Starting phenix.real_space_refine on Wed Mar 4 11:28:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bxu_30238/03_2026/7bxu_30238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bxu_30238/03_2026/7bxu_30238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bxu_30238/03_2026/7bxu_30238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bxu_30238/03_2026/7bxu_30238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bxu_30238/03_2026/7bxu_30238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bxu_30238/03_2026/7bxu_30238.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8704 2.51 5 N 2242 2.21 5 O 2414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13444 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1552 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5072 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5, 'GLU:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Restraints were copied for chains: D, B Time building chain proxies: 4.28, per 1000 atoms: 0.32 Number of scatterers: 13444 At special positions: 0 Unit cell: (104.76, 98.28, 140.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2414 8.00 N 2242 7.00 C 8704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 115 " distance=2.05 Simple disulfide: pdb=" SG CYS C 112 " - pdb=" SG CYS C 171 " distance=1.54 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 115 " distance=2.05 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 171 " distance=1.54 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 401 " - " ASN C 93 " " NAG C 402 " - " ASN C 263 " " NAG C 403 " - " ASN C 163 " " NAG C 404 " - " ASN C 184 " " NAG C 405 " - " ASN C 194 " " NAG C 406 " - " ASN C 216 " " NAG C 407 " - " ASN C 128 " " NAG D 401 " - " ASN D 93 " " NAG D 402 " - " ASN D 263 " " NAG D 403 " - " ASN D 163 " " NAG D 404 " - " ASN D 184 " " NAG D 405 " - " ASN D 194 " " NAG D 406 " - " ASN D 216 " " NAG D 407 " - " ASN D 128 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 595.1 milliseconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 6 sheets defined 61.1% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'C' and resid 84 through 105 removed outlier: 3.635A pdb=" N GLU C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 116 through 131 removed outlier: 4.050A pdb=" N GLN C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 153 through 170 Processing helix chain 'C' and resid 184 through 203 removed outlier: 3.991A pdb=" N PHE C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 removed outlier: 4.157A pdb=" N LYS C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 242 removed outlier: 4.458A pdb=" N THR C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 271 removed outlier: 3.562A pdb=" N THR C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 271 " --> pdb=" O LYS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 293 removed outlier: 4.339A pdb=" N SER C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 305 removed outlier: 3.898A pdb=" N LEU C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.658A pdb=" N ARG A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 163 removed outlier: 3.934A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.941A pdb=" N LEU A 178 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.948A pdb=" N ILE A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.780A pdb=" N ILE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 262' Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.783A pdb=" N ALA A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 303 through 315 removed outlier: 3.552A pdb=" N GLY A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 335 removed outlier: 3.637A pdb=" N THR A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 329 " --> pdb=" O TRP A 325 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.675A pdb=" N ILE A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 388 removed outlier: 3.593A pdb=" N ILE A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 407 removed outlier: 3.968A pdb=" N ALA A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 434 removed outlier: 3.772A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 415 " --> pdb=" O CYS A 411 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 Processing helix chain 'A' and resid 488 through 505 removed outlier: 3.727A pdb=" N VAL A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 532 removed outlier: 4.563A pdb=" N ILE A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 removed outlier: 4.222A pdb=" N TYR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 573 removed outlier: 3.783A pdb=" N VAL A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 593 removed outlier: 3.881A pdb=" N ILE A 583 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 592 " --> pdb=" O MET A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.535A pdb=" N MET A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 681 through 690 Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.959A pdb=" N ARG A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 753 through 764 