Starting phenix.real_space_refine on Wed Feb 4 20:51:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yy2_39664/02_2026/8yy2_39664.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yy2_39664/02_2026/8yy2_39664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yy2_39664/02_2026/8yy2_39664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yy2_39664/02_2026/8yy2_39664.map" model { file = "/net/cci-nas-00/data/ceres_data/8yy2_39664/02_2026/8yy2_39664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yy2_39664/02_2026/8yy2_39664.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 86 5.16 5 C 7915 2.51 5 N 2199 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12668 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3352 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 406} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2982 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 364} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2895 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'GDP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.55, per 1000 atoms: 0.20 Number of scatterers: 12668 At special positions: 0 Unit cell: (130.848, 140.624, 120.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 7 15.00 Mg 1 11.99 O 2460 8.00 N 2199 7.00 C 7915 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 467.7 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 50.9% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.985A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 removed outlier: 4.769A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 129 removed outlier: 4.753A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.491A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.561A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.533A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.602A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.104A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 296 through 301 removed outlier: 6.198A pdb=" N ALA A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.060A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.901A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.617A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 125 removed outlier: 4.458A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 4.155A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.564A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.601A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.642A pdb=" N VAL B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.651A pdb=" N LEU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 291 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 6.543A pdb=" N LYS B 297 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.991A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 388 removed outlier: 4.125A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.847A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.964A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 347 removed outlier: 3.640A pdb=" N VAL C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU C 320 " --> pdb=" O GLN C 316 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 392 Processing helix chain 'C' and resid 408 through 424 removed outlier: 3.673A pdb=" N SER C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Proline residue: C 417 - end of helix Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.513A pdb=" N ASP C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 470 Processing helix chain 'C' and resid 524 through 539 removed outlier: 3.526A pdb=" N ALA C 535 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 536 " --> pdb=" O MET C 532 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET C 537 " --> pdb=" O HIS C 533 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN C 538 " --> pdb=" O THR C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 615 removed outlier: 3.788A pdb=" N THR C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 624 removed outlier: 3.740A pdb=" N ASN C 624 " --> pdb=" O PRO C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 621 through 624' Processing helix chain 'C' and resid 625 through 631 Processing helix chain 'C' and resid 650 through 652 No H-bonds generated for 'chain 'C' and resid 650 through 652' Processing helix chain 'C' and resid 653 through 670 removed outlier: 3.829A pdb=" N PHE C 663 " --> pdb=" O LYS C 659 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 668 " --> pdb=" O ALA C 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 346 removed outlier: 3.714A pdb=" N GLU D 334 " --> pdb=" O GLN D 330 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D 337 " --> pdb=" O MET D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.596A pdb=" N GLU D 363 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 removed outlier: 3.742A pdb=" N SER D 389 " --> pdb=" O ALA D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 424 removed outlier: 3.759A pdb=" N ILE D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Proline residue: D 417 - end of helix removed outlier: 3.801A pdb=" N GLN D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.518A pdb=" N VAL D 458 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP D 459 " --> pdb=" O PRO D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 472 Processing helix chain 'D' and resid 524 through 539 Processing helix chain 'D' and resid 546 through 553 removed outlier: 4.098A pdb=" N SER D 550 " --> pdb=" O GLY D 546 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 553 " --> pdb=" O ARG D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 615 removed outlier: 3.506A pdb=" N LEU D 611 " --> pdb=" O THR D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 624 Processing helix chain 'D' and resid 625 through 631 Processing helix chain 'D' and resid 632 through 636 removed outlier: 3.643A pdb=" N LEU D 635 " --> pdb=" O MET D 632 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY D 636 " --> pdb=" O PRO D 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 632 through 636' Processing helix chain 'D' and resid 653 through 669 removed outlier: 3.509A pdb=" N LYS D 659 " --> pdb=" O GLN D 655 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE D 663 " --> pdb=" O LYS D 659 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA D 664 " --> pdb=" O SER D 660 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.691A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 removed outlier: 