Starting phenix.real_space_refine on Fri May 16 18:49:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3f_29694/05_2025/8g3f_29694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3f_29694/05_2025/8g3f_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_29694/05_2025/8g3f_29694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3f_29694/05_2025/8g3f_29694.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3f_29694/05_2025/8g3f_29694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3f_29694/05_2025/8g3f_29694.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14442 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'6OU': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.76, per 1000 atoms: 0.61 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: 3.40 Conformation dependent library (CDL) restraints added in 1.7 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 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: 1.50 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: 4.47 Time building geometry restraints manager: 4.06 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: 4.030 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.220 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (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 TRP 0.028 0.002 TRP D 153 HIS 0.008 0.001 HIS C 86 PHE 0.019 0.001 PHE A 124 TYR 0.022 0.001 TYR C 222 ARG 0.007 0.000 ARG C 212 Details of bonding type rmsd hydrogen bonds : bond 0.15782 ( 793) hydrogen bonds : angle 5.62434 ( 2268) covalent geometry : bond 0.00491 (14709) covalent geometry : angle 0.79097 (19778) *********************** 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 : 1.660 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: 0.7084 (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: 0.4750 (t-90) REVERT: E 18 PHE cc_start: 0.6522 (m-80) cc_final: 0.6121 (t80) REVERT: E 23 MET cc_start: 0.7482 (tpp) cc_final: 0.7075 (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: 0.7265 (tt) outliers start: 14 outliers final: 2 residues processed: 237 average time/residue: 0.2667 time to fit residues: 91.9369 Evaluate side-chains 187 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 149 optimal weight: 0.6980 chunk 134 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4485 r_free = 0.4485 target = 0.206341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.163608 restraints weight = 23554.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.158122 restraints weight = 36271.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153387 restraints weight = 31358.762| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14709 Z= 0.139 Angle : 0.608 9.745 19778 Z= 0.312 Chirality : 0.042 0.164 2246 Planarity : 0.004 0.057 2468 Dihedral : 11.754 166.578 2023 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.79 % Allowed : 9.02 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1779 helix: 1.60 (0.17), residues: 992 sheet: -0.36 (0.44), residues: 155 loop : -1.64 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 220 HIS 0.012 0.001 HIS C 160 PHE 0.015 0.001 PHE A 529 TYR 0.028 0.002 TYR E 151 ARG 0.011 0.001 ARG E 226 Details of bonding type rmsd hydrogen bonds : bond 0.05597 ( 793) hydrogen bonds : angle 4.68031 ( 2268) covalent geometry : bond 0.00297 (14709) covalent geometry : angle 0.60810 (19778) *********************** 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 232 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 THR cc_start: 0.7582 (m) cc_final: 0.7145 (p) REVERT: A 344 LEU cc_start: 0.7990 (mt) cc_final: 0.7710 (tp) REVERT: E 18 PHE cc_start: 0.6639 (m-80) cc_final: 0.6076 (t80) outliers start: 28 outliers final: 18 residues processed: 219 average time/residue: 0.2653 time to fit residues: 84.2485 Evaluate side-chains 193 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 528 MET Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 616 MET 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 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 18 optimal weight: 0.2980 chunk 127 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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 ** 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** B 65 HIS C 160 HIS D 20 GLN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 20 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 = 0.4386 r_free = 0.4386 target = 0.196401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.150867 restraints weight = 23369.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145538 restraints weight = 38880.