Starting phenix.real_space_refine on Fri Sep 11 06:23:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsn_30839/09_2026/7dsn_30839_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsn_30839/09_2026/7dsn_30839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsn_30839/09_2026/7dsn_30839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsn_30839/09_2026/7dsn_30839.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsn_30839/09_2026/7dsn_30839_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsn_30839/09_2026/7dsn_30839_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 27 5.16 5 C 4939 2.51 5 N 1192 2.21 5 O 1375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7534 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3670 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 22, 'TRANS': 448} Chain: "B" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3586 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 24, 'TRANS': 439} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 118 Unusual residues: {'HO9': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 17} Link IDs: {None: 19} Time building chain proxies: 1.74, per 1000 atoms: 0.23 Number of scatterers: 7534 At special positions: 0 Unit cell: (83.699, 86.96, 126.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 1 15.00 O 1375 8.00 N 1192 7.00 C 4939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.19 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 313.7 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 55.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 178 through 207 removed outlier: 3.671A pdb=" N ARG A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.778A pdb=" N GLN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.799A pdb=" N LYS A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.821A pdb=" N SER A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 342 removed outlier: 3.725A pdb=" N VAL A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.751A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.698A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 removed outlier: 3.670A pdb=" N THR A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.621A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.558A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'B' and resid 51 through 64 removed outlier: 3.563A pdb=" N GLY B 55 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 81 through 110 removed outlier: 3.681A pdb=" N LEU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.632A pdb=" N GLY B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 139 through 158 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 167 through 189 removed outlier: 3.681A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 180 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 220 removed outlier: 3.932A pdb=" N ALA B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.609A pdb=" N ALA B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 274 through 300 Proline residue: B 283 - end of helix removed outlier: 3.624A pdb=" N LEU B 287 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.651A pdb=" N LEU B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.504A pdb=" N VAL B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 356 removed outlier: 3.606A pdb=" N ASN B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.583A pdb=" N PHE B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 removed outlier: 3.610A pdb=" N SER B 390 " --> pdb=" O TYR B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 393 through 397 removed outlier: 3.834A pdb=" N ILE B 397 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 420 removed outlier: 4.098A pdb=" N VAL B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 448 removed outlier: 3.584A pdb=" N LEU B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 removed outlier: 3.567A pdb=" N LYS B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 476 removed