removed outlier: 3.550A pdb=" N LEU A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 789 removed outlier: 3.755A pdb=" N LEU A 787 " --> pdb=" O THR A 783 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 105 removed outlier: 3.635A pdb=" N GLU D 97 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER D 105 " --> pdb=" O CYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 116 through 131 removed outlier: 4.049A pdb=" N GLN D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN D 121 " --> pdb=" O PRO D 117 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 123 " --> pdb=" O PHE D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 153 through 170 Processing helix chain 'D' and resid 184 through 203 removed outlier: 3.992A pdb=" N PHE D 200 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 removed outlier: 4.158A pdb=" N LYS D 222 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 242 removed outlier: 4.458A pdb=" N THR D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 271 removed outlier: 3.562A pdb=" N THR D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 293 removed outlier: 4.338A pdb=" N SER D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 305 removed outlier: 3.898A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 removed outlier: 3.658A pdb=" N ARG B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 163 removed outlier: 3.934A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 134 " --> pdb=" O CYS B 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.941A pdb=" N LEU B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.949A pdb=" N ILE B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.780A pdb=" N ILE B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 257 through 262' Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.783A pdb=" N ALA B 291 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.552A pdb=" N GLY B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 335 removed outlier: 3.636A pdb=" N THR B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 333 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.675A pdb=" N ILE B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 374 through 388 removed outlier: 3.592A pdb=" N ILE B 379 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 407 removed outlier: 3.968A pdb=" N ALA B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 395 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR B 397 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 434 removed outlier: 3.771A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE B 415 " --> pdb=" O CYS B 411 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 Processing helix chain 'B' and resid 488 through 505 removed outlier: 3.726A pdb=" N VAL B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 532 removed outlier: 4.563A pdb=" N ILE B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 532 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 560 removed outlier: 4.222A pdb=" N TYR B 547 " --> pdb=" O ASP B 543 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 573 removed outlier: 3.783A pdb=" N VAL B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.880A pdb=" N ILE B 583 " --> pdb=" O TYR B 579 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 592 " --> pdb=" O MET B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 600 through 608 removed outlier: 3.535A pdb=" N MET B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 652 Processing helix chain 'B' and resid 681 through 690 Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.960A pdb=" N ARG B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 724 Processing helix chain 'B' and resid 753 through 764 removed outlier: 3.549A pdb=" N LEU B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 789 removed outlier: 3.755A pdb=" N LEU B 787 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 789 " --> pdb=" O LYS B 785 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AA2, first strand: chain 'A' and resid 660 through 662 Processing sheet with id=AA3, first strand: chain 'A' and resid 747 through 749 removed outlier: 3.831A pdb=" N GLY A 780 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 438 through 440 Processing sheet with id=AA5, first strand: chain 'B' and resid 660 through 662 Processing sheet with id=AA6, first strand: chain 'B' and resid 747 through 749 removed outlier: 3.831A pdb=" N GLY B 780 " --> pdb=" O VAL B 771 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1752 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: 1.93 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4161 1.34 - 1.46: 3322 1.46 - 1.58: 6119 1.58 - 1.71: 0 1.71 - 1.83: 128 Bond restraints: 13730 Sorted by residual: bond pdb=" CA GLU B 313 " pdb=" C GLU B 313 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.27e-02 6.20e+03 5.15e+00 bond pdb=" CA GLU A 313 " pdb=" C GLU A 313 " ideal model delta sigma weight residual 1.524 1.495 0.028 1.27e-02 6.20e+03 5.01e+00 bond pdb=" CA ALA D 106 " pdb=" C ALA D 106 " ideal model delta sigma weight residual 1.533 1.523 