Starting phenix.real_space_refine on Fri Jun 13 06:32:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3f_29694/06_2025/8g3f_29694.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3f_29694/06_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_29694/06_2025/8g3f_29694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3f_29694/06_2025/8g3f_29694.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3f_29694/06_2025/8g3f_29694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3f_29694/06_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-5710/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: 8.85, 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: 3.72 Conformation dependent library (CDL) restraints added in 1.9 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 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: 1.51 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: 4.82 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2343 1.32 - 1.44: 3765 1.44 - 1.57: 8465 1.57 - 1.69: 22 1.69 - 1.82: 114 Bond restraints: 14709 Sorted by residual: bond pdb=" C10 OLA E 401 " pdb=" C9 OLA E 401 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C16 6OU A 702 " pdb=" O18 6OU A 702 " ideal model delta sigma weight residual 1.327 1.464 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.462 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C31 6OU A 703 " pdb=" O30 6OU A 703 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C14 6OU A 702 " pdb=" C15 6OU A 702 " ideal model delta sigma weight residual 1.521 1.609 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 14704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.96: 19721 4.96 - 9.93: 51 9.93 - 14.89: 0 14.89 - 19.85: 4 19.85 - 24.81: 2 Bond angle restraints: 19778 Sorted by residual: angle pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " pdb=" C42 6OU A 703 " ideal model delta sigma weight residual 127.56 152.37 -24.81 3.00e+00 1.11e-01 6.84e+01 angle pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " pdb=" C42 6OU A 702 " ideal model delta sigma weight residual 127.56 152.10 -24.54 3.00e+00 1.11e-01 6.69e+01 angle pdb=" O22 6OU A 702 " pdb=" P23 6OU A 702 " pdb=" O26 6OU A 702 " ideal model delta sigma weight residual 93.95 110.79 -16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C39 6OU A 702 " pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " ideal model delta sigma weight residual 127.60 111.61 15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O22 6OU A 703 " pdb=" P23 6OU A 703 " pdb=" O26 6OU A 703 " ideal model delta sigma weight residual 93.95 109.65 -15.70 3.00e+00 1.11e-01 2.74e+01 ... (remaining 19773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 8665 35.61 - 71.21: 215 71.21 - 106.82: 16 106.82 - 142.42: 1 142.42 - 178.03: 4 Dihedral angle restraints: 8901 sinusoidal: 3689 harmonic: 5212 Sorted by residual: dihedral pdb=" CA ILE A 282 " pdb=" C ILE A 282 " pdb=" N MET A 283 " pdb=" CA MET A 283 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ARG D 139 " pdb=" C ARG D 139 " pdb=" N MET D 140 " pdb=" CA MET D 140 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" C21 6OU A 703 " pdb=" O22 6OU A 703 " ideal model delta sinusoidal sigma weight residual -59.00 119.03 -178.03 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1731 0.048 - 0.097: 402 0.097 - 0.145: 97 0.145 - 0.193: 13 0.193 - 0.241: 3 Chirality restraints: 2246 Sorted by residual: chirality pdb=" C20 6OU A 702 " pdb=" C19 6OU A 702 " pdb=" C21 6OU A 702 " pdb=" O30 6OU A 702 " both_signs ideal model delta sigma weight residual False 2.35 2.59 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA PHE A 174 " pdb=" N PHE A 174 " pdb=" C PHE A 174 " pdb=" CB PHE A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE E 156 " pdb=" N ILE E 156 " pdb=" C ILE E 156 " pdb=" CB ILE E 156 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2243 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " -0.197 2.00e-02 2.50e+03 1.52e-01 2.32e+02 pdb=" C11 OLA E 401 " 0.088 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " -0.088 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 173 " 0.021 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C THR A 173 " -0.068 2.00e-02 2.50e+03 pdb=" O THR A 173 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE A 174 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 30 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO E 31 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 31 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 31 " 0.030 5.00e-02 4.00e+02 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 260 2.70 - 3.25: 14113 3.25 - 3.80: 21907 3.80 - 4.35: 26921 4.35 - 4.90: 44883 Nonbonded interactions: 108084 Sorted by model distance: nonbonded pdb=" OD1 ASP C 168 " pdb=" N GLU C 169 " model vdw 2.148 3.120 nonbonded pdb=" O PHE A 251 " pdb=" OG SER A 255 " model vdw 2.227 3.040 nonbonded pdb=" OG SER A 421 " pdb=" O TYR A 437 " model vdw 2.241 3.040 nonbonded pdb=" ND2 ASN C 7 " pdb=" OD1 ASP C 27 " model vdw 2.250 3.120 nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.259 3.040 ... (remaining 108079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 35.020 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.360 ------------------------------------------------------------------------------- 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 : 1.646 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: 0.2684 time to fit residues: 93.0981 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 : 1.628 ------------------------------------------------------------------------------- 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 = 0.163607 restraints weight = 23554.