 0.8026 (mt) cc_final: 0.7735 (tp) REVERT: E 18 PHE cc_start: 0.6700 (m-80) cc_final: 0.6093 (t80) REVERT: E 23 MET cc_start: 0.7534 (tpp) cc_final: 0.7195 (tpp) outliers start: 30 outliers final: 20 residues processed: 213 average time/residue: 0.1138 time to fit residues: 35.9009 Evaluate side-chains 191 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 227 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 122 optimal weight: 7.9990 chunk 162 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 151 optimal weight: 0.0020 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 227 GLN E 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.204577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160062 restraints weight = 23651.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.155526 restraints weight = 35883.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.150476 restraints weight = 34098.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151235 restraints weight = 32270.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.148978 restraints weight = 24520.733| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14709 Z= 0.143 Angle : 0.613 11.217 19778 Z= 0.313 Chirality : 0.042 0.168 2246 Planarity : 0.003 0.052 2468 Dihedral : 11.165 163.332 2019 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.56 % Allowed : 12.80 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1779 helix: 1.62 (0.17), residues: 985 sheet: -0.36 (0.43), residues: 166 loop : -1.61 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 168 TYR 0.022 0.002 TYR E 151 PHE 0.016 0.001 PHE A 529 TRP 0.022 0.002 TRP D 220 HIS 0.009 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00313 (14709) covalent geometry : angle 0.61319 (19778) hydrogen bonds : bond 0.05690 ( 793) hydrogen bonds : angle 4.52339 ( 2268) *********************** 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 230 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8733 (tt) REVERT: A 173 THR cc_start: 0.7640 (m) cc_final: 0.7166 (p) REVERT: C 50 LEU cc_start: 0.4671 (OUTLIER) cc_final: 0.4458 (mm) REVERT: C 212 ARG cc_start: 0.8314 (ttt-90) cc_final: 0.7892 (ttt90) REVERT: E 18 PHE cc_start: 0.6709 (m-80) cc_final: 0.6109 (t80) REVERT: E 23 MET cc_start: 0.7548 (tpp) cc_final: 0.7129 (tpp) outliers start: 40 outliers final: 28 residues processed: 215 average time/residue: 0.1076 time to fit residues: 34.2825 Evaluate side-chains 198 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 13 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.0170 chunk 167 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 91 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN D 157 HIS E 19 GLN E 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.206519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.162027 restraints weight = 23698.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.156983 restraints weight = 32076.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.150722 restraints weight = 25897.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.148591 restraints weight = 28306.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.148107 restraints weight = 22975.834| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14709 Z= 0.116 Angle : 0.580 10.788 19778 Z= 0.294 Chirality : 0.041 0.172 2246 Planarity : 0.003 0.055 2468 Dihedral : 10.504 164.059 2018 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.43 % Allowed : 15.04 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.21), residues: 1779 helix: 1.72 (0.17), residues: 991 sheet: -0.38 (0.41), residues: 177 loop : -1.55 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 109 TYR 0.026 0.001 TYR E 151 PHE 0.012 0.001 PHE A 529 TRP 0.029 0.002 TRP E 122 HIS 0.008 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00238 (14709) covalent geometry : angle 0.57992 (19778) hydrogen bonds : bond 0.04951 ( 793) hydrogen bonds : angle 4.27166 ( 2268) *********************** 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 233 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6490 (ppp) cc_final: 0.6130 (ppp) REVERT: A 63 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 173 THR cc_start: 0.7469 (m) cc_final: 0.6969 (p) REVERT: C 74 MET cc_start: -0.0015 (tmm) cc_final: -0.0220 (tmm) REVERT: C 134 TYR cc_start: 0.7950 (t80) cc_final: 0.7727 (t80) REVERT: D 153 TRP cc_start: 0.7058 (t-100) cc_final: 0.6093 (t-100) REVERT: E 18 PHE cc_start: 0.6684 (m-80) cc_final: 0.6081 (t80) REVERT: E 23 MET cc_start: 0.7450 (tpp) cc_final: 0.7085 (tpp) REVERT: E 110 LEU cc_start: 0.9021 (tp) cc_final: 0.8800 (tt) REVERT: E 122 TRP cc_start: 0.8159 (t-100) cc_final: 0.7748 (t-100) outliers start: 38 outliers final: 26 residues processed: 216 average time/residue: 0.1215 time to fit residues: 38.7212 Evaluate side-chains 203 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 137 optimal weight: 30.0000 chunk 161 optimal weight: 8.9990 chunk 104 optimal weight: 0.0270 chunk 162 optimal weight: 5.