outlier: 3.530A pdb=" N THR B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) Proline residue: B 470 - end of helix Processing helix chain 'B' and resid 482 through 501 removed outlier: 3.860A pdb=" N GLN B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY B 488 " --> pdb=" O TRP B 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.548A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N GLY A 380 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 348 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 345 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 260 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A 308 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU A 262 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.547A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA6, first strand: chain 'B' and resid 365 through 366 334 hydrogen bonds defined for protein. 972 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: 0.82 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1168 1.31 - 1.43: 2050 1.43 - 1.56: 4424 1.56 - 1.68: 25 1.68 - 1.81: 40 Bond restraints: 7707 Sorted by residual: bond pdb=" CAI Y01 B 603 " pdb=" CAZ Y01 B 603 " ideal model delta sigma weight residual 1.332 1.555 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAI Y01 B 602 " pdb=" CAZ Y01 B 602 " ideal model delta sigma weight residual 1.332 1.554 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C22 HO9 B 601 " pdb=" C25 HO9 B 601 " ideal model delta sigma weight residual 1.380 1.564 -0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" C23 HO9 B 601 " pdb=" C28 HO9 B 601 " ideal model delta sigma weight residual 1.390 1.565 -0.175 2.00e-02 2.50e+03 7.68e+01 bond pdb=" CBG Y01 B 602 " pdb=" CBI Y01 B 602 " ideal model delta sigma weight residual 1.537 1.385 0.152 2.00e-02 2.50e+03 5.78e+01 ... (remaining 7702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 10135 2.66 - 5.32: 287 5.32 - 7.98: 58 7.98 - 10.64: 14 10.64 - 13.30: 3 Bond angle restraints: 10497 Sorted by residual: angle pdb=" N VAL B 396 " pdb=" CA VAL B 396 " pdb=" C VAL B 396 " ideal model delta sigma weight residual 112.83 106.26 6.57 9.90e-01 1.02e+00 4.40e+01 angle pdb=" C PRO A 209 " pdb=" N ARG A 210 " pdb=" CA ARG A 210 " ideal model delta sigma weight residual 121.54 131.91 -10.37 1.91e+00 2.74e-01 2.95e+01 angle pdb=" N ILE B 68 " pdb=" CA ILE B 68 " pdb=" C ILE B 68 " ideal model delta sigma weight residual 112.83 107.51 5.32 9.90e-01 1.02e+00 2.89e+01 angle pdb=" N THR A 163 " pdb=" CA THR A 163 " pdb=" C THR A 163 " ideal model delta sigma weight residual 111.71 105.32 6.39 1.34e+00 5.57e-01 2.27e+01 angle pdb=" C THR B 71 " pdb=" N PRO B 72 " pdb=" CA PRO B 72 " ideal model delta sigma weight residual 119.84 114.06 5.78 1.25e+00 6.40e-01 2.14e+01 ... (remaining 10492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.07: 4546 35.07 - 70.15: 124 70.15 - 105.22: 20 105.22 - 140.29: 31 140.29 - 175.37: 7 Dihedral angle restraints: 4728 sinusoidal: 2048 harmonic: 2680 Sorted by residual: dihedral pdb=" CA GLY A 410 " pdb=" C GLY A 410 " pdb=" N SER A 411 " pdb=" CA SER A 411 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA THR B 264 " pdb=" C THR B 264 " pdb=" N GLU B 265 " pdb=" CA GLU B 265 " ideal model delta harmonic sigma weight residual 180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ARG A 210 " pdb=" C ARG A 210 " pdb=" N CYS A 211 " pdb=" CA CYS A 211 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 4725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.192: 1223 1.192 - 2.383: 0 2.383 - 3.575: 0 3.575 - 4.766: 0 4.766 - 5.958: 10 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CBI Y01 B 602 " pdb=" CAU Y01 B 602 " pdb=" CBE Y01 B 602 " pdb=" CBG Y01 B 602 " both_signs ideal model delta sigma weight residual False 2.94 -3.02 5.96 2.00e-01 2.50e+01 8.87e+02 chirality pdb=" CBI Y01 B 603 " pdb=" CAU Y01 B 603 " pdb=" CBE Y01 B 603 " pdb=" CBG Y01 B 603 " both_signs ideal model delta sigma