Starting phenix.real_space_refine on Thu Jul 31 08:20:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bxu_30238/07_2025/7bxu_30238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bxu_30238/07_2025/7bxu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bxu_30238/07_2025/7bxu_30238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bxu_30238/07_2025/7bxu_30238.map" model { file = "/net/cci-nas-00/data/ceres_data/7bxu_30238/07_2025/7bxu_30238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bxu_30238/07_2025/7bxu_30238.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} 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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Restraints were copied for chains: B, D Time building chain proxies: 12.05, per 1000 atoms: 0.90 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.67 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: 3.48 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4161 1.34 - 1.46: 3322 1.46 - 1.58: 6119 1.58 - 1.71: 0 1.71 - 1.83: 128 Bond restraints: 13730 Sorted by residual: bond pdb=" CA GLU B 313 " pdb=" C GLU B 313 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.27e-02 6.20e+03 5.15e+00 bond pdb=" CA GLU A 313 " pdb=" C GLU A 313 " ideal model delta sigma weight residual 1.524 1.495 0.028 1.27e-02 6.20e+03 5.01e+00 bond pdb=" CA ALA D 106 " pdb=" C ALA D 106 " ideal model delta sigma weight residual 1.533 1.523 0.010 5.60e-03 3.19e+04 3.50e+00 bond pdb=" CA ALA C 106 " pdb=" C ALA C 106 " ideal model delta sigma weight residual 1.533 1.523 0.010 5.60e-03 3.19e+04 3.42e+00 bond pdb=" CA ASP D 257 " pdb=" C ASP D 257 " ideal model delta sigma weight residual 1.524 1.547 -0.024 1.29e-02 6.01e+03 3.39e+00 ... (remaining 13725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 17688 2.31 - 4.62: 829 4.62 - 6.92: 98 6.92 - 9.23: 47 9.23 - 11.54: 16 Bond angle restraints: 18678 Sorted by residual: angle pdb=" N ARG A 762 " pdb=" CA ARG A 762 " pdb=" C ARG A 762 " ideal model delta sigma weight residual 111.36 118.98 -7.62 1.09e+00 8.42e-01 4.89e+01 angle pdb=" N ARG B 762 " pdb=" CA ARG B 762 " pdb=" C ARG B 762 " ideal model delta sigma weight residual 111.36 118.93 -7.57 1.09e+00 8.42e-01 4.83e+01 angle pdb=" N PRO A 355 " pdb=" CA PRO A 355 " pdb=" CB PRO A 355 " ideal model delta sigma weight residual 103.51 109.92 -6.41 9.60e-01 1.09e+00 4.46e+01 angle pdb=" N PRO B 355 " pdb=" CA PRO B 355 " pdb=" CB PRO B 355 " ideal model delta sigma weight residual 103.51 109.92 -6.41 9.60e-01 1.09e+00 4.45e+01 angle pdb=" N PRO B 672 " pdb=" CA PRO B 672 " pdb=" CB PRO B 672 " ideal model delta sigma weight residual 103.00 110.30 -7.30 1.10e+00 8.26e-01 4.41e+01 ... (remaining 18673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7750 17.83 - 35.67: 434 35.67 - 53.50: 58 53.50 - 71.33: 12 71.33 - 89.16: 8 Dihedral angle restraints: 8262 sinusoidal: 3196 harmonic: 5066 Sorted by residual: dihedral pdb=" CB CYS C 112 " pdb=" SG CYS C 112 " pdb=" SG CYS C 171 " pdb=" CB CYS C 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.16 89.16 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS D 112 " pdb=" SG CYS D 112 " pdb=" SG CYS D 171 " pdb=" CB CYS D 171 " ideal model delta sinusoidal sigma weight residual -86.00 -175.11 89.11 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS D 84 " pdb=" SG CYS D 84 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual -86.00 -161.81 75.81 1 1.00e+01 1.00e-02 7.25e+01 ... (remaining 8259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1811 0.077 - 0.154: 361 0.154 - 0.232: 58 0.232 - 0.309: 17 0.309 - 0.386: 7 Chirality restraints: 2254 Sorted by residual: chirality pdb=" CA VAL A 221 " pdb=" N VAL A 221 " pdb=" C VAL A 221 " pdb=" CB VAL A 221 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA VAL B 221 " pdb=" N VAL B 221 " pdb=" C VAL B 221 " pdb=" CB VAL B 221 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA ARG A 762 " pdb=" N ARG A 762 " pdb=" C ARG A 762 " pdb=" CB ARG A 762 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 