6.737A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.185A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 200 removed outlier: 6.724A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 400 through 402 removed outlier: 9.488A pdb=" N GLN C 400 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 351 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N PHE C 402 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N CYS C 353 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG C 350 " --> pdb=" O MET C 643 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE C 645 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE C 352 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL C 647 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG C 354 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN C 427 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU C 642 " --> pdb=" O ASN C 427 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS C 429 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE C 644 " --> pdb=" O CYS C 429 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N PHE C 431 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN C 646 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR C 433 " --> pdb=" O ASN C 646 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 555 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS C 554 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 400 through 402 removed outlier: 9.488A pdb=" N GLN C 400 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 351 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N PHE C 402 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N CYS C 353 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG C 350 " --> pdb=" O MET C 643 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE C 645 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE C 352 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL C 647 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG C 354 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN C 427 " --> pdb=" O LYS C 640 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU C 642 " --> pdb=" O ASN C 427 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS C 429 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE C 644 " --> pdb=" O CYS C 429 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N PHE C 431 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN C 646 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR C 433 " --> pdb=" O ASN C 646 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 555 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS C 554 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 372 Processing sheet with id=AB1, first strand: chain 'C' and resid 502 through 504 Processing sheet with id=AB2, first strand: chain 'D' and resid 400 through 402 removed outlier: 4.130A pdb=" N GLN D 400 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS D 353 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ARG D 350 " --> pdb=" O MET D 643 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILE D 645 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE D 352 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL D 647 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG D 354 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS D 429 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE D 644 " --> pdb=" O CYS D 429 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE D 431 " --> pdb=" O PHE D 644 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN D 646 " --> pdb=" O PHE D 431 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR D 433 " --> pdb=" O ASN D 646 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 432 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY D 434 " --> pdb=" O LEU D 581 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY D 583 " --> pdb=" O GLY D 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 400 through 402 removed outlier: 4.130A pdb=" N GLN D 400 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS D 353 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ARG D 350 " --> pdb=" O MET D 643 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILE D 645 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE D 352 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL D 647 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG D 354 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS D 429 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE D 644 " --> pdb=" O CYS D 429 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE D 431 " --> pdb=" O PHE D 644 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN D 646 " --> pdb=" O PHE D 431 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR D 433 " --> pdb=" O ASN D 646 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 432 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY D 434 " --> pdb=" O LEU D 581 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY D 583 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE D 477 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 369 through 373 Processing sheet with id=AB5, first strand: chain 'D' and resid 502 through 504 removed outlier: 3.677A pdb=" N ARG D 503 " --> pdb=" O TYR D 513 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 513 " --> pdb=" O ARG D 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 656 hydrogen bonds defined for protein. 1878 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: 1.70 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4243 1.34 - 1.46: 2505 1.46 - 1.58: 6019 1.58 - 1.69: 11 1.69 - 1.81: 136 Bond restraints: 12914 Sorted by residual: bond pdb=" N LEU C 642 " pdb=" CA LEU C 642 " ideal model delta sigma weight residual 1.456 1.476 -0.020 1.22e-02 6.72e+03 2.66e+00 bond pdb=" C THR C 641 " pdb=" N LEU C 642 " ideal model delta sigma weight residual 1.331 1.346 -0.016 1.37e-02 5.33e+03 1.35e+00 bond pdb=" C5 GDP B 502 " pdb=" C4 GDP B 502 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" CA ILE D 599 " pdb=" CB ILE D 599 " ideal model delta sigma weight residual 1.540 1.568 -0.028 2.70e-02 1.37e+03 1.11e+00 bond pdb=" CA VAL A 260 " pdb=" CB VAL A 260 " ideal model delta sigma weight residual 1.526 1.541 -0.015 1.55e-02 4.16e+03 9.77e-01 ... (remaining 12909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 17257 1.66 - 3.33: 186 3.33 - 4.99: 39 4.99 - 6.65: 13 6.65 - 8.31: 3 Bond angle restraints: 17498 