weight residual False 2.94 -3.00 5.94 2.00e-01 2.50e+01 8.82e+02 chirality pdb=" CBH Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CAZ Y01 B 602 " pdb=" CBF Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.85 2.64 -5.50 2.00e-01 2.50e+01 7.56e+02 ... (remaining 1230 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 164 " -0.073 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO B 165 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 618 " -0.052 5.00e-02 4.00e+02 7.76e-02 9.63e+00 pdb=" N PRO A 619 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 282 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO B 283 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 283 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 283 " -0.032 5.00e-02 4.00e+02 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 199 2.69 - 3.24: 6731 3.24 - 3.79: 11474 3.79 - 4.35: 15599 4.35 - 4.90: 25421 Nonbonded interactions: 59424 Sorted by model distance: nonbonded pdb=" O VAL B 70 " pdb=" OG1 THR B 71 " model vdw 2.132 3.040 nonbonded pdb=" OG SER A 407 " pdb=" O LEU A 436 " model vdw 2.216 3.040 nonbonded pdb=" CG2 ILE B 397 " pdb=" O21 HO9 B 601 " model vdw 2.254 3.460 nonbonded pdb=" CG2 ILE B 147 " pdb=" C27 HO9 B 601 " model vdw 2.265 3.760 nonbonded pdb=" OG SER B 113 " pdb=" O THR B 264 " model vdw 2.271 3.040 ... (remaining 59419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic 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: 1.190 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.940 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.012 0.223 7716 Z= 0.583 Angle : 1.168 13.297 10523 Z= 0.603 Chirality : 0.490 5.958 1233 Planarity : 0.008 0.113 1282 Dihedral : 22.151 175.366 3003 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.97 % Allowed : 6.66 % Favored : 92.37 % Rotamer: Outliers : 1.52 % Allowed : 5.70 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.21), residues: 931 helix: -2.79 (0.17), residues: 486 sheet: -1.73 (0.59), residues: 63 loop : -3.19 (0.25), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 556 TYR 0.022 0.002 TYR B 103 PHE 0.022 0.002 PHE A 497 TRP 0.013 0.002 TRP A 220 HIS 0.005 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.01174 / 0.58 ( 7707) covalent geometry : angle 1.14298 / 0.60 (10497) SS BOND : bond 0.15911 / 8.37 ( 1) SS BOND : angle 5.72543 / 3.23 ( 2) hydrogen bonds : bond 0.21417 / 13.70 ( 334) hydrogen bonds : angle 7.35577 / 5.03 ( 972) link_BETA1-4 : bond 0.00722 / 0.37 ( 4) link_BETA1-4 : angle 4.44714 / 1.99 ( 12) link_NAG-ASN : bond 0.00789 / 0.41 ( 4) link_NAG-ASN : angle 5.23570 / 2.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.269 Fit side-chains REVERT: B 51 THR cc_start: 0.8410 (m) cc_final: 0.8194 (m) REVERT: B 195 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7056 (mtm180) REVERT: B 365 MET cc_start: 0.8597 (mtt) cc_final: 0.8290 (mtt) REVERT: B 401 SER cc_start: 0.7524 (OUTLIER) cc_final: 0.7022 (p) REVERT: B 438 PHE cc_start: 0.7291 (t80) cc_final: 0.7078 (t80) REVERT: B 496 CYS cc_start: 0.7983 (m) cc_final: 0.7733 (m) REVERT: B 500 MET cc_start: 0.8380 (mtt) cc_final: 0.8051 (mtm) outliers start: 12 outliers final: 5 residues processed: 155 average time/residue: 0.0797 time to fit residues: 16.6707 Evaluate side-chains 115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 505 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 74 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.5834 > 50:) overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 GLN A 353 ASN A 483 GLN A 539 HIS B 47 GLN B 261 ASN B 304 GLN B 367 HIS B 420 HIS B 501 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.151005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.112423 restraints weight = 9658.711| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.89 r_work: 0.2946 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7716 Z= 0.201 Angle : 1.279 32.613 10523 Z= 0.504 Chirality : 0.109 1.757 1233 