2251 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG C 401 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 404 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG C 404 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 404 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 404 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 404 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 402 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG D 402 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG D 402 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG D 402 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG D 402 " -0.008 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3584 2.79 - 3.32: 12390 3.32 - 3.85: 20377 3.85 - 4.37: 22351 4.37 - 4.90: 40193 Nonbonded interactions: 98895 Sorted by model distance: nonbonded pdb=" O ASN C 173 " pdb=" OG SER C 183 " model vdw 2.267 3.040 nonbonded pdb=" O ASN D 173 " pdb=" OG SER D 183 " model vdw 2.267 3.040 nonbonded pdb=" O4 NAG D 402 " pdb=" O6 NAG D 402 " model vdw 2.302 3.040 nonbonded pdb=" O4 NAG C 402 " pdb=" O6 NAG C 402 " model vdw 2.303 3.040 nonbonded pdb=" NH2 ARG B 640 " pdb=" OE1 GLN B 676 " model vdw 2.364 3.120 ... (remaining 98890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.410 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.720 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.491 13750 Z= 0.472 Angle : 1.275 42.377 18732 Z= 0.701 Chirality : 0.069 0.386 2254 Planarity : 0.009 0.072 2326 Dihedral : 11.207 75.404 4960 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.43 % Allowed : 6.81 % Favored : 92.75 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.061 0.003 TRP B 179 HIS 0.005 0.001 HIS A 658 PHE 0.047 0.003 PHE A 478 TYR 0.019 0.003 TYR A 156 ARG 0.007 0.001 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 14) link_NAG-ASN : angle 4.39490 ( 42) hydrogen bonds : bond 0.19292 ( 594) hydrogen bonds : angle 7.02833 ( 1752) SS BOND : bond 0.28365 ( 6) SS BOND : angle 18.42066 ( 12) covalent geometry : bond 0.00815 (13730) covalent geometry : angle 1.16965 (18678) *********************** 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 : 1.528 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: 0.8647 (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: 0.2528 time to fit residues: 96.9914 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 : 1.533 ------------------------------------------------------------------------------- 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 146 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 0.0670 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 101 optimal weight: 6.9990 chunk 158 optimal weight: 0.0370 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 191 ASN A 252 HIS A 460 ASN A 576 ASN A 657 ASN A 666 HIS D 191 ASN B 252 HIS B 460 ASN B 576 ASN B 623 HIS B 657 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.104579 restraints weight = 19318.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107348 restraints weight = 11381.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109117 restraints weight = 8037.339| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13750 Z= 0.123 Angle : 0.650 11.134 18732 Z= 0.336 Chirality : 0.041 0.156 2254 Planarity : 0.006 0.049 2326 Dihedral : 6.027 59.871 2156 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.09 % Allowed : 12.54 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.18), residues: 1708 helix: -1.43 (0.15), residues: 1030 sheet: -3.79 (0.91), residues: 20 loop : -2.92 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 179 HIS 0.012 0.001 HIS B 623 PHE 0.029 0.001 PHE C 119 TYR 0.011 0.001 TYR B 397 ARG 0.005 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 14) link_NAG-ASN : angle 1.64284 ( 42) hydrogen bonds : bond 0.04523 ( 594) hydrogen bonds : angle 4.59573 ( 1752) SS BOND : bond 0.01951 ( 6) SS BOND : angle 5.68674 ( 12) covalent geometry : bond 0.00254 (13730) covalent