0.010 5.60e-03 3.19e+04 3.50e+00 bond pdb=" CA ALA C 106 " pdb=" C ALA C 106 " ideal model delta sigma weight residual 1.533 1.523 0.010 5.60e-03 3.19e+04 3.42e+00 bond pdb=" CA ASP D 257 " pdb=" C ASP D 257 " ideal model delta sigma weight residual 1.524 1.547 -0.024 1.29e-02 6.01e+03 3.39e+00 ... (remaining 13725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 17688 2.31 - 4.62: 829 4.62 - 6.92: 98 6.92 - 9.23: 47 9.23 - 11.54: 16 Bond angle restraints: 18678 Sorted by residual: angle pdb=" N ARG A 762 " pdb=" CA ARG A 762 " pdb=" C ARG A 762 " ideal model delta sigma weight residual 111.36 118.98 -7.62 1.09e+00 8.42e-01 4.89e+01 angle pdb=" N ARG B 762 " pdb=" CA ARG B 762 " pdb=" C ARG B 762 " ideal model delta sigma weight residual 111.36 118.93 -7.57 1.09e+00 8.42e-01 4.83e+01 angle pdb=" N PRO A 355 " pdb=" CA PRO A 355 " pdb=" CB PRO A 355 " ideal model delta sigma weight residual 103.51 109.92 -6.41 9.60e-01 1.09e+00 4.46e+01 angle pdb=" N PRO B 355 " pdb=" CA PRO B 355 " pdb=" CB PRO B 355 " ideal model delta sigma weight residual 103.51 109.92 -6.41 9.60e-01 1.09e+00 4.45e+01 angle pdb=" N PRO B 672 " pdb=" CA PRO B 672 " pdb=" CB PRO B 672 " ideal model delta sigma weight residual 103.00 110.30 -7.30 1.10e+00 8.26e-01 4.41e+01 ... (remaining 18673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7750 17.83 - 35.67: 434 35.67 - 53.50: 58 53.50 - 71.33: 12 71.33 - 89.16: 8 Dihedral angle restraints: 8262 sinusoidal: 3196 harmonic: 5066 Sorted by residual: dihedral pdb=" CB CYS C 112 " pdb=" SG CYS C 112 " pdb=" SG CYS C 171 " pdb=" CB CYS C 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.16 89.16 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS D 112 " pdb=" SG CYS D 112 " pdb=" SG CYS D 171 " pdb=" CB CYS D 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.11 89.11 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS D 84 " pdb=" SG CYS D 84 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual -86.00 -161.81 75.81 1 1.00e+01 1.00e-02 7.25e+01 ... (remaining 8259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1811 0.077 - 0.154: 361 0.154 - 0.232: 58 0.232 - 0.309: 17 0.309 - 0.386: 7 Chirality restraints: 2254 Sorted by residual: chirality pdb=" CA VAL A 221 " pdb=" N VAL A 221 " pdb=" C VAL A 221 " pdb=" CB VAL A 221 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA VAL B 221 " pdb=" N VAL B 221 " pdb=" C VAL B 221 " pdb=" CB VAL B 221 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA ARG A 762 " pdb=" N ARG A 762 " pdb=" C ARG A 762 " pdb=" CB ARG A 762 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 2251 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG C 401 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 404 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG C 404 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 404 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 404 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 404 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 402 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG D 402 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG D 402 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG D 402 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG D 402 " -0.008 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3584 2.79 - 3.32: 12390 3.32 - 3.85: 20377 3.85 - 4.37: 22351 4.37 - 4.90: 40193 Nonbonded interactions: 98895 Sorted by model distance: nonbonded pdb=" O ASN C 173 " pdb=" OG SER C 183 " model vdw 2.267 3.040 nonbonded pdb=" O ASN D 173 " pdb=" OG SER D 183 " model vdw 2.267 3.040 nonbonded pdb=" O4 NAG D 402 " pdb=" O6 NAG D 402 " model vdw 2.302 3.040 nonbonded pdb=" O4 NAG C 402 " pdb=" O6 NAG C 402 " model vdw 2.303 3.040 nonbonded pdb=" NH2 ARG B 640 " pdb=" OE1 GLN B 676 " model vdw 2.364 3.120 ... (remaining 98890 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.010 0.491 13750 Z= 0.472 Angle : 1.275 42.377 18732 Z= 0.701 Chirality : 0.069 0.386 2254 Planarity : 0.009 0.072 2326 Dihedral : 11.207 75.404 4960 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.43 % Allowed : 6.81 % Favored : 92.75 % Cbeta Deviations : 0.12 % 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: -4.33 (0.16), residues: 1708 helix: -2.63 (0.13), residues: 1004 sheet: None (None), residues: 0 loop : -3.12 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 403 TYR 0.019 0.003 TYR A 156 PHE 0.047 0.003 PHE A 478 TRP 0.061 0.003 TRP B 179 HIS 0.005 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00815 (13730) covalent geometry : angle 1.16965 (18678) SS BOND : bond 0.28365 ( 6) SS BOND : angle 18.42066 ( 12) hydrogen bonds : bond 0.19292 ( 594) hydrogen bonds : angle 7.02833 ( 1752) link_NAG-ASN : bond 0.00518 ( 14) link_NAG-ASN : angle 4.39490 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9319 (p0) cc_final: 0.8994 (p0) REVERT: C 262 MET cc_start: 0.8715 (tpp) cc_final: 0.8359 (mmm) REVERT: A 332 MET cc_start: 0.8927 (tpp) cc_final: 0.8646 (tpp) REVERT: A 404 ILE cc_start: 0.8962 (tt) cc_final: 0.8507 (mt) REVERT: A 441 LEU cc_start: 