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.158124 restraints weight = 36274.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153400 restraints weight = 31289.993| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- 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 4.68032 ( 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 : 1.697 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: 0.7144 (p) REVERT: A 344 LEU cc_start: 0.7991 (mt) cc_final: 0.7711 (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: 0.2725 time to fit residues: 87.2986 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 : 1.581 ------------------------------------------------------------------------------- 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: 0.0570 chunk 127 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 139 optimal weight: 0.0050 chunk 159 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 overall best weight: 2.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** 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 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 = 0.4419 r_free = 0.4419 target = 0.199749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.155783 restraints weight = 23326.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.148951 restraints weight = 36429.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145565 restraints weight = 35566.813| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14709 Z= 0.263 Angle : 0.732 11.282 19778 Z= 0.378 Chirality : 0.046 0.190 2246 Planarity : 0.004 0.055 2468 Dihedral : 11.618 156.326 2019 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.82 % Allowed : 13.44 % Favored : 83.75 % 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: -0.03 (0.21), residues: 1779 helix: 1.11 (0.17), residues: 994 sheet: -0.42 (0.42), residues: 164 loop : -1.78 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 122 HIS 0.010 0.002 HIS E 157 PHE 0.025 0.002 PHE A 529 TYR 0.028 0.002 TYR A 561 ARG 0.008 0.001 ARG D 168 Details of bonding type rmsd hydrogen bonds : bond 0.07698 ( 793) hydrogen bonds : angle 4.92965 ( 2268) covalent geometry : bond 0.00627 (14709) covalent geometry : angle 0.73172 (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 229 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8931 (tt) REVERT: A 319 LYS cc_start: 0.8331 (tppt) cc_final: 0.7866 (mmtp) REVERT: A 556 ASP cc_start: 0.7650 (t0) cc_final: 0.7357 (t0) REVERT: B 5 GLU cc_start: 0.6110 (mp0) cc_final: 0.5906 (mp0) REVERT: C 50 LEU cc_start: 0.4187 (OUTLIER) cc_final: 0.3885 (mm) REVERT: C 212 ARG cc_start: 0.8402 (ttt-90) cc_final: 0.8113 (ttt90) REVERT: E 18 PHE cc_start: 0.6792 (m-80) cc_final: 0.6075 (t80) REVERT: E 110 LEU cc_start: 0.8859 (tt) cc_final: 0.8587 (tp) REVERT: E 290 MET cc_start: 0.4155 (mmp) cc_final: 0.3920 (mmp) outliers start: 44 outliers final: 32 residues processed: 215 average time/residue: 0.2608 time to fit residues: 82.8328 Evaluate side-chains 200 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 200 PHE 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 387 VAL Chi-restraints excluded: chain A residue 411 LEU 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 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 4 LEU 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 135 GLU Chi-restraints excluded: chain C residue 210 CYS 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 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: 0.0570 chunk 99 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 433 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** D 157 HIS E 157 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.203698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.159575 restraints weight = 23313.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.155598 restraints weight = 40590.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151182 restraints weight = 31427.025| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14709 Z= 0.146 Angle : 0.612 9.399 19778 Z= 0.315 Chirality : 0.042 0.148 2246 Planarity : 0.003 0.059 2468 Dihedral : 11.035 159.448 2019 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.43 % Allowed : 16.25 % Favored : 81.32 % 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: 0.26 (0.21), residues: 1779 helix: 1.42 (0.17), residues: 999 sheet: -0.50 (0.41), residues: 177 loop : -1.76 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 153 HIS 0.009 0.001 HIS C 160 PHE 0.015 0.001 PHE A 529 TYR 0.023 0.001 TYR E 151 ARG 0.007 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05950 ( 793) hydrogen bonds : angle 4.46031 ( 2268) covalent geometry : bond 0.00322 (14709) covalent geometry : angle 0.61178 (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 225 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.680 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 556 ASP cc_start: 0.7466 (t0) cc_final: 0.7147 (t0) REVERT: D 153 TRP cc_start: 0.6797 (t-100) cc_final: 0.5934 (t-100) REVERT: E 18 PHE cc_start: 0.6678 (m-80) cc_final: 0.6042 (t80) outliers start: 38 outliers final: 25 residues processed: 208 average time/residue: 0.2638 time to fit residues: 80.3982 Evaluate side-chains 192 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 284 PHE 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 591 VAL Chi-restraints excluded: chain A residue 616 MET 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 48 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 118 GLU 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: 1.9990 chunk 136 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 9 optimal weight: 0.0020 chunk 83 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 433 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.204609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.161289 restraints weight = 23513.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156215 restraints weight = 35242.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.152596 restraints weight = 27568.367| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 14709 Z= 0.134 Angle : 0.626 14.602 19778 Z= 0.312 Chirality : 0.042 0.158 2246 Planarity : 0.003 0.061 2468 Dihedral : 10.678 156.641 2018 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.24 % Allowed : 18.30 % Favored : 79.46 % 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: 0.45 (0.21), residues: 1779 helix: 1.55 (0.17), residues: 998 sheet: -0.38 (0.42), residues: 176 loop : -1.64 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 153 HIS 0.012 0.001 HIS D 157 PHE 0.016 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 0.05615 ( 793) hydrogen bonds : angle 4.34282 ( 2268) covalent geometry : bond 0.00289 (14709) covalent geometry : angle 0.62638 (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 225 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 1.638 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 319 LYS cc_start: 0.8101 (tppt) cc_final: 0.7672 (mmtp) REVERT: A 534 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7312 (mp) REVERT: A 556 ASP cc_start: 0.7474 (t0) cc_final: 0.7133 (t0) REVERT: C 217 LYS cc_start: 0.7891 (pptt) cc_final: 0.7323 (ptpt) REVERT: E 18 PHE cc_start: 0.6724 (m-80) cc_final: 0.6081 (t80) outliers start: 35 outliers final: 23 residues processed: 210 average time/residue: 0.2665 time to fit residues: 82.3062 Evaluate side-chains 198 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 284 PHE 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 591 VAL Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain 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 210 CYS Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 53 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 156 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** 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 = 0.4465 r_free = 0.4465 target = 0.204532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.159721 restraints weight = 23726.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156734 restraints weight = 36842.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.152352 restraints weight = 28997.204| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14709 Z= 0.139 Angle : 0.645 15.121 19778 Z= 0.320 Chirality : 0.042 0.213 2246 Planarity : 0.004 0.066 2468 Dihedral : 10.439 152.060 2018 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.88 % Allowed : 19.45 % Favored : 77.67 % 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 (0.21), residues: 1779 helix: 1.62 (0.17), residues: 989 sheet: -0.32 (0.42), residues: 176 loop : -1.54 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 153 HIS 0.008 0.001 HIS C 160 PHE 0.017 0.001 PHE A 529 TYR 0.023 0.001 TYR E 151 ARG 0.009 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05555 ( 793) hydrogen bonds : angle 4.31329 ( 2268) covalent geometry : bond 0.00303 (14709) covalent geometry : angle 0.64500 (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 226 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.611 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: 0.6475 (ppp) cc_final: 0.5978 (ppp) REVERT: A 534 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7349 (mp) REVERT: A 556 ASP cc_start: 0.7440 (t0) cc_final: 0.7056 (t0) REVERT: B 71 MET cc_start: 0.7334 (ppp) cc_final: 0.6710 (mmp) REVERT: C 50 LEU cc_start: 0.4354 (OUTLIER) cc_final: 0.4019 (mm) REVERT: E 18 PHE cc_start: 0.6711 (m-80) cc_final: 0.6092 (t80) outliers start: 45 outliers final: 32 residues processed: 207 average time/residue: 0.2686 time to fit residues: 82.4274 Evaluate side-chains 206 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 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 591 VAL Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 4 LEU 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 210 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 76 optimal weight: 0.0770 chunk 168 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 78 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 125 optimal weight: 20.0000 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** 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 C 160 HIS ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.206818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.163899 restraints weight = 23846.