geometry : angle 0.62974 (18678) *********************** 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 240 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9326 (p0) cc_final: 0.8961 (p0) REVERT: C 262 MET cc_start: 0.8695 (tpp) cc_final: 0.8218 (mmm) REVERT: A 102 SER cc_start: 0.8635 (m) cc_final: 0.8293 (p) REVERT: A 337 THR cc_start: 0.9343 (p) cc_final: 0.9048 (t) REVERT: A 404 ILE cc_start: 0.8883 (tt) cc_final: 0.8492 (mt) REVERT: A 441 LEU cc_start: 0.8162 (pt) cc_final: 0.7819 (tp) REVERT: A 741 MET cc_start: 0.8022 (ptt) cc_final: 0.7820 (ptt) REVERT: D 120 GLN cc_start: 0.8304 (tp-100) cc_final: 0.8072 (mp10) REVERT: D 150 ASP cc_start: 0.8927 (p0) cc_final: 0.8376 (p0) REVERT: D 195 HIS cc_start: 0.8177 (t70) cc_final: 0.7751 (t-170) REVERT: D 259 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7673 (mm-30) REVERT: D 262 MET cc_start: 0.8635 (tpp) cc_final: 0.8244 (mmm) REVERT: B 102 SER cc_start: 0.8714 (m) cc_final: 0.8324 (p) REVERT: B 124 ILE cc_start: 0.9360 (tp) cc_final: 0.8996 (tp) REVERT: B 404 ILE cc_start: 0.8833 (tt) cc_final: 0.8393 (mt) REVERT: B 441 LEU cc_start: 0.8009 (pt) cc_final: 0.7773 (tp) outliers start: 15 outliers final: 6 residues processed: 233 average time/residue: 0.2555 time to fit residues: 85.7344 Evaluate side-chains 198 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 88 optimal weight: 9.9990 chunk 107 optimal weight: 0.0060 chunk 73 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 163 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 195 HIS C 223 ASN C 242 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN A 623 HIS D 223 ASN D 242 ASN B 413 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.108184 restraints weight = 19251.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110991 restraints weight = 11082.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.112817 restraints weight = 7742.525| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13750 Z= 0.108 Angle : 0.577 6.800 18732 Z= 0.294 Chirality : 0.040 0.165 2254 Planarity : 0.005 0.042 2326 Dihedral : 4.903 41.341 2150 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.88 % Allowed : 14.42 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.19), residues: 1708 helix: -0.58 (0.16), residues: 1022 sheet: -3.66 (0.99), residues: 20 loop : -2.77 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 524 HIS 0.012 0.001 HIS A 623 PHE 0.031 0.001 PHE D 119 TYR 0.011 0.001 TYR A 397 ARG 0.002 0.000 ARG B 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 14) link_NAG-ASN : angle 1.53240 ( 42) hydrogen bonds : bond 0.03603 ( 594) hydrogen bonds : angle 4.00246 ( 1752) SS BOND : bond 0.00833 ( 6) SS BOND : angle 2.93626 ( 12) covalent geometry : bond 0.00226 (13730) covalent geometry : angle 0.56794 (18678) *********************** 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 232 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9296 (p0) cc_final: 0.8991 (p0) REVERT: C 152 MET cc_start: 0.8186 (ttm) cc_final: 0.7696 (ttm) REVERT: C 262 MET cc_start: 0.8649 (tpp) cc_final: 0.8187 (mmm) REVERT: A 102 SER cc_start: 0.8664 (m) cc_final: 0.8259 (p) REVERT: A 337 THR cc_start: 0.9297 (p) cc_final: 0.9030 (t) REVERT: A 404 ILE cc_start: 0.8794 (tt) cc_final: 0.8325 (mt) REVERT: A 441 LEU cc_start: 0.8163 (pt) cc_final: 0.7953 (tp) REVERT: A 560 VAL cc_start: 0.8477 (t) cc_final: 0.8234 (m) REVERT: D 121 GLN cc_start: 0.8245 (pt0) cc_final: 0.7899 (mt0) REVERT: D 150 ASP cc_start: 0.9061 (p0) cc_final: 0.8375 (p0) REVERT: D 195 HIS cc_start: 0.8176 (t70) cc_final: 0.7732 (t-170) REVERT: D 259 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 262 MET cc_start: 0.8528 (tpp) cc_final: 0.8143 (mmm) REVERT: B 102 SER cc_start: 0.8779 (m) cc_final: 0.8355 (p) REVERT: B 198 GLU cc_start: 0.8488 (pm20) cc_final: 0.7560 (pt0) REVERT: B 404 ILE cc_start: 0.8726 (tt) cc_final: 0.8209 (mt) REVERT: B 441 LEU cc_start: 0.8142 (pt) cc_final: 0.7920 (tp) REVERT: B 687 LEU cc_start: 0.9154 (mp) cc_final: 0.8868 (mp) REVERT: B 741 MET