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141332 restraints weight = 32271.351| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.009 0.073 14709 Z= 0.381 Angle : 0.863 11.079 19778 Z= 0.446 Chirality : 0.051 0.238 2246 Planarity : 0.005 0.056 2468 Dihedral : 11.741 151.659 2019 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.07 % Allowed : 14.08 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1779 helix: 0.63 (0.17), residues: 1004 sheet: -0.56 (0.42), residues: 163 loop : -1.97 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 122 HIS 0.012 0.002 HIS A 596 PHE 0.030 0.003 PHE A 33 TYR 0.033 0.003 TYR A 561 ARG 0.008 0.001 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.09054 ( 793) hydrogen bonds : angle 5.34393 ( 2268) covalent geometry : bond 0.00916 (14709) covalent geometry : angle 0.86265 (19778) *********************** 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 235 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 1.513 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 200 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6821 (t80) REVERT: A 319 LYS cc_start: 0.8374 (tppt) cc_final: 0.7932 (mmtp) REVERT: A 556 ASP cc_start: 0.7768 (t0) cc_final: 0.7346 (t0) REVERT: B 5 GLU cc_start: 0.6270 (mp0) cc_final: 0.6042 (mp0) REVERT: C 50 LEU cc_start: 0.4048 (OUTLIER) cc_final: 0.3672 (mm) REVERT: E 18 PHE cc_start: 0.6865 (m-80) cc_final: 0.6013 (t80) REVERT: E 110 LEU cc_start: 0.8923 (tt) cc_final: 0.8653 (tp) REVERT: E 290 MET cc_start: 0.4125 (mmp) cc_final: 0.3877 (mmp) outliers start: 48 outliers final: 35 residues processed: 220 average time/residue: 0.2436 time to fit residues: 79.1573 Evaluate side-chains 201 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 179 SER Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 LYS 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 537 THR 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 61 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 28 ILE 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 C residue 210 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 134 HIS 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 98 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 146 optimal weight: 0.7980 chunk 171 optimal weight: 0.0770 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.202511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159406 restraints weight = 23222.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154559 restraints weight = 35628.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149760 restraints weight = 27486.791| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14709 Z= 0.152 Angle : 0.633 10.449 19778 Z= 0.323 Chirality : 0.042 0.153 2246 Planarity : 0.004 0.060 2468 Dihedral : 11.311 155.994 2019 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.37 % Allowed : 17.21 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1779 helix: 1.27 (0.17), residues: 998 sheet: -0.37 (0.42), residues: 163 loop : -1.86 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 153 HIS 0.020 0.001 HIS C 160 PHE 0.017 0.001 PHE A 529 TYR 0.022 0.002 TYR E 151 ARG 0.007 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.06260 ( 793) hydrogen bonds : angle 4.56175 ( 2268) covalent geometry : bond 0.00331 (14709) covalent geometry : angle 0.63273 (19778) *********************** 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 217 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.621 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 319 LYS cc_start: 0.8241 (tppt) cc_final: 0.7862 (mmtp) REVERT: A 556 ASP cc_start: 0.7596 (t0) cc_final: 0.7200 (t0) REVERT: B 112 ILE cc_start: 0.8865 (mm) cc_final: 0.8441 (mt) REVERT: C 134 TYR cc_start: 0.7789 (t80) cc_final: 0.7582 (t80) REVERT: D 153 TRP cc_start: 0.6742 (t-100) cc_final: 0.5891 (t-100) REVERT: E 18 PHE cc_start: 0.6746 (m-80) cc_final: 0.6112 (t80) outliers start: 37 outliers final: 24 residues processed: 201 average time/residue: 0.2664 time to fit residues: 78.3305 Evaluate side-chains 186 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR 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 200 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 541 THR 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 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 48 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 134 HIS 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 70 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 9 optimal weight: 0.0370 chunk 83 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 165 optimal weight: 30.0000 chunk 65 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN C 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.204080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.160842 restraints weight = 23472.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156017 restraints weight = 35415.