Starting phenix.real_space_refine on Sat Sep 12 03:01:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bxu_30238/09_2026/7bxu_30238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bxu_30238/09_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_30238/09_2026/7bxu_30238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bxu_30238/09_2026/7bxu_30238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bxu_30238/09_2026/7bxu_30238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bxu_30238/09_2026/7bxu_30238.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bxu_30238/09_2026/7bxu_30238.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bxu_30238/09_2026/7bxu_30238.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 chiralities: 7 Restraints were copied for chains: D, B Time building chain proxies: 5.61, per 1000 atoms: 0.42 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: 1.14 Conformation dependent library (CDL) restraints added in 627.5 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: 0.38 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: 2.01 Time building geometry restraints manager: 1.54 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: 7484 17.83 - 35.67: 410 35.67 - 53.50: 58 53.50 - 71.33: 8 71.33 - 89.16: 8 Dihedral angle restraints: 7968 sinusoidal: 2902 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 7965 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: 0.03 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: 0.510 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.120 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 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 : 11.309 75.404 4666 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/Z covalent geometry : bond 0.00815 / 0.37 (13730) covalent geometry : angle 1.16965 / 0.66 (18678) SS BOND : bond 0.28365 / 24.90 ( 6) SS BOND : angle 18.42066 / 15.91 ( 12) hydrogen bonds : bond 0.19292 / 12.70 ( 594) hydrogen bonds : angle 7.02833 / 5.00 ( 1752) link_NAG-ASN : bond 0.00518 / 0.40 ( 14) link_NAG-ASN : angle 4.39490 / 3.46 ( 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 : 0.488 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: 0.1145 time to fit residues: 44.3899 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 : 0.509 ------------------------------------------------------------------------------- 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... C 167 GLN C 191 ASN A 252 HIS A 460 ASN A 576 ASN A 657 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.101445 restraints weight = 19434.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.104001 restraints weight = 11685.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.105615 restraints weight = 8483.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.106275 restraints weight = 6965.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107121 restraints weight = 6294.297| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13750 Z= 0.127 Angle : 0.659 10.190 18732 Z= 0.341 Chirality : 0.042 0.165 2254 Planarity : 0.006 0.049 2326 Dihedral : 5.465 45.109 1862 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.01 % Allowed : 12.39 % Favored : 86.59 % 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: -3.07 (0.18), residues: 1708 helix: -1.40 (0.15), residues: 1026 sheet: -3.82 (0.91), residues: 20 loop : -2.92 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 628 TYR 0.012 0.001 TYR B 397 PHE 0.027 0.001 PHE C 119 TRP 0.020 0.002 TRP B 179 HIS 0.011 0.001 HIS B 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (13730) covalent geometry : angle 0.64188 / 0.33 (18678) SS BOND : bond 0.00261 / 0.21 ( 6) SS BOND : angle 5.29625 / 2.89 ( 12) hydrogen bonds : bond 0.04696 / 3.23 ( 594) hydrogen bonds : angle 4.60582 / 3.33 ( 1752) link_NAG-ASN : bond 0.00264 / 0.19 ( 14) link_NAG-ASN : angle 1.61185 / 1.22 ( 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 232 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9342 (p0) cc_final: 0.8984 (p0) REVERT: C 152 MET cc_start: 0.7947 (ttm) cc_final: 0.7564 (ttm) REVERT: C 262 MET cc_start: 0.8707 (tpp) cc_final: 0.8233 (mmm) REVERT: A 102 SER cc_start: 0.8633 (m) cc_final: 0.8266 (p) REVERT: A 404 ILE cc_start: 0.8878 (tt) cc_final: 