cc_start: 0.8064 (ptt) cc_final: 0.7735 (ptt) outliers start: 26 outliers final: 14 residues processed: 226 average time/residue: 0.2321 time to fit residues: 78.7910 Evaluate side-chains 210 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 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 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 3 optimal weight: 10.0000 chunk 81 optimal weight: 0.0870 chunk 127 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 141 optimal weight: 0.0030 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 HIS A 359 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.099019 restraints weight = 19886.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.101538 restraints weight = 12294.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103160 restraints weight = 9052.000| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13750 Z= 0.099 Angle : 0.561 7.241 18732 Z= 0.288 Chirality : 0.040 0.158 2254 Planarity : 0.004 0.041 2326 Dihedral : 4.429 26.804 2150 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.67 % Allowed : 15.94 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.20), residues: 1708 helix: -0.04 (0.16), residues: 1020 sheet: -3.65 (1.03), residues: 20 loop : -2.67 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 524 HIS 0.011 0.001 HIS B 623 PHE 0.018 0.001 PHE D 119 TYR 0.011 0.001 TYR B 397 ARG 0.002 0.000 ARG B 762 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 14) link_NAG-ASN : angle 1.39826 ( 42) hydrogen bonds : bond 0.03155 ( 594) hydrogen bonds : angle 3.77741 ( 1752) SS BOND : bond 0.01100 ( 6) SS BOND : angle 2.86661 ( 12) covalent geometry : bond 0.00209 (13730) covalent geometry : angle 0.55340 (18678) *********************** 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 227 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9226 (p0) cc_final: 0.8736 (p0) REVERT: A 133 ILE cc_start: 0.8888 (tt) cc_final: 0.8681 (tt) REVERT: A 441 LEU cc_start: 0.8200 (pt) cc_final: 0.7999 (tp) REVERT: A 628 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8139 (ttm110) REVERT: A 741 MET cc_start: 0.8107 (ptt) cc_final: 0.7903 (ptt) REVERT: D 150 ASP cc_start: 0.8964 (p0) cc_final: 0.8422 (p0) REVERT: D 259 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7642 (mm-30) REVERT: D 262 MET cc_start: 0.8476 (tpp) cc_final: 0.8083 (mmm) REVERT: B 198 GLU cc_start: 0.8526 (pm20) cc_final: 0.8217 (pm20) REVERT: B 560 VAL cc_start: 0.8386 (t) cc_final: 0.8152 (m) REVERT: B 628 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8075 (ttp80) REVERT: B 687 LEU cc_start: 0.9109 (mp) cc_final: 0.8860 (mp) outliers start: 23 outliers final: 13 residues processed: 222 average time/residue: 0.2430 time to fit residues: 79.6443 Evaluate side-chains 202 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 381 MET Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 381 MET 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 70 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 195 HIS D 195 HIS D 242 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.101988 restraints weight = 19587.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.104788 restraints weight = 11231.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106553 restraints weight = 7909.607| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13750 Z= 0.177 Angle : 0.652 10.989 18732 Z= 0.327 Chirality : 0.043 0.160 2254 Planarity : 0.004 0.040 2326 Dihedral : 4.512 26.372 2150 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.19 % Allowed : 16.38 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 1708 helix: 0.08 (0.16), residues: 1030 sheet: -3.78 (1.01), residues: 20 loop : -2.62 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 179 HIS 0.005 0.001 HIS D 195 PHE 0.015 0.002 PHE B 581 TYR 0.011 0.001 TYR D 188 ARG 0.004 0.001 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 14) link_NAG-ASN : angle 1.71925 ( 42) hydrogen bonds : bond 0.04186 ( 594) hydrogen bonds : angle 3.87656 ( 1752) SS BOND : bond 