0.8240 (pt) cc_final: 0.8023 (tp) REVERT: A 623 HIS cc_start: 0.6532 (t-90) cc_final: 0.6176 (t70) REVERT: A 685 ILE cc_start: 0.9211 (pp) cc_final: 0.8984 (mt) REVERT: D 121 GLN cc_start: 0.7979 (pt0) cc_final: 0.7721 (mt0) REVERT: D 195 HIS cc_start: 0.7977 (t70) cc_final: 0.7717 (t-170) REVERT: B 102 SER cc_start: 0.8762 (m) cc_final: 0.8403 (p) REVERT: B 124 ILE cc_start: 0.9596 (tp) cc_final: 0.9390 (tp) REVERT: B 198 GLU cc_start: 0.8317 (pm20) cc_final: 0.8037 (pm20) REVERT: B 404 ILE cc_start: 0.8914 (tt) cc_final: 0.8449 (mt) REVERT: B 441 LEU cc_start: 0.8154 (pt) cc_final: 0.7908 (tp) outliers start: 6 outliers final: 4 residues processed: 265 average time/residue: 0.1106 time to fit residues: 42.6210 Evaluate side-chains 201 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 197 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain B residue 213 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 191 ASN A 252 HIS A 460 ASN A 576 ASN A 657 ASN A 774 ASN D 191 ASN B 252 HIS B 460 ASN B 576 ASN B 623 HIS B 657 ASN B 774 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.093908 restraints weight = 19789.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.096333 restraints weight = 12303.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.097914 restraints weight = 9105.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098743 restraints weight = 7541.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.099444 restraints weight = 6754.258| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13750 Z= 0.133 Angle : 0.657 9.745 18732 Z= 0.340 Chirality : 0.042 0.163 2254 Planarity : 0.006 0.050 2326 Dihedral : 6.068 57.966 2156 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.09 % Allowed : 12.54 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.10 (0.18), residues: 1708 helix: -1.43 (0.15), residues: 1026 sheet: -3.83 (0.91), residues: 20 loop : -2.92 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 628 TYR 0.011 0.001 TYR B 397 PHE 0.028 0.001 PHE C 119 TRP 0.021 0.002 TRP A 179 HIS 0.012 0.001 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00272 (13730) covalent geometry : angle 0.64053 (18678) SS BOND : bond 0.01454 ( 6) SS BOND : angle 4.97681 ( 12) hydrogen bonds : bond 0.04743 ( 594) hydrogen bonds : angle 4.62088 ( 1752) link_NAG-ASN : bond 0.00252 ( 14) link_NAG-ASN : angle 1.76587 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 221 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9346 (p0) cc_final: 0.8986 (p0) REVERT: C 152 MET cc_start: 0.7936 (ttm) cc_final: 0.7584 (ttm) REVERT: C 262 MET cc_start: 0.8701 (tpp) cc_final: 0.8227 (mmm) REVERT: A 102 SER cc_start: 0.8632 (m) cc_final: 0.8260 (p) REVERT: A 404 ILE cc_start: 0.8862 (tt) cc_final: 0.8482 (mt) REVERT: A 441 LEU cc_start: 0.8184 (pt) cc_final: 0.7899 (tp) REVERT: D 120 GLN cc_start: 0.8341 (tp-100) cc_final: 0.8063 (mp10) REVERT: D 150 ASP cc_start: 0.8939 (p0) cc_final: 0.8464 (p0) REVERT: D 195 HIS cc_start: 0.8270 (t70) cc_final: 0.7850 (t-170) REVERT: D 259 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7692 (mm-30) REVERT: D 262 MET cc_start: 0.8681 (tpp) cc_final: 0.8279 (mmm) REVERT: B 102 SER cc_start: 0.8714 (m) cc_final: 0.8293 (p) REVERT: B 124 ILE cc_start: 0.9365 (tp) cc_final: 0.8996 (tp) REVERT: B 404 ILE cc_start: 0.8825 (tt) cc_final: 0.8402 (mt) REVERT: B 441 LEU cc_start: 0.8008 (pt) cc_final: 0.7734 (tp) outliers start: 15 outliers final: 6 residues processed: 229 average time/residue: 0.1178 time to fit residues: 39.0138 Evaluate side-chains 191 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 185 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 751 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 165 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 164 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 139 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 242 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 676 GLN D 203 ASN D 242 ASN B 413 GLN B 774 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.089765 restraints weight = 20333.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.092312 restraints weight = 12656.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.093837 restraints weight = 9385.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.095014 restraints weight = 7802.