0.8493 (mt) REVERT: A 441 LEU cc_start: 0.8181 (pt) cc_final: 0.7892 (tp) REVERT: D 120 GLN cc_start: 0.8337 (tp-100) cc_final: 0.8067 (mp10) REVERT: D 150 ASP cc_start: 0.8910 (p0) cc_final: 0.8417 (p0) REVERT: D 195 HIS cc_start: 0.8257 (t70) cc_final: 0.7837 (t-170) REVERT: D 259 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 262 MET cc_start: 0.8688 (tpp) cc_final: 0.8289 (mmm) REVERT: B 102 SER cc_start: 0.8713 (m) cc_final: 0.8298 (p) REVERT: B 124 ILE cc_start: 0.9362 (tp) cc_final: 0.8998 (tp) REVERT: B 404 ILE cc_start: 0.8841 (tt) cc_final: 0.8413 (mt) REVERT: B 441 LEU cc_start: 0.8004 (pt) cc_final: 0.7734 (tp) outliers start: 14 outliers final: 6 residues processed: 226 average time/residue: 0.1137 time to fit residues: 37.7266 Evaluate side-chains 192 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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: 6.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 123 optimal weight: 0.0010 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 223 ASN C 242 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN A 623 HIS A 676 GLN D 203 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 = 0.3340 r_free = 0.3340 target = 0.123358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.087975 restraints weight = 20343.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.090514 restraints weight = 12689.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.092139 restraints weight = 9376.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.093047 restraints weight = 7770.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.093818 restraints weight = 6932.040| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13750 Z= 0.115 Angle : 0.589 6.795 18732 Z= 0.301 Chirality : 0.041 0.163 2254 Planarity : 0.005 0.044 2326 Dihedral : 4.645 18.416 1856 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.10 % Allowed : 13.77 % Favored : 84.13 % 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: -2.28 (0.19), residues: 1708 helix: -0.65 (0.16), residues: 1030 sheet: -3.74 (0.97), residues: 20 loop : -2.82 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 762 TYR 0.012 0.001 TYR A 397 PHE 0.031 0.001 PHE D 119 TRP 0.014 0.001 TRP B 524 HIS 0.012 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (13730) covalent geometry : angle 0.58176 / 0.30 (18678) SS BOND : bond 0.00183 / 0.10 ( 6) SS BOND : angle 2.73375 / 1.47 ( 12) hydrogen bonds : bond 0.03890 / 2.66 ( 594) hydrogen bonds : angle 4.07058 / 2.94 ( 1752) link_NAG-ASN : bond 0.00138 / 0.12 ( 14) link_NAG-ASN : angle 1.47337 / 1.14 ( 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 222 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9332 (p0) cc_final: 0.8994 (p0) REVERT: C 152 MET cc_start: 0.8046 (ttm) cc_final: 0.7657 (ttm) REVERT: C 262 MET cc_start: 0.8694 (tpp) cc_final: 0.8242 (mmm) REVERT: A 102 SER cc_start: 0.8672 (m) cc_final: 0.8217 (p) REVERT: A 404 ILE cc_start: 0.8775 (tt) cc_final: 0.8317 (mt) REVERT: A 441 LEU cc_start: 0.8264 (pt) cc_final: 0.8000 (tp) REVERT: A 741 MET cc_start: 0.8108 (ptt) cc_final: 0.7774 (ptt) REVERT: D 150 ASP cc_start: 0.9109 (p0) cc_final: 0.8401 (p0) REVERT: D 195 HIS cc_start: 0.8227 (t70) cc_final: 0.7796 (t-170) REVERT: D 259 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 262 MET cc_start: 0.8547 (tpp) cc_final: 0.8167 (mmm) REVERT: B 102 SER cc_start: 0.8788 (m) cc_final: 0.8319 (p) REVERT: B 198 GLU cc_start: 0.8518 (pm20) cc_final: 0.7771 (pt0) REVERT: B 441 LEU cc_start: 0.8071 (pt) cc_final: 0.7829 (tp) REVERT: B 687 LEU cc_start: 0.9121 (mp) cc_final: 0.8828 (mp) REVERT: B 741 MET cc_start: 0.8087 (ptt) cc_final: 0.7759 (ptt) outliers start: 29 outliers final: 17 residues processed: 216 average time/residue: 0.1089 time to fit residues: 35.2310 Evaluate side-chains 197 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 167 THR 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 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 187 VAL Chi-restraints excluded: chain B residue 239 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 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: 0.5980 chunk 115 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 128 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106321 restraints weight = 19367.