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.157903 restraints weight = 33517.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151714 restraints weight = 28523.516| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 14709 Z= 0.117 Angle : 0.636 13.477 19778 Z= 0.315 Chirality : 0.042 0.220 2246 Planarity : 0.003 0.064 2468 Dihedral : 9.957 143.233 2018 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.98 % Allowed : 20.60 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1779 helix: 1.78 (0.17), residues: 983 sheet: -0.25 (0.42), residues: 177 loop : -1.44 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 122 HIS 0.008 0.001 HIS C 160 PHE 0.016 0.001 PHE E 223 TYR 0.024 0.001 TYR E 151 ARG 0.010 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 793) hydrogen bonds : angle 4.14750 ( 2268) covalent geometry : bond 0.00237 (14709) covalent geometry : angle 0.63630 (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 222 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6472 (ppp) cc_final: 0.6104 (ppp) REVERT: A 173 THR cc_start: 0.7526 (m) cc_final: 0.6893 (p) REVERT: A 534 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7069 (mp) REVERT: A 556 ASP cc_start: 0.7332 (t0) cc_final: 0.6975 (t0) REVERT: B 112 ILE cc_start: 0.8838 (mm) cc_final: 0.8548 (mm) REVERT: C 50 LEU cc_start: 0.4549 (OUTLIER) cc_final: 0.4248 (mm) REVERT: E 18 PHE cc_start: 0.6693 (m-80) cc_final: 0.6086 (t80) outliers start: 31 outliers final: 26 residues processed: 213 average time/residue: 0.2839 time to fit residues: 89.6416 Evaluate side-chains 205 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 325 VAL 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 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 115 LEU Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain E residue 152 GLU 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: 6.9990 chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 174 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 9 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 GLN ** E 157 HIS ** 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 = 0.4470 r_free = 0.4470 target = 0.204911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.160243 restraints weight = 23559.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.157556 restraints weight = 37557.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153492 restraints weight = 31230.224| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2797 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 : 0.670 15.454 19778 Z= 0.329 Chirality : 0.043 0.205 2246 Planarity : 0.003 0.067 2468 Dihedral : 9.866 139.407 2018 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.43 % Allowed : 20.41 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.21), residues: 1779 helix: 1.71 (0.17), residues: 983 sheet: -0.28 (0.42), residues: 179 loop : -1.42 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 122 HIS 0.021 0.001 HIS D 157 PHE 0.019 0.001 PHE A 529 TYR 0.024 0.001 TYR E 151 ARG 0.012 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05297 ( 793) hydrogen bonds : angle 4.20915 ( 2268) covalent geometry : bond 0.00303 (14709) covalent geometry : angle 0.66979 (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 216 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 1.655 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: 0.6546 (ppp) cc_final: 0.6232 (ppp) REVERT: A 534 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7252 (mp) REVERT: A 556 ASP cc_start: 0.7447 (t0) cc_final: 0.7062 (t0) REVERT: B 112 ILE cc_start: 0.8865 (mm) cc_final: 0.8578 (mm) REVERT: C 50 LEU cc_start: 0.4257 (OUTLIER) cc_final: 0.3833 (mm) REVERT: E 18 PHE cc_start: 0.6716 (m-80) cc_final: 0.6118 (t80) outliers start: 38 outliers final: 30 residues processed: 203 average time/residue: 0.2554 time to fit residues: 77.7617 Evaluate side-chains 206 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 325 VAL 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 210 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 116 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** E 157 HIS ** 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 = 0.4472 r_free = 0.4472 target = 0.205149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.161887 restraints weight = 23353.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.157635 restraints weight = 33177.