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151014 restraints weight = 26658.049| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14709 Z= 0.133 Angle : 0.627 14.592 19778 Z= 0.314 Chirality : 0.042 0.157 2246 Planarity : 0.003 0.060 2468 Dihedral : 10.833 153.960 2019 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.30 % Allowed : 18.49 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1779 helix: 1.47 (0.17), residues: 999 sheet: -0.36 (0.42), residues: 175 loop : -1.71 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP D 153 HIS 0.014 0.001 HIS D 157 PHE 0.014 0.001 PHE A 529 TYR 0.023 0.001 TYR E 151 ARG 0.008 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05624 ( 793) hydrogen bonds : angle 4.37420 ( 2268) covalent geometry : bond 0.00281 (14709) covalent geometry : angle 0.62733 (19778) *********************** 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: 36 poor density : 191 time to evaluate : 1.472 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: symmetry clash REVERT: A 1 MET cc_start: 0.6420 (ppp) cc_final: 0.5950 (ppp) REVERT: A 534 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 556 ASP cc_start: 0.7471 (t0) cc_final: 0.7079 (t0) REVERT: B 112 ILE cc_start: 0.8907 (mm) cc_final: 0.8483 (mt) REVERT: C 217 LYS cc_start: 0.7949 (pptt) cc_final: 0.7360 (ptpt) REVERT: E 18 PHE cc_start: 0.6759 (m-80) cc_final: 0.6138 (t80) REVERT: E 110 LEU cc_start: 0.8787 (tt) cc_final: 0.8575 (tp) outliers start: 36 outliers final: 22 residues processed: 210 average time/residue: 0.2534 time to fit residues: 78.4727 Evaluate side-chains 195 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR 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 411 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR 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 115 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 53 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 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 = 0.4460 r_free = 0.4460 target = 0.204156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.163581 restraints weight = 23809.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.157064 restraints weight = 32244.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.152457 restraints weight = 28156.404| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2659 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= 0.138 Angle : 0.646 11.902 19778 Z= 0.320 Chirality : 0.042 0.194 2246 Planarity : 0.003 0.063 2468 Dihedral : 10.555 147.750 2018 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.30 % Allowed : 20.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1779 helix: 1.61 (0.17), residues: 989 sheet: -0.32 (0.42), residues: 176 loop : -1.58 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 153 HIS 0.019 0.001 HIS C 160 PHE 0.017 0.001 PHE C 158 TYR 0.023 0.001 TYR E 151 ARG 0.009 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05601 ( 793) hydrogen bonds : angle 4.32394 ( 2268) covalent geometry : bond 0.00300 (14709) covalent geometry : angle 0.64634 (19778) *********************** 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 216 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 1.649 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: symmetry clash REVERT: A 1 MET cc_start: 0.6258 (ppp) cc_final: 0.5838 (ppp) REVERT: A 319 LYS cc_start: 0.8106 (tppt) cc_final: 0.7706 (mmtp) REVERT: A 534 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7613 (mp) REVERT: A 556 ASP cc_start: 0.7567 (t0) cc_final: 0.7154 (t0) REVERT: B 71 MET cc_start: 0.7285 (ppp) cc_final: 0.6712 (mmp) REVERT: C 50 LEU cc_start: 0.4407 (OUTLIER) cc_final: 0.3967 (mm) REVERT: E 18 PHE cc_start: 0.6735 (m-80) cc_final: 0.6096 (t80) REVERT: E 226 ARG cc_start: 0.7419 (mmm160) cc_final: 0.7210 (mmm160) outliers start: 36 outliers final: 28 residues processed: 200 average time/residue: 0.2663 time to fit residues: 77.8906 Evaluate side-chains 201 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR 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 387 VAL Chi-restraints excluded: chain A residue 411 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 534 LEU Chi-restraints excluded: chain A residue 541 THR 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 199 MET 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 135 GLU Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 76 optimal weight: 0.0470 chunk 168 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 78 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 125 optimal weight: 30.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.203478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.158273 restraints weight = 23541.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.155815 restraints weight = 40683.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154275 restraints weight = 33505.471| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14709 Z= 0.151 Angle : 0.655 11.974 19778 Z= 0.329 Chirality : 0.043 0.238 2246 Planarity : 0.003 0.066 2468 Dihedral : 10.298 140.420 2018 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.75 % Allowed : 20.67 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1779 helix: 1.55 (0.17), residues: 990 sheet: -0.28 (0.42), residues: 176 loop : -1.55 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP D 153 HIS 0.013 0.001 HIS C 160 PHE 0.019 0.001 PHE A 529 TYR 0.024 0.001 TYR E 151 ARG 0.010 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05835 ( 793) hydrogen bonds : angle 4.31582 ( 2268) covalent geometry : bond 