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.109190 restraints weight = 11006.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111024 restraints weight = 7686.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112138 restraints weight = 6140.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112773 restraints weight = 5351.790| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2458 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= 0.108 Angle : 0.571 7.235 18732 Z= 0.293 Chirality : 0.040 0.163 2254 Planarity : 0.004 0.041 2326 Dihedral : 4.384 17.743 1856 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.54 % Allowed : 14.71 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.20), residues: 1708 helix: -0.18 (0.16), residues: 1032 sheet: -3.71 (1.03), residues: 20 loop : -2.71 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.011 0.001 TYR A 397 PHE 0.017 0.001 PHE D 119 TRP 0.015 0.001 TRP B 524 HIS 0.012 0.001 HIS B 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (13730) covalent geometry : angle 0.56364 / 0.29 (18678) SS BOND : bond 0.00791 / 0.38 ( 6) SS BOND : angle 2.73607 / 1.42 ( 12) hydrogen bonds : bond 0.03454 / 2.37 ( 594) hydrogen bonds : angle 3.84857 / 2.78 ( 1752) link_NAG-ASN : bond 0.00135 / 0.11 ( 14) link_NAG-ASN : angle 1.36252 / 1.05 ( 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 232 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9297 (p0) cc_final: 0.8984 (p0) REVERT: C 152 MET cc_start: 0.8125 (ttm) cc_final: 0.7821 (ttm) REVERT: A 441 LEU cc_start: 0.8281 (pt) cc_final: 0.8041 (tp) REVERT: A 560 VAL cc_start: 0.8423 (t) cc_final: 0.8177 (m) REVERT: A 562 MET cc_start: 0.8404 (mtm) cc_final: 0.8021 (mtm) REVERT: A 616 TRP cc_start: 0.7993 (OUTLIER) cc_final: 0.5398 (p-90) REVERT: A 628 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8191 (ttm110) REVERT: D 150 ASP cc_start: 0.9086 (p0) cc_final: 0.8517 (p0) REVERT: D 152 MET cc_start: 0.7887 (ttm) cc_final: 0.7452 (ttm) REVERT: D 195 HIS cc_start: 0.8160 (t70) cc_final: 0.7729 (t-170) REVERT: D 262 MET cc_start: 0.8549 (tpp) cc_final: 0.8182 (mmm) REVERT: B 198 GLU cc_start: 0.8495 (pm20) cc_final: 0.8205 (pm20) REVERT: B 441 LEU cc_start: 0.8180 (pt) cc_final: 0.7934 (tp) REVERT: B 616 TRP cc_start: 0.8040 (OUTLIER) cc_final: 0.5569 (p-90) REVERT: B 687 LEU cc_start: 0.9180 (mp) cc_final: 0.8904 (mp) outliers start: 35 outliers final: 16 residues processed: 225 average time/residue: 0.1084 time to fit residues: 36.6885 Evaluate side-chains 208 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 167 THR 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 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 381 MET 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: 0.0870 chunk 123 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.135117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.103634 restraints weight = 19588.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106443 restraints weight = 11221.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.108053 restraints weight = 7893.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109265 restraints weight = 6403.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109771 restraints weight = 5575.679| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2650 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= 0.108 Angle : 0.579 8.774 18732 Z= 0.292 Chirality : 0.040 0.160 2254 Planarity : 0.004 0.039 2326 Dihedral : 4.241 18.033 1856 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.97 % Allowed : 15.36 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.44 (0.20), residues: 1708 helix: 0.13 (0.16), residues: 1032 sheet: -3.71 (1.03), residues: 20 loop : -2.66 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 0.005 0.001 HIS C 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (13730) covalent geometry : angle 0.57021 / 0.29 (18678) SS BOND : bond 0.00343 / 0.17 ( 6) SS BOND : angle 3.27059 / 1.71 ( 12) hydrogen bonds : bond 0.03356 / 2.30 ( 594) hydrogen bonds : angle 3.75446 / 2.71 ( 1752) link_NAG-ASN : bond 0.00134 / 0.11 ( 14) link_NAG-ASN : angle 1.36302 / 1.04 ( 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 232 