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN E 19 GLN E 148 GLN E 157 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.203890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.157035 restraints weight = 23530.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.151641 restraints weight = 36611.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.147490 restraints weight = 30869.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147137 restraints weight = 26250.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146333 restraints weight = 20025.300| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14709 Z= 0.162 Angle : 0.649 14.562 19778 Z= 0.326 Chirality : 0.043 0.190 2246 Planarity : 0.003 0.059 2468 Dihedral : 10.425 158.552 2018 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.75 % Allowed : 16.89 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1779 helix: 1.51 (0.17), residues: 994 sheet: -0.42 (0.41), residues: 178 loop : -1.59 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 155 TYR 0.036 0.002 TYR D 151 PHE 0.020 0.001 PHE A 529 TRP 0.044 0.003 TRP D 153 HIS 0.014 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00368 (14709) covalent geometry : angle 0.64934 (19778) hydrogen bonds : bond 0.05911 ( 793) hydrogen bonds : angle 4.39757 ( 2268) *********************** 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 227 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8820 (tt) REVERT: A 534 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7331 (mp) REVERT: B 71 MET cc_start: 0.7536 (ppp) cc_final: 0.6777 (mmp) REVERT: C 50 LEU cc_start: 0.4178 (OUTLIER) cc_final: 0.3938 (mm) REVERT: D 114 ASN cc_start: 0.8625 (m110) cc_final: 0.8414 (m110) REVERT: D 155 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7349 (ttm110) REVERT: D 290 MET cc_start: 0.6430 (tpp) cc_final: 0.6130 (mmm) REVERT: E 18 PHE cc_start: 0.6692 (m-80) cc_final: 0.6140 (t80) REVERT: E 23 MET cc_start: 0.7509 (tpp) cc_final: 0.7165 (tpp) REVERT: E 110 LEU cc_start: 0.8969 (tp) cc_final: 0.8422 (tt) outliers start: 43 outliers final: 31 residues processed: 209 average time/residue: 0.1166 time to fit residues: 36.1914 Evaluate side-chains 200 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 104 optimal weight: 0.0050 chunk 4 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 503 GLN A 505 ASN B 58 GLN C 160 HIS ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.205422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161373 restraints weight = 23358.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.153811 restraints weight = 32233.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149313 restraints weight = 28924.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.149116 restraints weight = 26587.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.147536 restraints weight = 20986.944| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14709 Z= 0.131 Angle : 0.629 11.776 19778 Z= 0.314 Chirality : 0.042 0.195 2246 Planarity : 0.003 0.061 2468 Dihedral : 10.118 157.835 2018 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.26 % Allowed : 17.79 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1779 helix: 1.68 (0.17), residues: 984 sheet: -0.32 (0.42), residues: 175 loop : -1.48 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 155 TYR 0.041 0.001 TYR D 151 PHE 0.015 0.001 PHE A 529 TRP 0.025 0.003 TRP D 122 HIS 0.008 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00284 (14709) covalent geometry : angle 0.62896 (19778) hydrogen bonds : bond 0.05371 ( 793) hydrogen bonds : angle 4.22345 ( 2268) *********************** 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 228 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6469 (ppp) cc_final: 0.6059 (ppp) REVERT: A 63 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8680 (tt) REVERT: A 319 LYS cc_start: 0.8030 (tppt) cc_final: 0.7552 (mmtp) REVERT: B 221 MET cc_start: 0.7184 (tpt) cc_final: 0.6968 (mmt) REVERT: C 50 LEU cc_start: 0.4493 (OUTLIER) cc_final: 0.4280 (mm) REVERT: C 74 MET cc_start: -0.0119 (tmm) cc_final: -0.0484 (tmm) REVERT: D 114 ASN cc_start: 0.8689 (m110) cc_final: 0.8451 (m110) REVERT: D 155 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7854 (tpp80) REVERT: D 290 MET cc_start: 0.6466 (tpp) cc_final: 0.6189 (mmm) REVERT: E 18 PHE cc_start: 0.6696 (m-80) cc_final: 0.6104 (t80) REVERT: E 23 MET cc_start: 0.7494 (tpp) cc_final: 0.7104 (tpp) REVERT: E 110 LEU cc_start: 0.8957 (tp) cc_final: 0.8656 (tt) REVERT: E 226 ARG cc_start: 0.7672 (mmm160) cc_final: 0.7451 (mmm160) outliers start: 51 outliers final: 34 residues processed: 206 average time/residue: 0.1180 time to fit residues: 35.9043 Evaluate side-chains 206 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 197 TRP Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 124 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.205303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.162587 restraints weight = 23344.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.157803 restraints weight = 37661.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.153523 restraints weight = 28907.