Sorted by residual: angle pdb=" N ILE A 110 " pdb=" CA ILE A 110 " pdb=" C ILE A 110 " ideal model delta sigma weight residual 113.71 108.41 5.30 9.50e-01 1.11e+00 3.12e+01 angle pdb=" N MET A 413 " pdb=" CA MET A 413 " pdb=" C MET A 413 " ideal model delta sigma weight residual 108.34 113.61 -5.27 1.31e+00 5.83e-01 1.62e+01 angle pdb=" C GLY C 347 " pdb=" N ASN C 348 " pdb=" CA ASN C 348 " ideal model delta sigma weight residual 126.86 132.03 -5.17 1.57e+00 4.06e-01 1.09e+01 angle pdb=" N GLY A 412 " pdb=" CA GLY A 412 " pdb=" C GLY A 412 " ideal model delta sigma weight residual 113.18 120.26 -7.08 2.37e+00 1.78e-01 8.93e+00 angle pdb=" N THR C 544 " pdb=" CA THR C 544 " pdb=" C THR C 544 " ideal model delta sigma weight residual 114.04 110.34 3.70 1.24e+00 6.50e-01 8.91e+00 ... (remaining 17493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.34: 7509 26.34 - 52.69: 253 52.69 - 79.03: 30 79.03 - 105.37: 5 105.37 - 131.72: 3 Dihedral angle restraints: 7800 sinusoidal: 3158 harmonic: 4642 Sorted by residual: dihedral pdb=" O3B GTP B 501 " pdb=" O3A GTP B 501 " pdb=" PB GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sinusoidal sigma weight residual 291.08 159.36 131.72 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -26.75 131.34 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -162.59 -128.14 1 2.00e+01 2.50e-03 3.88e+01 ... (remaining 7797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1455 0.040 - 0.080: 344 0.080 - 0.120: 144 0.120 - 0.160: 8 0.160 - 0.200: 1 Chirality restraints: 1952 Sorted by residual: chirality pdb=" CB ILE D 599 " pdb=" CA ILE D 599 " pdb=" CG1 ILE D 599 " pdb=" CG2 ILE D 599 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE C 349 " pdb=" N ILE C 349 " pdb=" C ILE C 349 " pdb=" CB ILE C 349 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE D 620 " pdb=" N ILE D 620 " pdb=" C ILE D 620 " pdb=" CB ILE D 620 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1949 not shown) Planarity restraints: 2273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 641 " 0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C THR C 641 " -0.074 2.00e-02 2.50e+03 pdb=" O THR C 641 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU C 642 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 181 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO B 182 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 182 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 182 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 403 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO C 404 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 404 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 404 " 0.021 5.00e-02 4.00e+02 ... (remaining 2270 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 203 2.62 - 3.19: 11974 3.19 - 3.76: 21052 3.76 - 4.33: 29117 4.33 - 4.90: 45493 Nonbonded interactions: 107839 Sorted by model distance: nonbonded pdb=" OG1 THR D 441 " pdb="MG MG D 801 " model vdw 2.055 2.170 nonbonded pdb="MG MG D 801 " pdb=" O3B ADP D 802 " model vdw 2.073 2.170 nonbonded pdb=" O THR A 381 " pdb=" OH TYR A 432 " model vdw 2.090 3.040 nonbonded pdb=" O THR A 190 " pdb=" OG1 THR A 194 " model vdw 2.162 3.040 nonbonded pdb=" OG SER B 145 " pdb=" OG SER B 188 " model vdw 2.167 3.040 ... (remaining 107834 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 'C' and (resid 296 through 587 or resid 599 through 617 or (resid 618 and \ (name N or name CA or name C or name O or name CB )) or resid 619 through 670)) \ selection = (chain 'D' and (resid 296 through 308 or (resid 309 and (name N or name CA or na \ me C or name O or name CB )) or resid 310 through 670)) } 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: 19.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.950 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4500 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 : 0.002 0.038 12916 Z= 0.102 Angle : 0.505 8.313 17498 Z= 0.258 Chirality : 0.040 0.200 1952 Planarity : 0.004 0.059 2273 Dihedral : 13.151 131.717 4800 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.86 % Allowed : 5.38 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1584 helix: 0.68 (0.20), residues: 704 sheet: 0.07 (0.34), residues: 263 loop : -0.54 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 346 TYR 0.008 0.001 TYR C 433 PHE 0.009 0.001 PHE A 149 TRP 0.010 0.001 TRP B 344 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00206 (12914) covalent geometry : angle 0.50531 (17498) hydrogen bonds : bond 0.23892 ( 604) hydrogen bonds : angle 8.09794 ( 1878) Misc. bond : bond 0.00076 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 327 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6676 (mt0) REVERT: A 88 HIS cc_start: 0.7072 (t-90) cc_final: 0.6415 (t-170) REVERT: A 91 GLN cc_start: 0.6577 (mt0) cc_final: 0.6032 (mm-40) REVERT: A 112 LYS cc_start: 0.7300 (ptpt) cc_final: 0.6521 (pttt) REVERT: A 150 THR cc_start: 0.6528 (m) cc_final: 0.6322 (m) REVERT: A 155 GLU cc_start: 0.6984 (pp20) cc_final: 0.6774 (tt0) REVERT: A 176 GLN cc_start: 0.6691 (mm110) cc_final: 0.6455 (mm-40) REVERT: A 212 ILE cc_start: 0.6049 (mt) cc_final: 0.5782 (mt) REVERT: A 216 ASN cc_start: 0.7644 (m-40) cc_final: 0.7181 (m-40) REVERT: A 302 MET cc_start: 0.6782 (mmm) cc_final: 0.6321 (mmm) REVERT: A 372 GLN cc_start: 0.7564 (mm110) cc_final: 0.7272 (mt0) REVERT: A 397 LEU cc_start: 0.7156 (mt) cc_final: 0.6788 (mp) REVERT: A 398 MET cc_start: 0.5880 (mmp) cc_final: 0.5552 (mmt) REVERT: A 413 MET cc_start: 0.5526 (mpp) cc_final: 0.3994 (mpp) REVERT: A 437 VAL cc_start: 0.7156 (p) cc_final: 0.6830 (p) REVERT: B 36 TYR cc_start: 0.5961 (t80) cc_final: 0.5029 (t80) REVERT: B 37 HIS cc_start: 0.6669 (m-70) cc_final: 0.6180 (t-170) REVERT: B 41 ASP cc_start: 0.7871 (m-30) cc_final: 0.7509 (m-30) REVERT: B 126 SER cc_start: 0.6547 (t) cc_final: 0.6340 (p) REVERT: B 152 ILE cc_start: 0.7465 (mm) cc_final: 0.7008 (mm) REVERT: B 156 ARG cc_start: 0.6454 (tmm-80) cc_final: 0.6103 (ttm-80) REVERT: B 174 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7497 (tppt) REVERT: B 251 ARG cc_start: 0.6543 (mmm160) cc_final: 0.5783 (mtt-85) REVERT: B 267 MET cc_start: 0.7855 (mtt) cc_final: 0.7228 (mtp) REVERT: B 303 CYS cc_start: 0.6900 (m) cc_final: 0.6581 (m) REVERT: B 388 MET cc_start: 0.2921 (mmt) cc_final: 0.2575 (ptp) REVERT: B 406 MET cc_start: 0.7440 (tpp) cc_final: 0.6941 (ttp) REVERT: C 333 MET cc_start: 0.3213 (tmm) cc_final: 0.2238 (mtm) REVERT: C 500 MET cc_start: 0.5854 (mmp) cc_final: 0.5212 (mmp) REVERT: C 501 GLU cc_start: 0.5604 (pp20) cc_final: 0.4488 (mp0) REVERT: C 511 ASP cc_start: 0.3075 (m-30) cc_final: 0.2551 (t0) REVERT: C 537 MET cc_start: 0.2186 (pmm) cc_final: 0.1320 (tpt) REVERT: C 623 ARG cc_start: 0.4423 (mtt90) cc_final: 0.3934 (tpm170) REVERT: C 629 HIS cc_start: 0.5328 (t-170) cc_final: 0.5118 (t70) REVERT: C 643 MET cc_start: 0.4672 (tpt) cc_final: 0.4175 (ttt) REVERT: D 366 MET cc_start: 0.1858 (pmm) cc_final: -0.0915 (ttm) REVERT: D 500 MET cc_start: 0.4643 (mmm) cc_final: 0.4043 (mmt) outliers start: 12 outliers final: 3 residues processed: 337 average time/residue: 0.1097 time to fit residues: 52.4113 Evaluate side-chains 194 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 50.