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9228 (p0) cc_final: 0.8787 (p0) REVERT: C 262 MET cc_start: 0.8811 (mmm) cc_final: 0.8076 (mmm) REVERT: A 133 ILE cc_start: 0.8893 (tt) cc_final: 0.8646 (tt) REVERT: A 560 VAL cc_start: 0.8320 (t) cc_final: 0.8083 (m) REVERT: A 562 MET cc_start: 0.8336 (mtm) cc_final: 0.7941 (mtm) REVERT: A 616 TRP cc_start: 0.8017 (OUTLIER) cc_final: 0.5364 (p-90) REVERT: A 628 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8163 (ttm110) REVERT: D 150 ASP cc_start: 0.9033 (p0) cc_final: 0.8492 (p0) REVERT: D 195 HIS cc_start: 0.8172 (t70) cc_final: 0.7738 (t-170) REVERT: D 259 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7982 (mm-30) REVERT: D 262 MET cc_start: 0.8557 (tpp) cc_final: 0.8182 (mmm) REVERT: B 278 TYR cc_start: 0.8239 (t80) cc_final: 0.7967 (t80) REVERT: B 441 LEU cc_start: 0.8200 (pt) cc_final: 0.7958 (tp) REVERT: B 616 TRP cc_start: 0.8066 (OUTLIER) cc_final: 0.5529 (p-90) REVERT: B 687 LEU cc_start: 0.9174 (mp) cc_final: 0.8897 (mp) outliers start: 41 outliers final: 23 residues processed: 223 average time/residue: 0.1092 time to fit residues: 36.3900 Evaluate side-chains 207 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 167 THR 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 575 SER Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 748 VAL 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 381 MET 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: 0.9980 chunk 60 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 79 optimal weight: 0.0370 chunk 148 optimal weight: 2.9990 chunk 54 optimal weight: 0.0020 chunk 145 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 HIS A 359 ASN D 242 ASN ** 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 = 0.3391 r_free = 0.3391 target = 0.127337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.092043 restraints weight = 20310.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.094637 restraints weight = 12638.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.096310 restraints weight = 9333.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.097296 restraints weight = 7704.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.097827 restraints weight = 6851.181| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13750 Z= 0.099 Angle : 0.562 7.888 18732 Z= 0.285 Chirality : 0.040 0.212 2254 Planarity : 0.004 0.041 2326 Dihedral : 4.007 15.806 1856 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % 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: -1.09 (0.21), residues: 1708 helix: 0.47 (0.17), residues: 1024 sheet: -3.65 (1.04), residues: 20 loop : -2.60 (0.22), residues: 664 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 0.017 0.001 TRP B 524 HIS 0.006 0.000 HIS C 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (13730) covalent geometry : angle 0.55409 / 0.28 (18678) SS BOND : bond 0.00624 / 0.30 ( 6) SS BOND : angle 3.24305 / 1.66 ( 12) hydrogen bonds : bond 0.02891 / 1.98 ( 594) hydrogen bonds : angle 3.60037 / 2.60 ( 1752) link_NAG-ASN : bond 0.00134 / 0.11 ( 14) link_NAG-ASN : angle 1.25412 / 0.95 ( 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 230 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 MET cc_start: 0.8843 (mmm) cc_final: 0.8048 (mmm) REVERT: A 133 ILE cc_start: 0.8905 (tt) cc_final: 0.8665 (tt) REVERT: A 560 VAL cc_start: 0.8272 (t) cc_final: 0.8042 (m) REVERT: A 562 MET cc_start: 0.8239 (mtm) cc_final: 0.7891 (mtm) REVERT: A 628 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8105 (ttm110) REVERT: D 150 ASP cc_start: 0.8894 (p0) cc_final: 0.8648 (p0) REVERT: D 195 HIS cc_start: 0.8169 (t70) cc_final: 0.7735 (t-170) REVERT: D 203 ASN cc_start: 0.8301 (m110) cc_final: 0.8044 (t0) REVERT: D 259 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7822 (mm-30) REVERT: B 278 TYR cc_start: 0.8162 (t80) cc_final: 0.7913 (t80) REVERT: B 616 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.5437 (p-90) REVERT: B 687 LEU cc_start: 0.9130 (mp) cc_final: 0.8882 (mp) outliers start: 30 outliers final: 19 residues processed: 221 average time/residue: 0.1091 time to fit residues: 35.9376 Evaluate side-chains 203 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 642 GLU 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 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 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: 3.9990 chunk 116 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 1 optimal weight: 0.0010 chunk 113 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 117 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 167 GLN C 195 HIS B 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.138559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.107113 restraints weight = 19366.