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.150500 restraints weight = 30033.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.149603 restraints weight = 26330.531| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14709 Z= 0.137 Angle : 0.651 12.675 19778 Z= 0.323 Chirality : 0.042 0.196 2246 Planarity : 0.003 0.064 2468 Dihedral : 9.997 156.599 2018 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.20 % Allowed : 18.49 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1779 helix: 1.69 (0.17), residues: 985 sheet: -0.27 (0.42), residues: 176 loop : -1.45 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 155 TYR 0.032 0.001 TYR D 151 PHE 0.028 0.001 PHE E 223 TRP 0.058 0.003 TRP D 153 HIS 0.022 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00301 (14709) covalent geometry : angle 0.65119 (19778) hydrogen bonds : bond 0.05416 ( 793) hydrogen bonds : angle 4.22109 ( 2268) *********************** 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 226 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6410 (ppp) cc_final: 0.6101 (ppp) REVERT: A 63 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8560 (tt) REVERT: A 173 THR cc_start: 0.7638 (m) cc_final: 0.7155 (p) REVERT: A 534 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7279 (mp) REVERT: B 112 ILE cc_start: 0.8844 (mm) cc_final: 0.8564 (mm) REVERT: C 50 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.4060 (mm) REVERT: D 114 ASN cc_start: 0.8635 (m110) cc_final: 0.8377 (m110) REVERT: E 18 PHE cc_start: 0.6692 (m-80) cc_final: 0.6094 (t80) REVERT: E 23 MET cc_start: 0.7513 (tpp) cc_final: 0.7107 (tpp) outliers start: 50 outliers final: 41 residues processed: 204 average time/residue: 0.1206 time to fit residues: 36.6718 Evaluate side-chains 210 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 197 TRP Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 141 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.205974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.163573 restraints weight = 23081.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.158492 restraints weight = 37561.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.154934 restraints weight = 32691.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.153915 restraints weight = 27776.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.151438 restraints weight = 26271.334| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2759 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= 0.126 Angle : 0.657 15.447 19778 Z= 0.322 Chirality : 0.042 0.212 2246 Planarity : 0.003 0.066 2468 Dihedral : 9.818 154.902 2018 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.20 % Allowed : 19.32 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1779 helix: 1.74 (0.17), residues: 985 sheet: -0.19 (0.43), residues: 175 loop : -1.38 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 109 TYR 0.023 0.001 TYR E 151 PHE 0.014 0.001 PHE A 529 TRP 0.040 0.003 TRP E 122 HIS 0.006 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00270 (14709) covalent geometry : angle 0.65723 (19778) hydrogen bonds : bond 0.05175 ( 793) hydrogen bonds : angle 4.16509 ( 2268) *********************** 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 228 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6300 (ppp) cc_final: 0.6090 (ppp) REVERT: A 63 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8597 (tt) REVERT: A 173 THR cc_start: 0.7617 (m) cc_final: 0.7133 (p) REVERT: A 319 LYS cc_start: 0.7932 (tppt) cc_final: 0.7475 (mmtp) REVERT: A 455 MET cc_start: 0.7229 (mmm) cc_final: 0.6870 (mmp) REVERT: A 534 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7378 (mp) REVERT: B 112 ILE cc_start: 0.8864 (mm) cc_final: 0.8595 (mm) REVERT: D 114 ASN cc_start: 0.8574 (m110) cc_final: 0.8357 (m110) REVERT: E 18 PHE cc_start: 0.6675 (m-80) cc_final: 0.6078 (t80) REVERT: E 23 MET cc_start: 0.7533 (tpp) cc_final: 0.7102 (tpp) REVERT: E 122 TRP cc_start: 0.7729 (t-100) cc_final: 0.6992 (t-100) outliers start: 50 outliers final: 39 residues processed: 209 average time/residue: 0.1128 time to fit residues: 35.1642 Evaluate side-chains 213 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 197 TRP Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 77 optimal weight: 0.0980 chunk 129 optimal weight: 9.9990 chunk 117 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 106 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 15 optimal weight: 0.0020 chunk 133 optimal weight: 4.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.207884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.165358 restraints weight = 23526.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.161026 restraints weight = 35965.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157021 restraints weight = 29455.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.155451 restraints weight = 29104.