Planarity : 0.006 0.058 1282 Dihedral : 23.098 177.301 1367 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.77 % Favored : 92.91 % Rotamer: Outliers : 2.15 % Allowed : 10.90 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.24), residues: 931 helix: -1.27 (0.21), residues: 494 sheet: -1.09 (0.63), residues: 63 loop : -2.92 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 440 TYR 0.012 0.002 TYR A 554 PHE 0.016 0.002 PHE B 379 TRP 0.011 0.001 TRP A 220 HIS 0.010 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 7707) covalent geometry : angle 1.27031 / 0.50 (10497) SS BOND : bond 0.00278 / 0.15 ( 1) SS BOND : angle 2.40037 / 1.32 ( 2) hydrogen bonds : bond 0.06036 / 3.83 ( 334) hydrogen bonds : angle 4.73402 / 3.16 ( 972) link_BETA1-4 : bond 0.00367 / 0.19 ( 4) link_BETA1-4 : angle 2.53770 / 1.12 ( 12) link_NAG-ASN : bond 0.00534 / 0.27 ( 4) link_NAG-ASN : angle 3.98516 / 1.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.203 Fit side-chains REVERT: B 51 THR cc_start: 0.8025 (m) cc_final: 0.7783 (m) REVERT: B 195 ARG cc_start: 0.7835 (mtp180) cc_final: 0.7468 (mtm180) REVERT: B 271 TYR cc_start: 0.8900 (m-80) cc_final: 0.8538 (m-80) REVERT: B 438 PHE cc_start: 0.7671 (t80) cc_final: 0.7460 (t80) REVERT: B 500 MET cc_start: 0.8300 (mtt) cc_final: 0.7956 (mtm) outliers start: 17 outliers final: 11 residues processed: 119 average time/residue: 0.0831 time to fit residues: 13.6581 Evaluate side-chains 110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TRP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 431 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 GLN B 304 GLN B 501 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115763 restraints weight = 9569.911| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.90 r_work: 0.2973 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7716 Z= 0.128 Angle : 1.208 32.843 10523 Z= 0.464 Chirality : 0.109 1.863 1233 Planarity : 0.005 0.052 1282 Dihedral : 22.901 177.299 1357 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.12 % Favored : 93.56 % Rotamer: Outliers : 2.79 % Allowed : 11.91 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.26), residues: 931 helix: -0.39 (0.23), residues: 488 sheet: -0.89 (0.62), residues: 67 loop : -2.66 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.010 0.001 TYR B 146 PHE 0.012 0.001 PHE B 130 TRP 0.011 0.001 TRP B 477 HIS 0.005 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7707) covalent geometry : angle 1.19957 / 0.46 (10497) SS BOND : bond 0.00688 / 0.36 ( 1) SS BOND : angle 3.94589 / 2.08 ( 2) hydrogen bonds : bond 0.04633 / 2.92 ( 334) hydrogen bonds : angle 4.29124 / 2.86 ( 972) link_BETA1-4 : bond 0.00380 / 0.19 ( 4) link_BETA1-4 : angle 2.32472 / 1.04 ( 12) link_NAG-ASN : bond 0.00499 / 0.26 ( 4) link_NAG-ASN : angle 3.65406 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 249 LEU cc_start: 0.9294 (mt) cc_final: 0.9088 (mt) REVERT: A 260 LEU cc_start: 0.9015 (tp) cc_final: 0.8805 (tp) REVERT: A 593 LYS cc_start: 0.8031 (pptt) cc_final: 0.7395 (mtpt) REVERT: B 51 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7629 (m) REVERT: B 195 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7394 (mtm180) REVERT: B 271 TYR cc_start: 0.8867 (m-80) cc_final: 0.8561 (m-80) REVERT: B 365 MET cc_start: 0.8891 (mtt) cc_final: 0.8447 (mtt) REVERT: B 438 PHE cc_start: 0.7569 (t80) cc_final: 0.7342 (t80) REVERT: B 487 GLN cc_start: 0.7552 (tp40) cc_final: 0.7306 (tm-30) outliers start: 22 outliers final: 10 residues processed: 122 average time/residue: 0.0714 time to fit residues: 12.3389 Evaluate side-chains 109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 248 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 HIS A 296 GLN B 304 GLN B 501 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.114733 restraints weight = 9683.545| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.67 r_work: 0.2979 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7716 Z= 0.152 Angle : 1.210 