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109884 restraints weight = 11144.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111712 restraints weight = 7817.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.112836 restraints weight = 6259.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113262 restraints weight = 5450.363| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3130 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= 0.100 Angle : 0.565 8.161 18732 Z= 0.288 Chirality : 0.039 0.174 2254 Planarity : 0.004 0.039 2326 Dihedral : 3.815 14.971 1856 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.96 % Allowed : 17.68 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1708 helix: 0.69 (0.17), residues: 1022 sheet: -3.57 (1.02), residues: 20 loop : -2.52 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 151 TYR 0.014 0.001 TYR C 188 PHE 0.011 0.001 PHE D 119 TRP 0.024 0.001 TRP A 616 HIS 0.006 0.000 HIS C 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (13730) covalent geometry : angle 0.55494 / 0.28 (18678) SS BOND : bond 0.00851 / 0.41 ( 6) SS BOND : angle 3.65636 / 1.87 ( 12) hydrogen bonds : bond 0.02821 / 1.93 ( 594) hydrogen bonds : angle 3.52676 / 2.55 ( 1752) link_NAG-ASN : bond 0.00147 / 0.12 ( 14) link_NAG-ASN : angle 1.25173 / 0.95 ( 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 217 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.8901 (tt) cc_final: 0.8653 (tt) REVERT: A 560 VAL cc_start: 0.8220 (t) cc_final: 0.7962 (m) REVERT: A 562 MET cc_start: 0.8223 (mtm) cc_final: 0.7884 (mtt) REVERT: A 628 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8065 (ttm110) REVERT: D 83 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7762 (mp0) REVERT: D 195 HIS cc_start: 0.8178 (t70) cc_final: 0.7708 (t-170) REVERT: D 203 ASN cc_start: 0.8260 (m110) cc_final: 0.7775 (t0) REVERT: D 262 MET cc_start: 0.9001 (mmm) cc_final: 0.8288 (tmm) outliers start: 27 outliers final: 18 residues processed: 210 average time/residue: 0.1113 time to fit residues: 34.6699 Evaluate side-chains 198 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 748 VAL 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 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 ILE 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: 0.7980 chunk 110 optimal weight: 3.9990 chunk 156 optimal weight: 0.4980 chunk 73 optimal weight: 0.0980 chunk 93 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 69 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.107644 restraints weight = 19356.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110465 restraints weight = 11121.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112269 restraints weight = 7788.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113376 restraints weight = 6247.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.114012 restraints weight = 5443.606| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13750 Z= 0.102 Angle : 0.584 11.678 18732 Z= 0.294 Chirality : 0.040 0.166 2254 Planarity : 0.004 0.041 2326 Dihedral : 3.765 17.496 1856 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.74 % Allowed : 17.75 % Favored : 80.51 % 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: -0.67 (0.21), residues: 1708 helix: 0.83 (0.17), residues: 1022 sheet: -3.54 (1.00), residues: 20 loop : -2.46 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 151 TYR 0.011 0.001 TYR C 116 PHE 0.010 0.001 PHE D 119 TRP 0.023 0.001 TRP B 616 HIS 0.006 0.000 HIS C 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (13730) covalent geometry : angle 0.57348 / 0.29 (18678) SS BOND : bond 0.00656 / 0.32 ( 6) SS BOND : angle 3.78856 / 1.94 ( 12) hydrogen bonds : bond 0.02776 / 1.90 ( 594) hydrogen bonds : angle 