0.00338 (14709) covalent geometry : angle 0.65549 (19778) *********************** 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 213 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.523 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: 0.6381 (ppp) cc_final: 0.6057 (ppp) REVERT: A 534 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7433 (mp) REVERT: A 556 ASP cc_start: 0.7545 (t0) cc_final: 0.7125 (t0) REVERT: E 18 PHE cc_start: 0.6678 (m-80) cc_final: 0.6066 (t80) REVERT: E 26 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7239 (tt) outliers start: 43 outliers final: 35 residues processed: 197 average time/residue: 0.2465 time to fit residues: 71.8043 Evaluate side-chains 203 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 118 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 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 488 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 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 199 MET 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 50 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 132 optimal weight: 20.0000 chunk 170 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 4 optimal weight: 0.0370 chunk 174 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 92 optimal weight: 0.0570 chunk 9 optimal weight: 0.2980 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.206445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161167 restraints weight = 23353.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.156373 restraints weight = 36901.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.152909 restraints weight = 27872.842| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14709 Z= 0.127 Angle : 0.649 15.459 19778 Z= 0.320 Chirality : 0.042 0.203 2246 Planarity : 0.003 0.068 2468 Dihedral : 9.832 137.894 2018 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.05 % Allowed : 21.88 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1779 helix: 1.71 (0.17), residues: 994 sheet: -0.24 (0.41), residues: 184 loop : -1.47 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 153 HIS 0.013 0.001 HIS C 160 PHE 0.010 0.001 PHE E 223 TYR 0.025 0.001 TYR E 151 ARG 0.010 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.04943 ( 793) hydrogen bonds : angle 4.14617 ( 2268) covalent geometry : bond 0.00264 (14709) covalent geometry : angle 0.64872 (19778) *********************** 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 217 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 1.500 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 1 MET cc_start: 0.6356 (ppp) cc_final: 0.6012 (ppp) REVERT: A 173 THR cc_start: 0.7609 (m) cc_final: 0.6948 (p) REVERT: A 319 LYS cc_start: 0.7991 (tppt) cc_final: 0.7490 (mmtp) REVERT: A 534 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7461 (mp) REVERT: A 556 ASP cc_start: 0.7473 (t0) cc_final: 0.7089 (t0) REVERT: B 71 MET cc_start: 0.7526 (ppp) cc_final: 0.6794 (mmp) REVERT: E 18 PHE cc_start: 0.6726 (m-80) cc_final: 0.6062 (t80) outliers start: 32 outliers final: 28 residues processed: 205 average time/residue: 0.2608 time to fit residues: 79.0615 Evaluate side-chains 202 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 22 VAL 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 50 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 135 GLU 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 297 LYS Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 152 GLU 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 116 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 109 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 9 optimal weight: 0.0870 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 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 = 0.4466 r_free = 0.4466 target = 0.204378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.160344 restraints weight = 23426.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.155531 restraints weight = 38018.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150792 restraints weight = 33894.322| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3019 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= 0.144 Angle : 0.684 15.738 19778 Z= 0.335 Chirality : 0.043 0.194 2246 Planarity : 0.003 0.070 2468 Dihedral : 9.845 139.908 2018 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.43 % Allowed : 21.56 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1779 helix: 1.62 (0.17), residues: 989 sheet: -0.14 (0.42), residues: 178 loop : -1.50 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP D 197 HIS 0.013 0.001 HIS C 160 PHE 0.033 0.001 PHE E 223 TYR 0.024 0.001 TYR E 151 ARG 0.011 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05528 ( 793) hydrogen bonds : angle 4.23970 ( 2268) covalent geometry : bond 0.00318 (14709) covalent geometry : angle 0.68376 (19778) *********************** 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: 38 poor density : 175 time to evaluate : 1.563 