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.0270 chunk 149 optimal weight: 30.0000 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN B 14 ASN B 15 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN B 334 GLN B 335 ASN B 424 GLN C 305 GLN C 332 ASN C 547 ASN D 435 GLN D 516 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.237561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.182914 restraints weight = 17719.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.175599 restraints weight = 25571.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.178539 restraints weight = 20703.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.177921 restraints weight = 11122.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.178255 restraints weight = 10307.936| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12916 Z= 0.152 Angle : 0.646 8.616 17498 Z= 0.331 Chirality : 0.045 0.201 1952 Planarity : 0.005 0.046 2273 Dihedral : 8.005 135.516 1768 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.73 % Allowed : 10.70 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1584 helix: 0.68 (0.19), residues: 731 sheet: 0.34 (0.34), residues: 260 loop : -0.73 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 390 TYR 0.017 0.001 TYR B 208 PHE 0.024 0.002 PHE B 20 TRP 0.011 0.001 TRP A 21 HIS 0.008 0.001 HIS C 527 Details of bonding type rmsd covalent geometry : bond 0.00327 (12914) covalent geometry : angle 0.64583 (17498) hydrogen bonds : bond 0.05303 ( 604) hydrogen bonds : angle 5.49506 ( 1878) Misc. bond : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.6775 (t0) cc_final: 0.6381 (t70) REVERT: A 154 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7530 (mmp) REVERT: A 300 ASN cc_start: 0.8238 (m-40) cc_final: 0.7718 (m-40) REVERT: A 352 LYS cc_start: 0.5744 (mmtt) cc_final: 0.5299 (mmtt) REVERT: A 398 MET cc_start: 0.6781 (mmp) cc_final: 0.6393 (mmt) REVERT: A 432 TYR cc_start: 0.6454 (t80) cc_final: 0.5549 (t80) REVERT: B 251 ARG cc_start: 0.6848 (mmm160) cc_final: 0.6332 (mtt-85) REVERT: B 267 MET cc_start: 0.8155 (mtt) cc_final: 0.7875 (mtp) REVERT: B 300 MET cc_start: 0.7876 (mmm) cc_final: 0.7623 (mtt) REVERT: C 333 MET cc_start: 0.3284 (tmm) cc_final: 0.2037 (mtm) REVERT: C 500 MET cc_start: 0.5834 (mmp) cc_final: 0.5274 (mmp) REVERT: C 501 GLU cc_start: 0.5970 (pp20) cc_final: 0.4968 (mp0) REVERT: C 511 ASP cc_start: 0.3258 (m-30) cc_final: 0.3009 (t0) REVERT: C 524 ASP cc_start: 0.5600 (p0) cc_final: 0.5369 (p0) REVERT: C 537 MET cc_start: 0.1618 (pmm) cc_final: 0.1038 (tpt) REVERT: D 366 MET cc_start: 0.1648 (pmm) cc_final: -0.1171 (ttm) REVERT: D 435 GLN cc_start: -0.0577 (OUTLIER) cc_final: -0.0836 (pt0) REVERT: D 500 MET cc_start: 0.4420 (mmm) cc_final: 0.3754 (mmt) outliers start: 38 outliers final: 19 residues processed: 257 average time/residue: 0.0918 time to fit residues: 35.4330 Evaluate side-chains 195 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 435 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 29 optimal weight: 6.9990 chunk 149 optimal weight: 50.0000 chunk 139 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 88 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS B 14 ASN B 100 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN C 538 ASN ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 GLN D 332 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.236251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.181489 restraints weight = 17922.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.170864 restraints weight = 25434.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.173987 restraints weight = 21677.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.173648 restraints weight = 12403.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.174281 restraints weight = 10509.542| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12916 Z= 0.139 Angle : 0.601 7.610 17498 Z= 0.307 Chirality : 0.043 0.192 1952 Planarity : 0.004 0.061 2273 Dihedral : 7.980 137.364 1768 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.51 % Allowed : 14.64 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1584 helix: 0.85 (0.19), residues: 721 sheet: 0.26 (0.33), residues: 265 loop : -0.76 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 390 TYR 0.013 0.001 TYR A 83 PHE 0.018 0.002 PHE B 266 TRP 0.012 0.001 TRP A 346 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00300 (12914) covalent geometry : angle 0.60115 (17498) hydrogen bonds : bond 0.04837 ( 604) hydrogen bonds : angle 5.04970 ( 1878) Misc. bond : bond 0.00108 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7353 (mm110) cc_final: 0.7146 (mt0) REVERT: A 203 MET cc_start: 0.7346 (mmm) cc_final: 0.6894 (mmm) REVERT: A 217 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6508 (mm) REVERT: A 300 ASN cc_start: 0.8218 (m-40) cc_final: 0.7745 (m-40) REVERT: A 302 MET cc_start: 0.8272 (mmm) cc_final: 0.7974 (mmm) REVERT: A 352 LYS cc_start: 0.5599 (mmtt) cc_final: 0.5282 (mmtt) REVERT: A 398 MET cc_start: 0.6842 (mmp) cc_final: 0.6412 (mmt) REVERT: B 251 ARG cc_start: 0.6852 (mmm160) cc_final: 0.6424 (mtt-85) REVERT: B 267 MET cc_start: 0.8119 (mtt) cc_final: 0.7888 (mtp) REVERT: C 333 MET cc_start: 0.3467 (tmm) cc_final: 0.2873 (ttm) REVERT: C 500 MET cc_start: 0.5794 (mmp) cc_final: 0.5179 (mmp) REVERT: C 501 GLU cc_start: 0.5974 (pp20) cc_final: 0.5080 (mp0) REVERT: C 537 MET cc_start: 0.1679 (pmm) cc_final: 0.1059 (tpt) REVERT: C 593 MET cc_start: 0.4285 (tpt) cc_final: 0.4055 (tpt) REVERT: C 632 MET cc_start: 0.4784 (tmm) cc_final: 0.4584 (tpt) REVERT: D 366 MET cc_start: 0.1697 (pmm) cc_final: -0.1077 (ttm) REVERT: D 391 MET cc_start: 0.1193 (ptp) cc_final: 0.0498 (mmt) REVERT: D 500 MET cc_start: 0.4378 (mmm) cc_final: 0.3726 (mmt) outliers start: 35 outliers final: 21 residues processed: 218 average time/residue: 0.0816 time to fit residues: 26.9411 Evaluate side-chains 188 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 22 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 143 optimal weight: 0.0000 chunk 153 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 100 ASN B 190 HIS ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN C 420 GLN ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 GLN C 617 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.237746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.184227 restraints weight = 17828.