3.47662 / 2.52 ( 1752) link_NAG-ASN : bond 0.00121 / 0.08 ( 14) link_NAG-ASN : angle 1.27110 / 0.97 ( 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 211 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.8925 (tt) cc_final: 0.8676 (tt) REVERT: A 560 VAL cc_start: 0.8136 (t) cc_final: 0.7882 (m) REVERT: A 562 MET cc_start: 0.8216 (mtm) cc_final: 0.7894 (mtt) REVERT: A 628 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8063 (ttm110) REVERT: D 83 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7778 (mp0) REVERT: D 150 ASP cc_start: 0.9135 (p0) cc_final: 0.8864 (p0) REVERT: D 203 ASN cc_start: 0.8238 (m110) cc_final: 0.7792 (t0) REVERT: D 259 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7655 (mm-30) REVERT: B 325 TRP cc_start: 0.8775 (t-100) cc_final: 0.8415 (t60) outliers start: 24 outliers final: 18 residues processed: 206 average time/residue: 0.1127 time to fit residues: 34.6365 Evaluate side-chains 199 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 748 VAL 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 297 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 ILE 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: 5.9990 chunk 108 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 GLN C 195 HIS D 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.138373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.106700 restraints weight = 19436.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109547 restraints weight = 11146.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111247 restraints weight = 7829.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112455 restraints weight = 6316.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113132 restraints weight = 5463.972| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13750 Z= 0.107 Angle : 0.594 11.487 18732 Z= 0.298 Chirality : 0.041 0.170 2254 Planarity : 0.004 0.038 2326 Dihedral : 3.726 16.572 1856 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.59 % Allowed : 18.41 % 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: -0.59 (0.21), residues: 1708 helix: 0.87 (0.17), residues: 1038 sheet: -3.59 (0.96), residues: 20 loop : -2.45 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 266 TYR 0.014 0.001 TYR D 188 PHE 0.011 0.001 PHE D 119 TRP 0.014 0.001 TRP A 524 HIS 0.007 0.001 HIS C 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13730) covalent geometry : angle 0.58469 / 0.30 (18678) SS BOND : bond 0.00707 / 0.34 ( 6) SS BOND : angle 3.45959 / 1.75 ( 12) hydrogen bonds : bond 0.02929 / 2.01 ( 594) hydrogen bonds : angle 3.47571 / 2.52 ( 1752) link_NAG-ASN : bond 0.00162 / 0.14 ( 14) link_NAG-ASN : angle 1.31290 / 1.00 ( 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 208 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.8961 (tt) cc_final: 0.8704 (tt) REVERT: A 198 GLU cc_start: 0.8604 (pm20) cc_final: 0.8257 (pm20) REVERT: A 325 TRP cc_start: 0.8834 (t-100) cc_final: 0.8424 (t60) REVERT: A 560 VAL cc_start: 0.8066 (t) cc_final: 0.7775 (m) REVERT: A 562 MET cc_start: 0.8227 (mtm) cc_final: 0.7935 (mtt) REVERT: A 628 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8064 (ttm110) REVERT: A 687 LEU cc_start: 0.9135 (mp) cc_final: 0.8862 (mp) REVERT: D 83 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7728 (mp0) REVERT: D 150 ASP cc_start: 0.9163 (p0) cc_final: 0.8898 (p0) REVERT: D 168 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7686 (tm-30) REVERT: D 203 ASN cc_start: 0.8339 (m110) cc_final: 0.7959 (t0) REVERT: D 259 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 325 TRP cc_start: 0.8778 (t-100) cc_final: 0.8433 (t60) REVERT: B 560 VAL cc_start: 0.8173 (t) cc_final: 0.7934 (m) outliers start: 22 outliers final: 18 residues processed: 204 average time/residue: 0.1050 time to fit residues: 31.8082 Evaluate side-chains 204 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 VAL 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 297 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 ILE 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: 0.0870 chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 GLN C 195 HIS D 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106660 restraints weight = 19334.