0.00299 ( 6) SS BOND : angle 3.11112 ( 12) covalent geometry : bond 0.00427 (13730) covalent geometry : angle 0.64301 (18678) *********************** 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 227 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9393 (p0) cc_final: 0.8875 (p0) REVERT: C 152 MET cc_start: 0.8082 (ttm) cc_final: 0.7650 (ttm) REVERT: C 262 MET cc_start: 0.8888 (mmm) cc_final: 0.8092 (mmm) REVERT: A 133 ILE cc_start: 0.9047 (tt) cc_final: 0.8755 (tt) REVERT: A 198 GLU cc_start: 0.8614 (pm20) cc_final: 0.8279 (pm20) REVERT: A 441 LEU cc_start: 0.8311 (pt) cc_final: 0.8052 (tp) REVERT: A 616 TRP cc_start: 0.8152 (OUTLIER) cc_final: 0.5320 (p-90) REVERT: A 628 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8265 (ttm110) REVERT: D 150 ASP cc_start: 0.9071 (p0) cc_final: 0.8477 (p0) REVERT: D 152 MET cc_start: 0.7966 (ttm) cc_final: 0.7520 (ttm) REVERT: D 262 MET cc_start: 0.8692 (tpp) cc_final: 0.8362 (mmm) REVERT: B 198 GLU cc_start: 0.8612 (pm20) cc_final: 0.8221 (pm20) REVERT: B 616 TRP cc_start: 0.8201 (OUTLIER) cc_final: 0.5379 (p-90) REVERT: B 628 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8138 (ttp80) REVERT: B 687 LEU cc_start: 0.9138 (mp) cc_final: 0.8876 (mp) REVERT: B 751 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6922 (tp30) outliers start: 44 outliers final: 26 residues processed: 217 average time/residue: 0.2581 time to fit residues: 82.1490 Evaluate side-chains 210 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 301 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 575 SER 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 129 ILE 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 168 GLU 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 507 LEU Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 102 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 35 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 195 HIS D 195 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.096076 restraints weight = 20325.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.098907 restraints weight = 11838.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.100737 restraints weight = 8421.413| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13750 Z= 0.102 Angle : 0.580 8.383 18732 Z= 0.292 Chirality : 0.040 0.156 2254 Planarity : 0.004 0.039 2326 Dihedral : 4.095 16.568 2150 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.32 % Allowed : 17.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1708 helix: 0.41 (0.17), residues: 1024 sheet: -3.70 (1.04), residues: 20 loop : -2.56 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 524 HIS 0.006 0.001 HIS D 195 PHE 0.014 0.001 PHE D 119 TYR 0.011 0.001 TYR B 397 ARG 0.003 0.000 ARG B 113 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 14) link_NAG-ASN : angle 1.41805 ( 42) hydrogen bonds : bond 0.03153 ( 594) hydrogen bonds : angle 3.67708 ( 1752) SS BOND : bond 0.00310 ( 6) SS BOND : angle 3.26189 ( 12) covalent geometry : bond 0.00220 (13730) covalent geometry : angle 0.57124 (18678) *********************** 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 220 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 MET cc_start: 0.8084 (ttm) cc_final: 0.7851 (ttm) REVERT: C 262 MET cc_start: 0.8886 (mmm) cc_final: 0.8099 (mmm) REVERT: A 441 LEU cc_start: 0.8261 (pt) cc_final: 0.8043 (tp) REVERT: A 616 TRP cc_start: 0.7917 (OUTLIER) cc_final: 0.5323 (p-90) REVERT: A 628 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8103 (ttp80) REVERT: D 150 ASP cc_start: 0.8989 (p0) cc_final: 0.8560 (p0) REVERT: B 616 TRP cc_start: 0.8037 (OUTLIER) cc_final: 0.5413 (p-90) REVERT: B 628 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8045 (ttp80) REVERT: B 687 LEU cc_start: 0.9105 (mp) cc_final: 0.8865 (mp) outliers start: 32 outliers final: 18 residues processed: 210 average time/residue: 0.3035 time to fit residues: 93.5051 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 : 1.639 ------------------------------------------------------------------------------- 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 381 MET Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 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 167 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 157 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 195 HIS A 607 GLN D 195 HIS D 242 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.097194 restraints weight = 19773.