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: 0.6358 (ppp) cc_final: 0.6054 (ppp) REVERT: A 200 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6822 (t80) REVERT: A 534 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7299 (mp) REVERT: A 556 ASP cc_start: 0.7532 (t0) cc_final: 0.7100 (t0) REVERT: C 50 LEU cc_start: 0.4373 (OUTLIER) cc_final: 0.4138 (mm) REVERT: E 18 PHE cc_start: 0.6736 (m-80) cc_final: 0.6126 (t80) REVERT: E 26 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7263 (tt) REVERT: E 140 MET cc_start: 0.3656 (ppp) cc_final: 0.2737 (ppp) outliers start: 38 outliers final: 29 residues processed: 199 average time/residue: 0.2487 time to fit residues: 73.7296 Evaluate side-chains 202 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 200 PHE 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 449 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 541 THR 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 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 50 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 197 TRP Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.0060 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 135 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** 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 = 0.4467 r_free = 0.4467 target = 0.204571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.161309 restraints weight = 23561.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.158271 restraints weight = 38249.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153623 restraints weight = 31058.824| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3095 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= 0.142 Angle : 0.707 16.124 19778 Z= 0.346 Chirality : 0.043 0.247 2246 Planarity : 0.003 0.071 2468 Dihedral : 9.777 141.874 2018 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.37 % Allowed : 21.88 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1779 helix: 1.60 (0.17), residues: 994 sheet: -0.11 (0.42), residues: 178 loop : -1.48 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 197 HIS 0.013 0.001 HIS C 160 PHE 0.019 0.001 PHE E 223 TYR 0.025 0.001 TYR E 151 ARG 0.011 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05528 ( 793) hydrogen bonds : angle 4.23577 ( 2268) covalent geometry : bond 0.00311 (14709) covalent geometry : angle 0.70697 (19778) ********************** 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 208 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.609 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 200 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6818 (t80) REVERT: A 319 LYS cc_start: 0.7866 (tppt) cc_final: 0.7343 (mmtp) REVERT: A 376 MET cc_start: 0.5845 (ppp) cc_final: 0.5561 (ppp) REVERT: A 534 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7689 (mp) REVERT: A 556 ASP cc_start: 0.7511 (t0) cc_final: 0.7079 (t0) REVERT: B 5 GLU cc_start: 0.6316 (mp0) cc_final: 0.6104 (mm-30) REVERT: C 50 LEU cc_start: 0.4397 (OUTLIER) cc_final: 0.4191 (mm) REVERT: E 18 PHE cc_start: 0.6717 (m-80) cc_final: 0.6103 (t80) REVERT: E 26 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7201 (tt) outliers start: 37 outliers final: 31 residues processed: 195 average time/residue: 0.2473 time to fit residues: 72.8574 Evaluate side-chains 203 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 118 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 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 534 LEU Chi-restraints excluded: chain A residue 541 THR 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 199 MET Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 197 TRP Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 142 optimal weight: 0.0570 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 GLN B 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.205060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.163722 restraints weight = 23300.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.157263 restraints weight = 33451.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.152557 restraints weight = 29783.183| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3169 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= 0.136 Angle : 0.703 15.616 19778 Z= 0.343 Chirality : 0.043 0.237 2246 Planarity : 0.003 0.071 2468 Dihedral : 9.611 143.449 2018 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.37 % Allowed : 22.20 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1779 helix: 1.61 (0.17), residues: 994 sheet: -0.19 (0.43), residues: 181 loop : -1.38 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP E 153 HIS 0.013 0.001 HIS C 160 PHE 0.016 0.001 PHE A 529 TYR 0.025 0.001 TYR E 151 ARG 0.012 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05371 ( 793) hydrogen bonds : angle 4.19534 ( 2268) covalent geometry : bond 0.00294 (14709) covalent geometry : angle 0.70258 (19778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4318.96 seconds wall clock time: 76 minutes 50.43 seconds (4610.43 seconds total)