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151294 restraints weight = 26768.495| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2882 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= 0.131 Angle : 0.677 15.822 19778 Z= 0.330 Chirality : 0.043 0.214 2246 Planarity : 0.003 0.069 2468 Dihedral : 9.735 140.120 2018 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.43 % Allowed : 20.67 % Favored : 76.90 % 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: 0.67 (0.21), residues: 1779 helix: 1.69 (0.17), residues: 989 sheet: -0.28 (0.42), residues: 176 loop : -1.43 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 153 HIS 0.015 0.001 HIS D 157 PHE 0.016 0.001 PHE A 529 TYR 0.025 0.001 TYR E 151 ARG 0.011 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05232 ( 793) hydrogen bonds : angle 4.17916 ( 2268) covalent geometry : bond 0.00284 (14709) covalent geometry : angle 0.67731 (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 217 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 2.438 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: 0.6315 (ppp) cc_final: 0.6078 (ppp) REVERT: A 376 MET cc_start: 0.6027 (ppp) cc_final: 0.5742 (ppp) REVERT: A 534 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7361 (mp) REVERT: A 556 ASP cc_start: 0.7430 (t0) cc_final: 0.7021 (t0) REVERT: B 112 ILE cc_start: 0.8862 (mm) cc_final: 0.8578 (mm) REVERT: C 50 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.3928 (mm) REVERT: E 18 PHE cc_start: 0.6741 (m-80) cc_final: 0.6152 (t80) REVERT: E 140 MET cc_start: 0.3487 (ppp) cc_final: 0.2669 (ppp) outliers start: 38 outliers final: 31 residues processed: 203 average time/residue: 0.2679 time to fit residues: 82.2074 Evaluate side-chains 209 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 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 222 LEU Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 325 VAL 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 210 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain D residue 128 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 135 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 173 optimal weight: 9.9990 chunk 129 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 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 = 0.4478 r_free = 0.4478 target = 0.205751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.162493 restraints weight = 23582.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157615 restraints weight = 36544.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.152500 restraints weight = 34318.238| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14709 Z= 0.131 Angle : 0.701 15.122 19778 Z= 0.341 Chirality : 0.043 0.214 2246 Planarity : 0.003 0.071 2468 Dihedral : 9.645 140.102 2018 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.18 % Allowed : 20.92 % Favored : 76.90 % 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: 0.67 (0.21), residues: 1779 helix: 1.66 (0.17), residues: 994 sheet: -0.25 (0.43), residues: 176 loop : -1.41 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP E 153 HIS 0.013 0.001 HIS D 157 PHE 0.016 0.001 PHE A 529 TYR 0.025 0.001 TYR E 151 ARG 0.012 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 793) hydrogen bonds : angle 4.14829 ( 2268) covalent geometry : bond 0.00282 (14709) covalent geometry : angle 0.70083 (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 210 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.5951 (ppp) cc_final: 0.5704 (ppp) REVERT: A 534 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7367 (mp) REVERT: A 556 ASP cc_start: 0.7458 (t0) cc_final: 0.7069 (t0) REVERT: B 112 ILE cc_start: 0.8868 (mm) cc_final: 0.8584 (mm) REVERT: C 50 LEU cc_start: 0.4309 (OUTLIER) cc_final: 0.3925 (mm) REVERT: E 18 PHE cc_start: 0.6722 (m-80) cc_final: 0.6125 (t80) REVERT: E 140 MET cc_start: 0.3332 (ppp) cc_final: 0.2570 (ppp) outliers start: 34 outliers final: 28 residues processed: 197 average time/residue: 0.2603 time to fit residues: 77.9569 Evaluate side-chains 200 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 222 LEU Chi-restraints excluded: chain A residue 325 VAL 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 210 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 142 optimal weight: 0.0470 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 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 = 0.4470 r_free = 0.4470 target = 0.205054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.160312 restraints weight = 23449.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.155940 restraints weight = 35086.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.150700 restraints weight = 29041.393| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14709 Z= 0.135 Angle : 0.701 14.695 19778 Z= 0.342 Chirality : 0.043 0.217 2246 Planarity : 0.003 0.071 2468 Dihedral : 9.596 139.409 2018 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.24 % Allowed : 20.92 % Favored : 76.84 % 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: 1.63 (0.17), residues: 995 sheet: -0.28 (0.43), residues: 177 loop : -1.40 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRP E 153 HIS 0.012 0.001 HIS D 157 PHE 0.017 0.001 PHE A 529 TYR 0.023 0.001 TYR E 151 ARG 0.012 0.001 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.05307 ( 793) hydrogen bonds : angle 4.16989 ( 2268) covalent geometry : bond 0.00296 (14709) covalent geometry : angle 0.70074 (19778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4720.75 seconds wall clock time: 84 minutes 4.63 seconds (5044.63 seconds total)