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109482 restraints weight = 11124.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.111279 restraints weight = 7844.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112393 restraints weight = 6291.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113051 restraints weight = 5486.430| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13750 Z= 0.110 Angle : 0.605 10.450 18732 Z= 0.303 Chirality : 0.041 0.173 2254 Planarity : 0.004 0.036 2326 Dihedral : 3.755 17.907 1856 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.52 % Allowed : 18.77 % Favored : 79.71 % 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: -0.52 (0.21), residues: 1708 helix: 0.92 (0.17), residues: 1042 sheet: -3.54 (0.93), residues: 20 loop : -2.42 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 271 TYR 0.013 0.001 TYR D 188 PHE 0.010 0.001 PHE D 119 TRP 0.014 0.001 TRP A 524 HIS 0.007 0.001 HIS D 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (13730) covalent geometry : angle 0.59594 / 0.30 (18678) SS BOND : bond 0.00943 / 0.45 ( 6) SS BOND : angle 3.64260 / 1.86 ( 12) hydrogen bonds : bond 0.02957 / 2.03 ( 594) hydrogen bonds : angle 3.47775 / 2.52 ( 1752) link_NAG-ASN : bond 0.00146 / 0.13 ( 14) link_NAG-ASN : angle 1.32639 / 1.01 ( 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 217 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.8966 (tt) cc_final: 0.8718 (tt) REVERT: A 198 GLU cc_start: 0.8598 (pm20) cc_final: 0.8308 (pm20) REVERT: A 313 GLU cc_start: 0.7998 (tt0) cc_final: 0.7794 (tt0) REVERT: A 325 TRP cc_start: 0.8821 (t-100) cc_final: 0.8438 (t60) REVERT: A 560 VAL cc_start: 0.8108 (t) cc_final: 0.7807 (m) REVERT: A 562 MET cc_start: 0.8217 (mtm) cc_final: 0.7928 (mtt) REVERT: A 628 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8060 (ttm110) REVERT: A 687 LEU cc_start: 0.9148 (mp) cc_final: 0.8881 (mp) REVERT: D 83 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7677 (mp0) REVERT: D 150 ASP cc_start: 0.9179 (p0) cc_final: 0.8876 (p0) REVERT: D 203 ASN cc_start: 0.8298 (m110) cc_final: 0.7926 (t0) REVERT: B 325 TRP cc_start: 0.8788 (t-100) cc_final: 0.8458 (t60) REVERT: B 560 VAL cc_start: 0.8152 (t) cc_final: 0.7881 (m) outliers start: 21 outliers final: 18 residues processed: 214 average time/residue: 0.1079 time to fit residues: 33.9579 Evaluate side-chains 206 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 A residue 168 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 VAL 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 297 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 ILE 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: 0.0570 chunk 97 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 GLN C 195 HIS D 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.125428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.089094 restraints weight = 20399.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.091648 restraints weight = 12816.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.093321 restraints weight = 9551.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.094294 restraints weight = 7913.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.095010 restraints weight = 7064.330| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13750 Z= 0.124 Angle : 0.623 11.895 18732 Z= 0.310 Chirality : 0.042 0.200 2254 Planarity : 0.004 0.035 2326 Dihedral : 3.814 16.773 1856 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.45 % Allowed : 18.91 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1708 helix: 0.91 (0.17), residues: 1040 sheet: None (None), residues: 0 loop : -2.49 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 271 TYR 0.013 0.001 TYR D 188 PHE 0.010 0.001 PHE D 119 TRP 0.011 0.001 TRP A 524 HIS 0.007 0.001 HIS D 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (13730) covalent geometry : angle 0.61333 / 0.31 (18678) SS BOND : bond 0.00703 / 0.34 ( 6) SS BOND : angle 3.68974 / 1.88 ( 12) hydrogen bonds : bond 0.03254 / 2.25 ( 594) hydrogen bonds : angle 3.52759 / 2.55 ( 1752) link_NAG-ASN : bond 0.00164 / 0.15 ( 14) link_NAG-ASN : angle 1.44091 / 1.09 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.40 seconds wall clock time: 36 minutes 41.58 seconds (2201.58 seconds total)