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.095608 restraints weight = 6897.686| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13750 Z= 0.109 Angle : 0.578 6.800 18732 Z= 0.296 Chirality : 0.040 0.168 2254 Planarity : 0.005 0.044 2326 Dihedral : 5.045 45.445 2150 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.74 % Allowed : 14.42 % Favored : 83.84 % 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: -2.30 (0.19), residues: 1708 helix: -0.67 (0.16), residues: 1030 sheet: -3.75 (0.98), residues: 20 loop : -2.81 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 762 TYR 0.012 0.001 TYR A 397 PHE 0.031 0.001 PHE D 119 TRP 0.015 0.001 TRP B 524 HIS 0.012 0.001 HIS A 623 Details of bonding type rmsd covalent geometry : bond 0.00228 (13730) covalent geometry : angle 0.56940 (18678) SS BOND : bond 0.00634 ( 6) SS BOND : angle 2.80585 ( 12) hydrogen bonds : bond 0.03694 ( 594) hydrogen bonds : angle 4.06322 ( 1752) link_NAG-ASN : bond 0.00124 ( 14) link_NAG-ASN : angle 1.55641 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9315 (p0) cc_final: 0.8982 (p0) REVERT: C 152 MET cc_start: 0.8006 (ttm) cc_final: 0.7697 (ttm) REVERT: C 262 MET cc_start: 0.8642 (tpp) cc_final: 0.8183 (mmm) REVERT: A 102 SER cc_start: 0.8649 (m) cc_final: 0.8226 (p) REVERT: A 404 ILE cc_start: 0.8770 (tt) cc_final: 0.8302 (mt) REVERT: A 441 LEU cc_start: 0.8233 (pt) cc_final: 0.7979 (tp) REVERT: A 741 MET cc_start: 0.8047 (ptt) cc_final: 0.7721 (ptt) REVERT: D 150 ASP cc_start: 0.9094 (p0) cc_final: 0.8391 (p0) REVERT: D 168 GLU cc_start: 0.7858 (tt0) cc_final: 0.7631 (tm-30) REVERT: D 195 HIS cc_start: 0.8214 (t70) cc_final: 0.7764 (t-170) REVERT: D 259 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 262 MET cc_start: 0.8514 (tpp) cc_final: 0.8134 (mmm) REVERT: B 102 SER cc_start: 0.8770 (m) cc_final: 0.8322 (p) REVERT: B 198 GLU cc_start: 0.8509 (pm20) cc_final: 0.7810 (pt0) REVERT: B 404 ILE cc_start: 0.8704 (tt) cc_final: 0.8198 (mt) REVERT: B 441 LEU cc_start: 0.8117 (pt) cc_final: 0.7857 (tp) REVERT: B 560 VAL cc_start: 0.8472 (t) cc_final: 0.8211 (m) REVERT: B 687 LEU cc_start: 0.9133 (mp) cc_final: 0.8844 (mp) REVERT: B 741 MET cc_start: 0.8029 (ptt) cc_final: 0.7713 (ptt) outliers start: 24 outliers final: 11 residues processed: 223 average time/residue: 0.1041 time to fit residues: 34.8688 Evaluate side-chains 203 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 753 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 58 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 128 optimal weight: 0.0970 chunk 130 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS B 676 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.137792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106777 restraints weight = 19349.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109596 restraints weight = 11005.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.111397 restraints weight = 7687.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112562 restraints weight = 6146.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113258 restraints weight = 5335.241| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13750 Z= 0.107 Angle : 0.570 7.288 18732 Z= 0.292 Chirality : 0.041 0.164 2254 Planarity : 0.004 0.041 2326 Dihedral : 4.557 30.047 2150 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.32 % Allowed : 15.14 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1708 helix: -0.18 (0.16), residues: 1032 sheet: -3.78 (1.02), residues: 20 loop : -2.69 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.010 0.001 TYR A 397 PHE 0.018 0.001 PHE D 119 TRP 0.014 0.001 TRP B 524 HIS 0.011 0.001 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00239 (13730) covalent geometry : angle 0.56224 (18678) SS BOND : bond 0.00656 ( 6) SS BOND : angle 2.68298 ( 12) hydrogen bonds : bond 0.03454 ( 594) hydrogen bonds : angle 3.84435 ( 1752) link_NAG-ASN : bond 0.00127 ( 14) link_NAG-ASN : angle 1.46745 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9308 (p0) cc_final: 0.8961 (p0) REVERT: C 152 MET cc_start: 0.8096 (ttm) cc_final: 0.7801 (ttm) REVERT: C 262 MET cc_start: 0.8671 (tpp) cc_final: 0.8227 (mmm) REVERT: A 441 LEU cc_start: 0.8267 (pt) cc_final: 0.8037 (tp) REVERT: A 560 VAL cc_start: 0.8424 (t) cc_final: 0.8188 (m) REVERT: A 562 MET cc_start: 0.8375 (mtm) cc_final: 0.7995 (mtm) REVERT: A 616 TRP cc_start: 0.7969 (OUTLIER) cc_final: 0.5411 (p-90) REVERT: D 150 ASP cc_start: 0.9060 (p0) cc_final: 0.8497 (p0) REVERT: D 152 MET cc_start: 0.7844 (ttm) cc_final: 0.7406 (ttm) REVERT: D 262 MET cc_start: 0.8532 (tpp) cc_final: 0.8166 (mmm) REVERT: B 198 GLU cc_start: 0.8530 (pm20) cc_final: 0.8223 (pm20) REVERT: B 616 TRP cc_start: 0.8018 (OUTLIER) cc_final: 0.5588 (p-90) REVERT: B 687 LEU cc_start: 0.9182 (mp) cc_final: 0.8914 (mp) outliers start: 32 outliers final: 15 residues processed: 229 average time/residue: 0.1060 time to fit residues: 35.8170 Evaluate side-chains 208 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 778 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.107232 restraints weight = 19483.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110047 restraints weight = 11101.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.111791 restraints weight = 7779.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.112902 restraints weight = 6256.