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099759 restraints weight = 12039.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.101388 restraints weight = 8791.611| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2928 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= 0.123 Angle : 0.602 7.921 18732 Z= 0.304 Chirality : 0.041 0.163 2254 Planarity : 0.004 0.038 2326 Dihedral : 4.003 16.014 2150 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.25 % Allowed : 18.19 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1708 helix: 0.53 (0.17), residues: 1028 sheet: -3.73 (0.99), residues: 20 loop : -2.48 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 524 HIS 0.006 0.001 HIS D 195 PHE 0.012 0.001 PHE D 119 TYR 0.010 0.001 TYR B 397 ARG 0.004 0.000 ARG C 225 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 14) link_NAG-ASN : angle 1.50620 ( 42) hydrogen bonds : bond 0.03448 ( 594) hydrogen bonds : angle 3.66193 ( 1752) SS BOND : bond 0.00767 ( 6) SS BOND : angle 3.69497 ( 12) covalent geometry : bond 0.00287 (13730) covalent geometry : angle 0.59153 (18678) *********************** 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 219 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9455 (p0) cc_final: 0.9248 (p0) REVERT: A 441 LEU cc_start: 0.8267 (pt) cc_final: 0.8053 (tp) REVERT: A 616 TRP cc_start: 0.8064 (OUTLIER) cc_final: 0.5310 (p-90) REVERT: A 628 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8153 (ttm110) REVERT: A 687 LEU cc_start: 0.9092 (mp) cc_final: 0.8814 (mp) REVERT: D 83 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7776 (mp0) REVERT: D 150 ASP cc_start: 0.8998 (p0) cc_final: 0.8632 (p0) REVERT: D 259 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7660 (mm-30) REVERT: D 262 MET cc_start: 0.8977 (mmm) cc_final: 0.8225 (tmm) REVERT: B 616 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.5272 (p-90) REVERT: B 628 ARG cc_start: 0.8271 (ttp80) cc_final: 0.8061 (ttp80) REVERT: B 687 LEU cc_start: 0.9090 (mp) cc_final: 0.8869 (mp) outliers start: 31 outliers final: 24 residues processed: 212 average time/residue: 0.3365 time to fit residues: 104.9821 Evaluate side-chains 210 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 167 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 616 TRP 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 129 ILE 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 167 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 165 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 31 optimal weight: 0.0040 chunk 6 optimal weight: 8.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 195 HIS D 195 HIS D 242 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.092733 restraints weight = 20239.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.095516 restraints weight = 11870.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.097268 restraints weight = 8502.175| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13750 Z= 0.142 Angle : 0.631 8.828 18732 Z= 0.320 Chirality : 0.042 0.178 2254 Planarity : 0.004 0.039 2326 Dihedral : 4.069 16.851 2150 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.39 % Allowed : 18.26 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1708 helix: 0.53 (0.17), residues: 1034 sheet: -3.78 (0.93), residues: 20 loop : -2.47 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 524 HIS 0.006 0.001 HIS C 195 PHE 0.011 0.001 PHE B 581 TYR 0.015 0.001 TYR C 188 ARG 0.005 0.000 ARG D 225 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 14) link_NAG-ASN : angle 1.57307 ( 42) hydrogen bonds : bond 0.03653 ( 594) hydrogen bonds : angle 3.69023 ( 1752) SS BOND : bond 0.00794 ( 6) SS BOND : angle 3.95664 ( 12) covalent geometry : bond 0.00337 (13730) covalent geometry : angle 0.61975 (18678) *********************** 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 217 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9436 (p0) cc_final: 0.9105 (p0) REVERT: A 198 GLU cc_start: 0.8603 (pm20) cc_final: 0.8271 (pm20) REVERT: A 441 LEU cc_start: 0.8338 (pt) cc_final: 0.8119 (tp) REVERT: A 616 TRP cc_start: 0.8104 (OUTLIER) cc_final: 0.5223 (p-90) REVERT: A 628 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8207 (ttm110) REVERT: A 687 LEU cc_start: 0.9151 (mp) cc_final: 0.8902 (mp) REVERT: D 83 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7807 (mp0) REVERT: D 150 ASP cc_start: 0.8992 (p0) cc_final: 0.8628 (p0) REVERT: D 259 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7762 (mm-30) REVERT: D 262 MET cc_start: 0.9006 (mmm) cc_final: 0.8213 (tmm) REVERT: B 616 TRP cc_start: 0.8122 (OUTLIER) cc_final: 0.5249 (p-90) REVERT: B 687 LEU cc_start: 0.9112 (mp) cc_final: 0.8895 (mp) outliers start: 33 outliers final: 26 residues processed: 208 average time/residue: 0.3396 time to fit residues: 102.4632 Evaluate side-chains 210 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 129 ILE 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 167 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 0.0770 chunk 132 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 195 HIS C 242 ASN D 195 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.094797 restraints weight = 19755.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.097275 restraints weight = 12013.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.098846 restraints weight = 8784.734| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13750 Z= 0.207 Angle : 0.701 9.210 18732 Z= 0.355 Chirality : 0.045 0.175 2254 Planarity : 0.004 0.042 2326 Dihedral : 4.390 18.605 2150 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.32 % Allowed : 18.41 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1708 helix: 0.41 (0.17), residues: 1032 sheet: -4.03 (0.85), residues: 20 loop : -2.50 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 179 HIS 0.006 0.001 HIS D 195 PHE 0.017 0.002 PHE B 581 TYR 0.013 0.001 TYR A 433 ARG 0.005 0.001 ARG C 225 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 14) link_NAG-ASN : angle 1.84076 ( 42) hydrogen bonds : bond 0.04518 ( 594) hydrogen bonds : angle 3.87009 ( 1752) SS BOND : bond 0.00864 ( 6) SS BOND : angle 4.48791 ( 12) covalent geometry : bond 0.00503 (13730) covalent geometry : angle 0.68768 (18678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9418 (p0) cc_final: 0.8869 (p0) REVERT: A 198 GLU cc_start: 0.8612 (pm20) cc_final: 0.8218 (pm20) REVERT: A 616 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.5245 (p-90) REVERT: A 628 ARG cc_start: 0.8540 (ttp80) cc_final: 0.8241 (ttp80) REVERT: A 687 LEU cc_start: 0.9136 (mp) cc_final: 0.8931 (mp) REVERT: A 751 GLU cc_start: 0.7702 (pm20) cc_final: 0.7497 (pm20) REVERT: D 83 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7784 (mp0) REVERT: D 150 ASP cc_start: 0.9123 (p0) cc_final: 0.8520 (p0) REVERT: D 259 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7796 (mm-30) REVERT: B 616 TRP cc_start: 0.8257 (OUTLIER) cc_final: 0.5267 (p-90) REVERT: B 687 LEU cc_start: 0.9121 (mp) cc_final: 0.8892 (mp) outliers start: 32 outliers final: 29 residues processed: 197 average time/residue: 0.3498 time to fit residues: 101.4729 Evaluate side-chains 203 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 129 ILE 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 167 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 781 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 12 optimal weight: 0.0870 chunk 137 optimal weight: 5.9990 chunk 105 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 167 GLN C 195 HIS C 242 ASN D 195 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.104550 restraints weight = 19274.