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.179395 restraints weight = 23414.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.181808 restraints weight = 19977.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.181107 restraints weight = 11433.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.181635 restraints weight = 10749.860| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12916 Z= 0.118 Angle : 0.568 8.623 17498 Z= 0.288 Chirality : 0.043 0.197 1952 Planarity : 0.004 0.054 2273 Dihedral : 7.888 136.876 1768 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.58 % Allowed : 15.43 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1584 helix: 0.89 (0.19), residues: 727 sheet: 0.46 (0.34), residues: 259 loop : -0.79 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 359 TYR 0.015 0.001 TYR B 208 PHE 0.014 0.001 PHE D 329 TRP 0.013 0.001 TRP A 346 HIS 0.008 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00248 (12914) covalent geometry : angle 0.56838 (17498) hydrogen bonds : bond 0.04235 ( 604) hydrogen bonds : angle 4.76843 ( 1878) Misc. bond : bond 0.00164 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.6641 (t0) cc_final: 0.6335 (t70) REVERT: A 203 MET cc_start: 0.7338 (mmm) cc_final: 0.6890 (mmm) REVERT: A 217 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6477 (mm) REVERT: A 300 ASN cc_start: 0.8249 (m-40) cc_final: 0.7760 (m-40) REVERT: A 352 LYS cc_start: 0.5669 (mmtt) cc_final: 0.5278 (mmtt) REVERT: A 398 MET cc_start: 0.6802 (mmp) cc_final: 0.6491 (mmt) REVERT: B 208 TYR cc_start: 0.7547 (m-80) cc_final: 0.7313 (m-80) REVERT: B 251 ARG cc_start: 0.6910 (mmm160) cc_final: 0.6463 (mtt-85) REVERT: B 267 MET cc_start: 0.8135 (mtt) cc_final: 0.7869 (mtp) REVERT: B 375 GLN cc_start: 0.7617 (pp30) cc_final: 0.7095 (pp30) REVERT: B 415 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6759 (ttm) REVERT: C 333 MET cc_start: 0.3692 (tmm) cc_final: 0.3167 (ttm) REVERT: C 500 MET cc_start: 0.5645 (mmp) cc_final: 0.5223 (mmp) REVERT: C 501 GLU cc_start: 0.5777 (pp20) cc_final: 0.5067 (mp0) REVERT: C 506 LYS cc_start: 0.3778 (mmmm) cc_final: 0.2762 (mttp) REVERT: C 537 MET cc_start: 0.1808 (pmm) cc_final: 0.1326 (tpt) REVERT: D 366 MET cc_start: 0.1616 (pmm) cc_final: -0.1347 (ttm) REVERT: D 391 MET cc_start: 0.1192 (ptp) cc_final: 0.0557 (mmt) REVERT: D 500 MET cc_start: 0.4605 (mmm) cc_final: 0.3885 (mmt) outliers start: 36 outliers final: 20 residues processed: 211 average time/residue: 0.0867 time to fit residues: 28.0247 Evaluate side-chains 184 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 56 optimal weight: 10.0000 chunk 156 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 chunk 117 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 101 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 424 GLN C 420 GLN C 435 GLN ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.231368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.175973 restraints weight = 18000.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.167972 restraints weight = 24198.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.169981 restraints weight = 24208.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.170188 restraints weight = 12759.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.170388 restraints weight = 11107.297| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12916 Z= 0.184 Angle : 0.666 8.814 17498 Z= 0.337 Chirality : 0.046 0.195 1952 Planarity : 0.005 0.046 2273 Dihedral : 8.160 143.083 1767 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.45 % Allowed : 16.15 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1584 helix: 0.71 (0.19), residues: 727 sheet: 0.20 (0.34), residues: 268 loop : -0.83 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 390 TYR 0.023 0.002 TYR D 622 PHE 0.021 0.002 PHE B 90 TRP 0.019 0.002 TRP A 346 HIS 0.007 0.001 HIS D 339 Details of bonding type rmsd covalent geometry : bond 0.00417 (12914) covalent geometry : angle 0.66626 (17498) hydrogen bonds : bond 0.04729 ( 604) hydrogen bonds : angle 4.81529 ( 1878) Misc. bond : bond 0.00219 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7407 (mm110) cc_final: 0.7187 (mt0) REVERT: A 217 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6615 (mm) REVERT: A 230 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8419 (mp) REVERT: A 286 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6538 (mm) REVERT: A 352 LYS cc_start: 0.5354 (mmtt) cc_final: 0.5144 (mmtt) REVERT: A 398 MET cc_start: 0.7003 (mmp) cc_final: 0.6668 (mmt) REVERT: B 208 TYR cc_start: 0.7598 (m-80) cc_final: 0.7354 (m-80) REVERT: B 251 ARG cc_start: 0.7238 (mmm160) cc_final: 0.6896 (tpp-160) REVERT: B 267 MET cc_start: 0.8263 (mtt) cc_final: 0.8029 (mtp) REVERT: B 375 GLN cc_start: 0.7806 (pp30) cc_final: 0.7228 (pp30) REVERT: B 415 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6756 (ttm) REVERT: B 423 GLN cc_start: 0.7540 (pp30) cc_final: 0.7042 (pp30) REVERT: C 333 MET cc_start: 0.3907 (tmm) cc_final: 0.2760 (mtt) REVERT: C 500 MET cc_start: 0.5848 (mmp) cc_final: 0.5540 (mmp) REVERT: C 501 GLU cc_start: 0.5996 (pp20) cc_final: 0.5092 (mp0) REVERT: C 506 LYS cc_start: 0.3940 (mmmm) cc_final: 0.2935 (mttp) REVERT: C 537 MET cc_start: 0.1698 (OUTLIER) cc_final: 0.1330 (tpt) REVERT: C 593 MET cc_start: 0.5316 (tpt) cc_final: 0.4873 (tpt) REVERT: D 339 HIS cc_start: 0.2394 (OUTLIER) cc_final: 0.2135 (t-170) REVERT: D 366 MET cc_start: 0.1934 (pmm) cc_final: -0.1071 (ttm) REVERT: D 391 MET cc_start: 0.1249 (ptp) cc_final: 0.0564 (mmt) REVERT: D 500 MET cc_start: 0.4419 (mmm) cc_final: 0.3754 (mmt) REVERT: D 632 MET cc_start: 0.2000 (mmp) cc_final: 0.0350 (ttp) REVERT: D 662 ARG cc_start: 0.0768 (OUTLIER) cc_final: 0.0028 (tpt170) outliers start: 48 outliers final: 29 residues processed: 208 average time/residue: 0.0866 time to fit residues: 27.4623 Evaluate side-chains 192 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 537 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 339 HIS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 662 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 124 optimal weight: 20.0000 chunk 98 optimal weight: 0.1980 chunk 30 optimal weight: 0.2980 chunk 130 optimal weight: 0.0030 chunk 122 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 107 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 118 optimal weight: 50.0000 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 88 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 15 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 347 ASN C 339 HIS C 565 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.234801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.179987 restraints weight = 17879.