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113490 restraints weight = 5449.034| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13750 Z= 0.107 Angle : 0.578 9.037 18732 Z= 0.292 Chirality : 0.040 0.159 2254 Planarity : 0.004 0.039 2326 Dihedral : 4.284 21.294 2150 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.83 % Allowed : 15.94 % Favored : 81.23 % 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: -1.41 (0.20), residues: 1708 helix: 0.14 (0.16), residues: 1034 sheet: -3.75 (1.03), residues: 20 loop : -2.64 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.011 0.001 TYR D 188 PHE 0.015 0.001 PHE D 119 TRP 0.015 0.001 TRP B 524 HIS 0.006 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00239 (13730) covalent geometry : angle 0.56959 (18678) SS BOND : bond 0.00622 ( 6) SS BOND : angle 3.12088 ( 12) hydrogen bonds : bond 0.03295 ( 594) hydrogen bonds : angle 3.74611 ( 1752) link_NAG-ASN : bond 0.00114 ( 14) link_NAG-ASN : angle 1.44627 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9239 (p0) cc_final: 0.8765 (p0) REVERT: A 560 VAL cc_start: 0.8384 (t) cc_final: 0.8165 (m) REVERT: A 562 MET cc_start: 0.8289 (mtm) cc_final: 0.7937 (mtm) REVERT: A 616 TRP cc_start: 0.7961 (OUTLIER) cc_final: 0.5384 (p-90) REVERT: A 628 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8144 (ttm110) REVERT: D 150 ASP cc_start: 0.8971 (p0) cc_final: 0.8430 (p0) REVERT: D 262 MET cc_start: 0.8568 (tpp) cc_final: 0.8183 (mmm) REVERT: B 198 GLU cc_start: 0.8510 (pm20) cc_final: 0.7449 (pt0) REVERT: B 278 TYR cc_start: 0.8225 (t80) cc_final: 0.7963 (t80) REVERT: B 616 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.5559 (p-90) REVERT: B 687 LEU cc_start: 0.9172 (mp) cc_final: 0.8914 (mp) REVERT: B 741 MET cc_start: 0.8192 (ptt) cc_final: 0.7984 (ptt) outliers start: 39 outliers final: 21 residues processed: 225 average time/residue: 0.1023 time to fit residues: 34.0130 Evaluate side-chains 211 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 778 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 63 optimal weight: 0.0270 chunk 79 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 145 optimal weight: 0.1980 chunk 47 optimal weight: 0.0470 chunk 131 optimal weight: 3.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS A 359 ASN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.127453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.091990 restraints weight = 20358.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.094582 restraints weight = 12696.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.096258 restraints weight = 9361.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.097296 restraints weight = 7723.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.097891 restraints weight = 6836.720| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13750 Z= 0.099 Angle : 0.566 8.081 18732 Z= 0.286 Chirality : 0.040 0.174 2254 Planarity : 0.004 0.041 2326 Dihedral : 3.971 16.181 2150 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.17 % Allowed : 16.38 % Favored : 81.45 % 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: -1.05 (0.21), residues: 1708 helix: 0.50 (0.17), residues: 1022 sheet: -3.66 (1.04), residues: 20 loop : -2.58 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 113 TYR 0.010 0.001 TYR A 397 PHE 0.013 0.001 PHE D 119 TRP 0.016 0.001 TRP B 524 HIS 0.006 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00210 (13730) covalent geometry : angle 0.55657 (18678) SS BOND : bond 0.00538 ( 6) SS BOND : angle 3.31824 ( 12) hydrogen bonds : bond 0.02922 ( 594) hydrogen bonds : angle 3.60124 ( 1752) link_NAG-ASN : bond 0.00138 ( 14) link_NAG-ASN : angle 1.35037 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 MET cc_start: 0.7114 (tpp) cc_final: 0.6481 (mtt) REVERT: C 262 MET cc_start: 0.8773 (mmm) cc_final: 0.8095 (mmm) REVERT: A 560 VAL cc_start: 0.8280 (t) cc_final: 0.8054 (m) REVERT: A 562 MET cc_start: 0.8273 (mtm) cc_final: 0.7930 (mtm) REVERT: A 628 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8068 (ttm110) REVERT: D 150 ASP cc_start: 0.8870 (p0) cc_final: 0.8586 (p0) REVERT: D 152 MET cc_start: 0.7757 (ttm) cc_final: 0.7534 (ttm) REVERT: D 259 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 278 TYR cc_start: 0.8152 (t80) cc_final: 0.7885 (t80) REVERT: B 325 TRP cc_start: 0.8872 (t-100) cc_final: 0.8427 (t60) REVERT: B 560 VAL cc_start: 0.8341 (t) cc_final: 0.8108 (m) REVERT: B 616 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.5440 (p-90) REVERT: B 687 LEU cc_start: 0.9068 (mp) cc_final: 0.8860 (mp) REVERT: B 741 MET cc_start: 0.7980 (ptt) cc_final: 0.7764 (ptt) outliers start: 30 outliers final: 20 residues processed: 221 average time/residue: 0.1062 time to fit residues: 34.4230 Evaluate side-chains 206 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 158 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 195 HIS ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.095737 restraints weight = 19845.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.098270 restraints weight = 12146.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.099912 restraints weight = 8905.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100786 restraints weight = 7322.