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.153659 restraints weight = 26286.771| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14709 Z= 0.120 Angle : 0.678 15.788 19778 Z= 0.333 Chirality : 0.042 0.223 2246 Planarity : 0.003 0.068 2468 Dihedral : 9.552 153.057 2018 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.11 % Allowed : 20.15 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.22), residues: 1779 helix: 1.80 (0.17), residues: 996 sheet: -0.19 (0.42), residues: 185 loop : -1.28 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 109 TYR 0.024 0.001 TYR D 293 PHE 0.010 0.001 PHE A 529 TRP 0.041 0.003 TRP E 122 HIS 0.022 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00245 (14709) covalent geometry : angle 0.67819 (19778) hydrogen bonds : bond 0.04690 ( 793) hydrogen bonds : angle 4.10183 ( 2268) *********************** 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 213 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 173 THR cc_start: 0.7581 (m) cc_final: 0.7116 (p) REVERT: A 376 MET cc_start: 0.6085 (ppp) cc_final: 0.5829 (ppp) REVERT: A 534 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7209 (mp) REVERT: D 114 ASN cc_start: 0.8548 (m110) cc_final: 0.8309 (m110) REVERT: E 18 PHE cc_start: 0.6638 (m-80) cc_final: 0.6015 (t80) REVERT: E 140 MET cc_start: 0.3460 (ppp) cc_final: 0.2626 (ppp) outliers start: 33 outliers final: 27 residues processed: 200 average time/residue: 0.1118 time to fit residues: 33.8396 Evaluate side-chains 204 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 197 TRP Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 0.0770 chunk 159 optimal weight: 8.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.205840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.165270 restraints weight = 23160.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.158974 restraints weight = 32533.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.151458 restraints weight = 27879.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.147604 restraints weight = 29517.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146268 restraints weight = 28331.817| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2962 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= 0.134 Angle : 0.695 15.012 19778 Z= 0.341 Chirality : 0.043 0.205 2246 Planarity : 0.003 0.071 2468 Dihedral : 9.581 147.675 2018 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.24 % Allowed : 20.22 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1779 helix: 1.72 (0.17), residues: 999 sheet: -0.18 (0.42), residues: 185 loop : -1.27 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 109 TYR 0.030 0.001 TYR D 293 PHE 0.017 0.001 PHE A 529 TRP 0.075 0.004 TRP E 122 HIS 0.014 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00292 (14709) covalent geometry : angle 0.69510 (19778) hydrogen bonds : bond 0.05204 ( 793) hydrogen bonds : angle 4.15488 ( 2268) ********************** 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 210 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8549 (tt) REVERT: A 173 THR cc_start: 0.7652 (m) cc_final: 0.7197 (p) REVERT: A 376 MET cc_start: 0.6309 (ppp) cc_final: 0.6088 (ppp) REVERT: A 534 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7166 (mp) REVERT: B 112 ILE cc_start: 0.8802 (mm) cc_final: 0.8588 (mm) REVERT: D 114 ASN cc_start: 0.8711 (m110) cc_final: 0.8429 (m110) REVERT: E 18 PHE cc_start: 0.6650 (m-80) cc_final: 0.6047 (t80) REVERT: E 140 MET cc_start: 0.3809 (ppp) cc_final: 0.2968 (ppp) outliers start: 35 outliers final: 32 residues processed: 198 average time/residue: 0.1113 time to fit residues: 32.8883 Evaluate side-chains 201 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 155 ARG Chi-restraints excluded: chain D residue 197 TRP Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 135 optimal weight: 0.2980 chunk 168 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN C 160 HIS D 20 GLN E 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.205180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.162334 restraints weight = 23438.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.157204 restraints weight = 33493.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.152528 restraints weight = 27177.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.150389 restraints weight = 28430.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.148520 restraints weight = 25595.528| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14709 Z= 0.136 Angle : 0.700 14.676 19778 Z= 0.345 Chirality : 0.043 0.218 2246 Planarity : 0.004 0.071 2468 Dihedral : 9.507 141.449 2018 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.43 % Allowed : 20.35 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1779 helix: 1.67 (0.17), residues: 997 sheet: -0.13 (0.42), residues: 185 loop : -1.27 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 226 TYR 0.030 0.001 TYR D 293 PHE 0.016 0.001 PHE A 529 TRP 0.092 0.004 TRP E 122 HIS 0.027 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00297 (14709) covalent geometry : angle 0.70039 (19778) hydrogen bonds : bond 0.05372 ( 793) hydrogen bonds : angle 4.17152 ( 2268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.41 seconds wall clock time: 40 minutes 47.27 seconds (2447.27 seconds total)