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.172536 restraints weight = 23986.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.174212 restraints weight = 23132.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.174597 restraints weight = 12302.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.174779 restraints weight = 10540.651| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12916 Z= 0.117 Angle : 0.584 6.450 17498 Z= 0.295 Chirality : 0.043 0.241 1952 Planarity : 0.004 0.051 2273 Dihedral : 7.960 140.685 1767 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.66 % Allowed : 18.02 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1584 helix: 0.85 (0.19), residues: 731 sheet: 0.21 (0.34), residues: 269 loop : -0.83 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 390 TYR 0.015 0.001 TYR D 622 PHE 0.021 0.001 PHE B 266 TRP 0.015 0.001 TRP A 346 HIS 0.009 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00254 (12914) covalent geometry : angle 0.58438 (17498) hydrogen bonds : bond 0.04073 ( 604) hydrogen bonds : angle 4.59447 ( 1878) Misc. bond : bond 0.00142 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.7456 (mmm) cc_final: 0.6877 (mmm) REVERT: A 217 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6676 (mm) REVERT: A 302 MET cc_start: 0.8071 (mmm) cc_final: 0.7722 (mtt) REVERT: A 352 LYS cc_start: 0.5346 (mmtt) cc_final: 0.5113 (mmtm) REVERT: A 398 MET cc_start: 0.7012 (mmp) cc_final: 0.6654 (mmt) REVERT: B 208 TYR cc_start: 0.7553 (m-80) cc_final: 0.7293 (m-80) REVERT: B 251 ARG cc_start: 0.7119 (mmm160) cc_final: 0.6827 (tpp-160) REVERT: B 257 MET cc_start: 0.8321 (mmm) cc_final: 0.8082 (mmm) REVERT: B 267 MET cc_start: 0.8195 (mtt) cc_final: 0.7898 (mtp) REVERT: B 375 GLN cc_start: 0.7764 (pp30) cc_final: 0.7279 (pp30) REVERT: B 415 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6798 (ttm) REVERT: B 423 GLN cc_start: 0.7541 (pp30) cc_final: 0.7029 (pp30) REVERT: C 333 MET cc_start: 0.3882 (tmm) cc_final: 0.2661 (mtm) REVERT: C 500 MET cc_start: 0.5882 (mmp) cc_final: 0.5586 (mmp) REVERT: C 501 GLU cc_start: 0.5813 (pp20) cc_final: 0.5056 (mp0) REVERT: C 506 LYS cc_start: 0.3818 (mmmm) cc_final: 0.2978 (mttp) REVERT: C 537 MET cc_start: 0.1781 (pmm) cc_final: 0.1463 (tpp) REVERT: D 339 HIS cc_start: 0.2095 (OUTLIER) cc_final: 0.1564 (t70) REVERT: D 366 MET cc_start: 0.1893 (pmm) cc_final: -0.1043 (ttm) REVERT: D 482 LEU cc_start: 0.1297 (OUTLIER) cc_final: 0.0797 (mp) REVERT: D 500 MET cc_start: 0.4363 (mmm) cc_final: 0.3676 (mmt) REVERT: D 662 ARG cc_start: 0.0915 (OUTLIER) cc_final: 0.0180 (tpt170) outliers start: 37 outliers final: 24 residues processed: 210 average time/residue: 0.0869 time to fit residues: 28.1520 Evaluate side-chains 190 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 339 HIS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 662 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 30 optimal weight: 9.9990 chunk 136 optimal weight: 0.4980 chunk 84 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 chunk 143 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 0.0980 chunk 86 optimal weight: 5.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 347 ASN B 424 GLN C 615 GLN C 617 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.239197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.185212 restraints weight = 17700.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.177741 restraints weight = 22628.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.180631 restraints weight = 19809.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.180433 restraints weight = 10239.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.180764 restraints weight = 9236.017| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12916 Z= 0.111 Angle : 0.589 12.033 17498 Z= 0.292 Chirality : 0.043 0.203 1952 Planarity : 0.004 0.054 2273 Dihedral : 7.846 137.863 1767 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.09 % Allowed : 17.88 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1584 helix: 0.84 (0.19), residues: 730 sheet: 0.22 (0.33), residues: 284 loop : -0.74 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.012 0.001 TYR A 83 PHE 0.017 0.001 PHE B 266 TRP 0.014 0.001 TRP A 388 HIS 0.011 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00234 (12914) covalent geometry : angle 0.58899 (17498) hydrogen bonds : bond 0.03824 ( 604) hydrogen bonds : angle 4.49747 ( 1878) Misc. bond : bond 0.00138 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6516 (mm) REVERT: A 286 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6593 (mm) REVERT: A 295 CYS cc_start: 0.7423 (p) cc_final: 0.7201 (p) REVERT: A 302 MET cc_start: 0.8001 (mmm) cc_final: 0.7720 (mtt) REVERT: A 352 LYS cc_start: 0.5515 (mmtt) cc_final: 0.5257 (mmtm) REVERT: A 398 MET cc_start: 0.6875 (mmp) cc_final: 0.6578 (mmt) REVERT: A 432 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6294 (t80) REVERT: B 208 TYR cc_start: 0.7533 (m-80) cc_final: 0.7033 (m-80) REVERT: B 251 ARG cc_start: 0.7059 (mmm160) cc_final: 0.6583 (mtt-85) REVERT: B 267 MET cc_start: 0.8101 (mtt) cc_final: 0.7832 (mtp) REVERT: B 321 MET cc_start: 0.7157 (ptp) cc_final: 0.6668 (ptp) REVERT: B 375 GLN cc_start: 0.7698 (pp30) cc_final: 0.7246 (pp30) REVERT: B 415 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6546 (ttm) REVERT: B 423 GLN cc_start: 0.7445 (pp30) cc_final: 0.7013 (pp30) REVERT: C 333 MET cc_start: 0.3884 (tmm) cc_final: 0.2666 (mtm) REVERT: C 414 MET cc_start: 0.4263 (pmm) cc_final: 0.2754 (ttt) REVERT: C 500 MET cc_start: 0.5706 (mmp) cc_final: 0.5445 (mmp) REVERT: C 501 GLU cc_start: 0.5738 (pp20) cc_final: 