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.101538 restraints weight = 6530.560| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13750 Z= 0.124 Angle : 0.594 8.325 18732 Z= 0.302 Chirality : 0.041 0.179 2254 Planarity : 0.004 0.039 2326 Dihedral : 3.973 19.484 2150 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.88 % Allowed : 17.39 % Favored : 80.72 % 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: -0.94 (0.21), residues: 1708 helix: 0.55 (0.17), residues: 1034 sheet: -3.67 (1.02), residues: 20 loop : -2.50 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.014 0.001 TYR C 188 PHE 0.011 0.001 PHE D 119 TRP 0.018 0.001 TRP A 616 HIS 0.006 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00290 (13730) covalent geometry : angle 0.58345 (18678) SS BOND : bond 0.00762 ( 6) SS BOND : angle 3.73634 ( 12) hydrogen bonds : bond 0.03406 ( 594) hydrogen bonds : angle 3.64822 ( 1752) link_NAG-ASN : bond 0.00117 ( 14) link_NAG-ASN : angle 1.49778 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 MET cc_start: 0.8920 (mmm) cc_final: 0.8053 (mmm) REVERT: A 198 GLU cc_start: 0.8608 (pm20) cc_final: 0.8207 (pm20) REVERT: A 562 MET cc_start: 0.8298 (mtm) cc_final: 0.7966 (mtt) REVERT: A 628 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8144 (ttm110) REVERT: D 83 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7744 (mp0) REVERT: D 203 ASN cc_start: 0.8339 (m110) cc_final: 0.7925 (t0) REVERT: D 259 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 616 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.5439 (p-90) REVERT: B 687 LEU cc_start: 0.9122 (mp) cc_final: 0.8890 (mp) REVERT: B 741 MET cc_start: 0.8197 (ptt) cc_final: 0.7965 (ptt) outliers start: 26 outliers final: 20 residues processed: 203 average time/residue: 0.1068 time to fit residues: 32.0950 Evaluate side-chains 201 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.089416 restraints weight = 20329.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.091965 restraints weight = 12716.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.093605 restraints weight = 9445.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.094624 restraints weight = 7838.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.094968 restraints weight = 6974.172| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13750 Z= 0.113 Angle : 0.595 7.940 18732 Z= 0.303 Chirality : 0.041 0.180 2254 Planarity : 0.004 0.044 2326 Dihedral : 3.871 16.391 2150 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.74 % Allowed : 17.83 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.81 (0.21), residues: 1708 helix: 0.67 (0.17), residues: 1030 sheet: None (None), residues: 0 loop : -2.52 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 113 TYR 0.011 0.001 TYR C 188 PHE 0.011 0.001 PHE D 119 TRP 0.015 0.001 TRP B 524 HIS 0.006 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00258 (13730) covalent geometry : angle 0.58391 (18678) SS BOND : bond 0.00765 ( 6) SS BOND : angle 3.87811 ( 12) hydrogen bonds : bond 0.03190 ( 594) hydrogen bonds : angle 3.58572 ( 1752) link_NAG-ASN : bond 0.00110 ( 14) link_NAG-ASN : angle 1.49076 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 MET cc_start: 0.7588 (mmm) cc_final: 0.7300 (tpp) REVERT: C 262 MET cc_start: 0.8906 (mmm) cc_final: 0.8038 (mmm) REVERT: A 198 GLU cc_start: 0.8611 (pm20) cc_final: 0.8238 (pm20) REVERT: A 560 VAL cc_start: 0.8243 (t) cc_final: 0.7971 (m) REVERT: A 628 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8103 (ttm110) REVERT: A 687 LEU cc_start: 0.9135 (mp) cc_final: 0.8894 (mp) REVERT: D 83 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7801 (mp0) REVERT: D 150 ASP cc_start: 0.9223 (p0) cc_final: 0.8828 (p0) REVERT: D 203 ASN cc_start: 0.8412 (m110) cc_final: 0.7965 (t0) REVERT: D 259 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7763 (mm-30) REVERT: B 616 TRP cc_start: 0.7971 (OUTLIER) cc_final: 0.5404 (p-90) REVERT: B 741 MET cc_start: 0.8147 (ptt) cc_final: 0.7349 (ptt) outliers start: 24 outliers final: 21 residues processed: 204 average time/residue: 0.1062 time to fit residues: 31.9347 Evaluate side-chains 205 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 2 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 93 optimal weight: 10.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS D 167 GLN D 195 HIS D 242 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.100172 restraints weight = 19522.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.102918 restraints weight = 11302.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.104618 restraints weight = 7996.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.105709 restraints weight = 6462.