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.107395 restraints weight = 10921.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109198 restraints weight = 7621.735| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13750 Z= 0.119 Angle : 0.622 9.201 18732 Z= 0.317 Chirality : 0.041 0.162 2254 Planarity : 0.004 0.036 2326 Dihedral : 4.095 18.360 2150 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.03 % Allowed : 18.77 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1708 helix: 0.67 (0.17), residues: 1026 sheet: -4.10 (0.78), residues: 20 loop : -2.43 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 524 HIS 0.007 0.001 HIS C 195 PHE 0.012 0.001 PHE D 119 TYR 0.012 0.001 TYR C 188 ARG 0.005 0.000 ARG D 266 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 14) link_NAG-ASN : angle 1.55220 ( 42) hydrogen bonds : bond 0.03474 ( 594) hydrogen bonds : angle 3.67238 ( 1752) SS BOND : bond 0.00919 ( 6) SS BOND : angle 4.26992 ( 12) covalent geometry : bond 0.00268 (13730) covalent geometry : angle 0.60919 (18678) ********************** 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 211 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 ASP cc_start: 0.9428 (p0) cc_final: 0.8899 (p0) REVERT: C 152 MET cc_start: 0.8321 (ttm) cc_final: 0.7910 (ttm) REVERT: C 262 MET cc_start: 0.8937 (mmm) cc_final: 0.8181 (mmm) REVERT: A 198 GLU cc_start: 0.8614 (pm20) cc_final: 0.8207 (pm20) REVERT: A 441 LEU cc_start: 0.8365 (pt) cc_final: 0.8138 (tp) REVERT: A 616 TRP cc_start: 0.8041 (OUTLIER) cc_final: 0.5173 (p-90) REVERT: A 628 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8192 (ttm110) REVERT: A 687 LEU cc_start: 0.9133 (mp) cc_final: 0.8920 (mp) REVERT: D 83 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7676 (mp0) REVERT: D 150 ASP cc_start: 0.9126 (p0) cc_final: 0.8588 (p0) REVERT: D 259 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 616 TRP cc_start: 0.8085 (OUTLIER) cc_final: 0.5215 (p-90) REVERT: B 687 LEU cc_start: 0.9090 (mp) cc_final: 0.8863 (mp) outliers start: 28 outliers final: 25 residues processed: 202 average time/residue: 0.2852 time to fit residues: 84.3741 Evaluate side-chains 204 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 616 TRP Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain D residue 129 ILE 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 167 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 616 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 741 MET 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 85 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 150 optimal weight: 6.9990 chunk 144 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 167 GLN C 195 HIS A 607 GLN A 666 HIS D 195 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.094827 restraints weight = 20087.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.097640 restraints weight = 11699.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.099427 restraints weight = 8314.078| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13750 Z= 0.115 Angle : 0.613 11.130 18732 Z= 0.312 Chirality : 0.041 0.237 2254 Planarity : 0.004 0.037 2326 Dihedral : 3.873 17.333 2150 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.10 % Allowed : 18.91 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1708 helix: 0.78 (0.17), residues: 1038 sheet: None (None), residues: 0 loop : -2.50 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 524 HIS 0.007 0.001 HIS C 195 PHE 0.012 0.001 PHE D 119 TYR 0.012 0.001 TYR C 188 ARG 0.005 0.000 ARG D 225 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 14) link_NAG-ASN : angle 1.46133 ( 42) hydrogen bonds : bond 0.03247 ( 594) hydrogen bonds : angle 3.56758 ( 1752) SS BOND : bond 0.00926 ( 6) SS BOND : angle 3.79472 ( 12) covalent geometry : bond 0.00254 (13730) covalent geometry : angle 0.60235 (18678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4589.52 seconds wall clock time: 84 minutes 14.01 seconds (5054.01 seconds total)