0.5034 (mp0) REVERT: C 506 LYS cc_start: 0.3790 (mmmm) cc_final: 0.2907 (mttp) REVERT: C 537 MET cc_start: 0.1778 (OUTLIER) cc_final: 0.1514 (tpp) REVERT: C 580 ASP cc_start: 0.1680 (p0) cc_final: 0.1213 (m-30) REVERT: C 593 MET cc_start: 0.5177 (tpt) cc_final: 0.4764 (tpt) REVERT: D 339 HIS cc_start: 0.1932 (OUTLIER) cc_final: 0.1442 (t70) REVERT: D 366 MET cc_start: 0.1816 (pmm) cc_final: -0.1089 (ttm) REVERT: D 482 LEU cc_start: 0.1277 (OUTLIER) cc_final: 0.0801 (mp) REVERT: D 500 MET cc_start: 0.4338 (mmm) cc_final: 0.3686 (mmt) REVERT: D 662 ARG cc_start: 0.1150 (OUTLIER) cc_final: 0.0373 (tpt170) outliers start: 43 outliers final: 20 residues processed: 217 average time/residue: 0.0989 time to fit residues: 32.0337 Evaluate side-chains 187 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 537 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 339 HIS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 662 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 4 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 154 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN C 538 ASN C 617 GLN D 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.235706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.181365 restraints weight = 17500.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.170913 restraints weight = 22570.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.173836 restraints weight = 21271.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.173939 restraints weight = 11186.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.174271 restraints weight = 9680.955| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12916 Z= 0.138 Angle : 0.620 11.547 17498 Z= 0.308 Chirality : 0.044 0.162 1952 Planarity : 0.005 0.054 2273 Dihedral : 7.922 139.810 1767 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.09 % Allowed : 17.66 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1584 helix: 0.84 (0.19), residues: 731 sheet: 0.04 (0.32), residues: 278 loop : -0.73 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 549 TYR 0.012 0.001 TYR A 357 PHE 0.025 0.002 PHE B 266 TRP 0.017 0.002 TRP A 346 HIS 0.008 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00310 (12914) covalent geometry : angle 0.62000 (17498) hydrogen bonds : bond 0.04062 ( 604) hydrogen bonds : angle 4.49282 ( 1878) Misc. bond : bond 0.00209 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 217 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6627 (mm) REVERT: A 286 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6506 (mm) REVERT: A 295 CYS cc_start: 0.7445 (p) cc_final: 0.7213 (p) REVERT: A 302 MET cc_start: 0.8090 (mmm) cc_final: 0.7823 (mtt) REVERT: A 352 LYS cc_start: 0.5599 (mmtt) cc_final: 0.5266 (mmtm) REVERT: A 398 MET cc_start: 0.7010 (mmp) cc_final: 0.6678 (mmt) REVERT: A 432 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6240 (t80) REVERT: B 208 TYR cc_start: 0.7549 (m-80) cc_final: 0.7064 (m-80) REVERT: B 251 ARG cc_start: 0.7140 (mmm160) cc_final: 0.6884 (tpp-160) REVERT: B 267 MET cc_start: 0.8168 (mtt) cc_final: 0.7884 (mtp) REVERT: B 375 GLN cc_start: 0.7830 (pp30) cc_final: 0.7257 (pp30) REVERT: B 415 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6600 (ttm) REVERT: B 423 GLN cc_start: 0.7585 (pp30) cc_final: 0.7141 (pp30) REVERT: C 414 MET cc_start: 0.4259 (pmm) cc_final: 0.2698 (ttt) REVERT: C 500 MET cc_start: 0.5960 (mmp) cc_final: 0.5356 (mmp) REVERT: C 504 MET cc_start: 0.5118 (tmm) cc_final: 0.4363 (tmm) REVERT: C 506 LYS cc_start: 0.3785 (mmmm) cc_final: 0.2938 (mttp) REVERT: C 537 MET cc_start: 0.2060 (OUTLIER) cc_final: 0.1764 (tpp) REVERT: C 624 ASN cc_start: 0.6022 (t0) cc_final: 0.5244 (t0) REVERT: D 339 HIS cc_start: 0.2066 (OUTLIER) cc_final: 0.1612 (t70) REVERT: D 366 MET cc_start: 0.1731 (pmm) cc_final: -0.1110 (ttm) REVERT: D 391 MET cc_start: 0.1263 (ptp) cc_final: 0.0504 (mmt) REVERT: D 482 LEU cc_start: 0.1372 (OUTLIER) cc_final: 0.0825 (mp) REVERT: D 500 MET cc_start: 0.4181 (mmm) cc_final: 0.3533 (mmt) REVERT: D 632 MET cc_start: 0.2627 (mmp) cc_final: 0.2350 (mmm) REVERT: D 662 ARG cc_start: 0.1108 (OUTLIER) cc_final: 0.0325 (tpt170) outliers start: 43 outliers final: 24 residues processed: 206 average time/residue: 0.0954 time to fit residues: 29.3303 Evaluate side-chains 194 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 537 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 339 HIS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 662 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 103 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 3 optimal weight: 0.3980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.236527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.182145 restraints weight = 17620.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.176637 restraints weight = 23075.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.178243 restraints weight = 21572.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.178677 restraints weight = 11143.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.178620 restraints weight = 10066.777| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12916 Z= 0.126 Angle : 0.620 10.107 17498 Z= 0.307 Chirality : 0.044 0.168 1952 Planarity : 0.004 0.055 2273 Dihedral : 7.926 140.091 1767 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.66 % Allowed : 18.88 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1584 helix: 0.83 (0.19), residues: 729 sheet: 0.03 (0.33), residues: 277 loop : -0.71 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 592 TYR 0.013 0.001 TYR A 357 PHE 0.011 0.001 PHE D 329 TRP 0.022 0.002 TRP A 388 HIS 0.008 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00282 (12914) covalent geometry : angle 0.61997 (17498) hydrogen bonds : bond 0.03937 ( 604) hydrogen bonds : angle 4.45124 ( 1878) Misc. bond : bond 0.00172 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7646 (p90) cc_final: 0.7156 (p90) REVERT: A 217 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6618 (mm) REVERT: A 286 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6507 (mm) REVERT: A 295 CYS cc_start: 0.7444 (p) cc_final: 0.7213 (p) REVERT: A 302 MET cc_start: 0.8078 (mmm) cc_final: 0.7828 (mtt) REVERT: A 352 LYS cc_start: 0.5472 (mmtt) cc_final: 0.5212 (mmtm) REVERT: A 398 MET cc_start: 0.6995 (mmp) cc_final: 0.6697 (mmt) REVERT: A 432 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6318 (t80) REVERT: B 208 TYR cc_start: 0.7448 (m-80) cc_final: 0.6906 (m-80) REVERT: B 267 MET cc_start: 0.8141 (mtt) cc_final: 0.7900 (mtp) REVERT: B 375 GLN cc_start: 0.7841 (pp30) cc_final: 0.7280 (pp30) REVERT: B 406 MET cc_start: 0.5200 (ttm) cc_final: 0.4905 (ttm) REVERT: B 415 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6528 (ttm) REVERT: B 423 GLN cc_start: 0.7560 (pp30) cc_final: 0.7121 (pp30) REVERT: C 414 MET cc_start: 0.4196 (pmm) cc_final: 0.2778 (ttt) REVERT: C 489 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7146 (mp) REVERT: C 500 MET cc_start: 0.5775 (mmp) cc_final: 0.5349 (mmp) REVERT: C 504 MET cc_start: 0.5095 (tmm) cc_final: 0.4266 (tmm) REVERT: C 506 LYS cc_start: 0.3472 (mmmm) cc_final: 0.2848 (mttp) REVERT: C 537 MET cc_start: 0.2090 (OUTLIER) cc_final: 0.1836 (tpp) REVERT: C 580 ASP cc_start: 0.1472 (p0) cc_final: 0.1115 (m-30) REVERT: C 593 MET cc_start: 0.5368 (tpt) cc_final: 0.5112 (tpt) REVERT: C 624 ASN cc_start: 0.6121 (t0) cc_final: 0.5327 (t0) REVERT: D 366 MET cc_start: 0.1864 (pmm) cc_final: -0.1211 (ttm) REVERT: D 391 MET cc_start: 0.1136 (ptp) cc_final: 0.0514 (mmt) REVERT: D 482 LEU cc_start: 0.1321 (OUTLIER) cc_final: 0.0790 (mp) REVERT: D 662 ARG cc_start: 0.1142 (OUTLIER) cc_final: 0.0362 (tpt170) outliers start: 37 outliers final: 25 residues processed: 201 average time/residue: 0.0987 time to fit residues: 30.0204 Evaluate side-chains 192 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 537 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 662 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 65 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 153 optimal weight: 30.0000 chunk 154 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 31 GLN A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 617 GLN C 651 GLN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.230026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.175169 restraints weight = 17960.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.167097 restraints weight = 22934.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.168837 restraints weight = 22608.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.169724 restraints weight = 11646.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.170018 restraints weight = 9647.739| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12916 Z= 0.236 Angle : 0.752 11.145 17498 Z= 0.380 Chirality : 0.049 0.197 1952 Planarity : 0.006 0.064 2273 Dihedral : 8.408 146.898 1767 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.16 % Allowed : 18.16 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.21), residues: 1584 helix: 0.45 (0.19), residues: 729 sheet: -0.25 (0.33), residues: 279 loop : -0.89 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 62 TYR 0.032 0.002 TYR B 425 PHE 0.027 0.003 PHE B 90 TRP 0.024 0.003 TRP A 346 HIS 0.008 0.002 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00547 (12914) covalent geometry : angle 0.75222 (17498) hydrogen bonds : bond 0.04986 ( 604) hydrogen bonds : angle 4.78773 ( 1878) Misc. bond : bond 0.00299 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7664 (p90) cc_final: 0.7110 (p90) REVERT: A 60 LYS cc_start: 0.4089 (pttt) cc_final: 0.2979 (tttt) REVERT: A 154 MET cc_start: 0.8317 (mmt) cc_final: 0.7975 (mmt) REVERT: A 213 CYS cc_start: 0.6451 (p) cc_final: 0.6076 (t) REVERT: A 286 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6499 (mm) REVERT: A 302 MET cc_start: 0.8133 (mmm) cc_final: 0.7891 (mtt) REVERT: A 398 MET cc_start: 0.7256 (mmp) cc_final: 0.7017 (mmt) REVERT: A 432 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6358 (t80) REVERT: B 208 TYR cc_start: 0.7487 (m-80) cc_final: 0.7086 (m-80) REVERT: B 267 MET cc_start: 0.8175 (mtt) cc_final: 0.7931 (mtp) REVERT: B 375 GLN cc_start: 0.7904 (pp30) cc_final: 0.7292 (pp30) REVERT: B 415 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6668 (ttm) REVERT: C 414 MET cc_start: 0.4252 (pmm) cc_final: 0.2451 (ttt) REVERT: C 489 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7222 (mp) REVERT: C 500 MET cc_start: 0.5906 (mmp) cc_final: 0.5552 (mmp) REVERT: C 506 LYS cc_start: 0.3629 (mmmm) cc_final: 0.2670 (mttp) REVERT: C 537 MET cc_start: 0.2036 (OUTLIER) cc_final: 0.1759 (tpp) REVERT: C 580 ASP cc_start: 0.1505 (p0) cc_final: 0.1093 (m-30) REVERT: C 597 LYS cc_start: 0.4520 (mmtp) cc_final: 0.4318 (mmtt) REVERT: C 624 ASN cc_start: 0.6075 (t0) cc_final: 0.5237 (t0) REVERT: D 391 MET cc_start: 0.1264 (ptp) cc_final: 0.0607 (mmt) REVERT: D 482 LEU cc_start: 0.1431 (OUTLIER) cc_final: 0.0773 (mp) REVERT: D 500 MET cc_start: 0.4238 (mmm) cc_final: 0.3864 (mmt) REVERT: D 532 MET cc_start: 0.4381 (tpt) cc_final: 0.1876 (ttp) REVERT: D 662 ARG cc_start: 0.0922 (OUTLIER) cc_final: 0.0099 (tpt170) outliers start: 44 outliers final: 29 residues processed: 198 average time/residue: 0.0916 time to fit residues: 27.6494 Evaluate side-chains 179 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 537 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 662 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 138 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 145 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN D 373 HIS D 393 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.233769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.178865 restraints weight = 17830.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.169981 restraints weight = 20316.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.171979 restraints weight = 18164.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.172523 restraints weight = 9884.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.172972 restraints weight = 8791.307| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12916 Z= 0.137 Angle : 0.658 8.796 17498 Z= 0.326 Chirality : 0.045 0.210 1952 Planarity : 0.005 0.053 2273 Dihedral : 8.195 143.848 1765 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.44 % Allowed : 18.88 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1584 helix: 0.65 (0.19), residues: 730 sheet: -0.21 (0.33), residues: 277 loop : -0.88 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.034 0.002 TYR B 36 PHE 0.015 0.001 PHE A 169 TRP 0.020 0.002 TRP A 388 HIS 0.008 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00307 (12914) covalent geometry : angle 0.65761 (17498) hydrogen bonds : bond 0.04241 ( 604) hydrogen bonds : angle 4.58096 ( 1878) Misc. bond : bond 0.00191 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.39 seconds wall clock time: 39 minutes 15.18 seconds (2355.18 seconds total)