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106315 restraints weight = 5675.292| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13750 Z= 0.159 Angle : 0.646 10.584 18732 Z= 0.328 Chirality : 0.043 0.216 2254 Planarity : 0.004 0.038 2326 Dihedral : 4.054 18.432 2150 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.81 % Allowed : 18.19 % Favored : 80.00 % 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: -0.87 (0.21), residues: 1708 helix: 0.59 (0.17), residues: 1036 sheet: None (None), residues: 0 loop : -2.53 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.011 0.001 TYR C 116 PHE 0.012 0.001 PHE A 581 TRP 0.013 0.001 TRP B 179 HIS 0.006 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00384 (13730) covalent geometry : angle 0.63326 (18678) SS BOND : bond 0.00764 ( 6) SS BOND : angle 4.16396 ( 12) hydrogen bonds : bond 0.03899 ( 594) hydrogen bonds : angle 3.71829 ( 1752) link_NAG-ASN : bond 0.00171 ( 14) link_NAG-ASN : angle 1.66452 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7575 (mp0) REVERT: C 152 MET cc_start: 0.7673 (mmm) cc_final: 0.7202 (tpp) REVERT: A 198 GLU cc_start: 0.8609 (pm20) cc_final: 0.8177 (pm20) REVERT: A 628 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8181 (ttm110) REVERT: D 83 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7781 (mp0) REVERT: D 150 ASP cc_start: 0.9289 (p0) cc_final: 0.8898 (p0) REVERT: D 203 ASN cc_start: 0.8321 (m110) cc_final: 0.7806 (t0) REVERT: D 259 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7783 (mm-30) REVERT: B 616 TRP cc_start: 0.8136 (OUTLIER) cc_final: 0.5246 (p-90) REVERT: B 741 MET cc_start: 0.8192 (ptt) cc_final: 0.7968 (ptt) outliers start: 25 outliers final: 21 residues processed: 201 average time/residue: 0.1091 time to fit residues: 31.9020 Evaluate side-chains 201 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105214 restraints weight = 19313.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.108062 restraints weight = 10979.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109848 restraints weight = 7685.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110926 restraints weight = 6152.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111459 restraints weight = 5373.723| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13750 Z= 0.126 Angle : 0.622 12.849 18732 Z= 0.317 Chirality : 0.042 0.244 2254 Planarity : 0.004 0.037 2326 Dihedral : 3.971 18.569 2150 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.67 % Allowed : 18.48 % Favored : 79.86 % 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: -0.73 (0.21), residues: 1708 helix: 0.73 (0.17), residues: 1030 sheet: None (None), residues: 0 loop : -2.49 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 271 TYR 0.011 0.001 TYR C 116 PHE 0.012 0.001 PHE D 119 TRP 0.017 0.001 TRP A 524 HIS 0.007 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00294 (13730) covalent geometry : angle 0.61022 (18678) SS BOND : bond 0.00861 ( 6) SS BOND : angle 4.04354 ( 12) hydrogen bonds : bond 0.03450 ( 594) hydrogen bonds : angle 3.63198 ( 1752) link_NAG-ASN : bond 0.00158 ( 14) link_NAG-ASN : angle 1.53916 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7616 (mp0) REVERT: C 152 MET cc_start: 0.7562 (mmm) cc_final: 0.7271 (tpp) REVERT: C 262 MET cc_start: 0.8917 (mmm) cc_final: 0.8129 (tmm) REVERT: A 560 VAL cc_start: 0.8223 (t) cc_final: 0.7913 (m) REVERT: A 628 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8189 (ttm110) REVERT: A 687 LEU cc_start: 0.9149 (mp) cc_final: 0.8920 (mp) REVERT: D 83 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7692 (mp0) REVERT: D 150 ASP cc_start: 0.9279 (p0) cc_final: 0.8870 (p0) REVERT: D 203 ASN cc_start: 0.8330 (m110) cc_final: 0.7751 (t0) REVERT: D 259 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7829 (mm-30) REVERT: B 325 TRP cc_start: 0.8872 (t-100) cc_final: 0.8403 (t60) REVERT: B 616 TRP cc_start: 0.8056 (OUTLIER) cc_final: 0.5175 (p-90) REVERT: B 741 MET cc_start: 0.8184 (ptt) cc_final: 0.7337 (ptt) outliers start: 23 outliers final: 22 residues processed: 202 average time/residue: 0.1130 time to fit residues: 33.4190 Evaluate side-chains 204 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 150 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 195 HIS ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS D 242 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.099111 restraints weight = 19730.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.101679 restraints weight = 11876.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.103326 restraints weight = 8629.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.104287 restraints weight = 7072.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.104726 restraints weight = 6272.252| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13750 Z= 0.112 Angle : 0.606 11.994 18732 Z= 0.308 Chirality : 0.041 0.237 2254 Planarity : 0.004 0.038 2326 Dihedral : 3.766 16.600 2150 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.59 % Allowed : 18.62 % Favored : 79.78 % 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: -0.59 (0.21), residues: 1708 helix: 0.85 (0.17), residues: 1028 sheet: None (None), residues: 0 loop : -2.43 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 271 TYR 0.011 0.001 TYR A 397 PHE 0.012 0.001 PHE D 119 TRP 0.018 0.001 TRP A 524 HIS 0.007 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00251 (13730) covalent geometry : angle 0.59500 (18678) SS BOND : bond 0.00859 ( 6) SS BOND : angle 3.77946 ( 12) hydrogen bonds : bond 0.03146 ( 594) hydrogen bonds : angle 3.55190 ( 1752) link_NAG-ASN : bond 0.00154 ( 14) link_NAG-ASN : angle 1.46511 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1956.80 seconds wall clock time: 34 minutes 30.18 seconds (2070.18 seconds total)