32.797 10523 Z= 0.463 Chirality : 0.108 1.816 1233 Planarity : 0.004 0.050 1282 Dihedral : 22.864 175.014 1357 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.12 % Favored : 93.56 % Rotamer: Outliers : 3.17 % Allowed : 13.56 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.27), residues: 931 helix: 0.02 (0.23), residues: 497 sheet: -0.71 (0.62), residues: 67 loop : -2.42 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.013 0.002 TYR A 226 PHE 0.016 0.001 PHE B 351 TRP 0.013 0.001 TRP B 477 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 7707) covalent geometry : angle 1.20234 / 0.46 (10497) SS BOND : bond 0.00563 / 0.30 ( 1) SS BOND : angle 2.90930 / 1.60 ( 2) hydrogen bonds : bond 0.04710 / 2.98 ( 334) hydrogen bonds : angle 4.18203 / 2.78 ( 972) link_BETA1-4 : bond 0.00360 / 0.18 ( 4) link_BETA1-4 : angle 2.33215 / 1.04 ( 12) link_NAG-ASN : bond 0.00492 / 0.25 ( 4) link_NAG-ASN : angle 3.53446 / 1.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9068 (tp) cc_final: 0.8848 (tp) REVERT: A 593 LYS cc_start: 0.8013 (pptt) cc_final: 0.7406 (mtpt) REVERT: B 51 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7646 (m) REVERT: B 271 TYR cc_start: 0.8846 (m-80) cc_final: 0.8545 (m-80) REVERT: B 401 SER cc_start: 0.6898 (m) cc_final: 0.6305 (p) REVERT: B 438 PHE cc_start: 0.7527 (t80) cc_final: 0.7315 (t80) REVERT: B 487 GLN cc_start: 0.7605 (tp40) cc_final: 0.7370 (tm-30) outliers start: 25 outliers final: 16 residues processed: 113 average time/residue: 0.0628 time to fit residues: 10.3455 Evaluate side-chains 116 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 267 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116268 restraints weight = 9600.388| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.72 r_work: 0.3014 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7716 Z= 0.121 Angle : 1.186 32.913 10523 Z= 0.449 Chirality : 0.108 1.819 1233 Planarity : 0.004 0.048 1282 Dihedral : 22.843 175.754 1357 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.66 % Favored : 93.02 % Rotamer: Outliers : 2.41 % Allowed : 15.08 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.27), residues: 931 helix: 0.36 (0.23), residues: 498 sheet: -0.62 (0.61), residues: 67 loop : -2.26 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.011 0.001 TYR A 226 PHE 0.020 0.001 PHE B 474 TRP 0.015 0.001 TRP B 477 HIS 0.005 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7707) covalent geometry : angle 1.17854 / 0.45 (10497) SS BOND : bond 0.00529 / 0.28 ( 1) SS BOND : angle 2.33885 / 1.29 ( 2) hydrogen bonds : bond 0.04135 / 2.61 ( 334) hydrogen bonds : angle 4.03068 / 2.67 ( 972) link_BETA1-4 : bond 0.00398 / 0.20 ( 4) link_BETA1-4 : angle 2.25590 / 1.00 ( 12) link_NAG-ASN : bond 0.00456 / 0.23 ( 4) link_NAG-ASN : angle 3.43998 / 1.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 593 LYS cc_start: 0.7985 (pptt) cc_final: 0.7387 (mtpt) REVERT: B 51 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7580 (m) REVERT: B 271 TYR cc_start: 0.8815 (m-80) cc_final: 0.8564 (m-80) REVERT: B 401 SER cc_start: 0.6894 (m) cc_final: 0.6344 (p) REVERT: B 438 PHE cc_start: 0.7501 (t80) cc_final: 0.7279 (t80) REVERT: B 487 GLN cc_start: 0.7628 (tp40) cc_final: 0.7382 (tm-30) outliers start: 19 outliers final: 11 residues processed: 117 average time/residue: 0.0570 time to fit residues: 9.8384 Evaluate side-chains 116 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 248 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 89 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.158688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122924 restraints weight = 9526.674| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.64 r_work: 0.3012 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7716 Z= 0.131 Angle : 1.189 32.786 10523 Z= 0.451 Chirality : 0.108 1.816 1233 Planarity : 0.004 0.047 1282 Dihedral : 22.837 176.475 1357 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.12 % Favored : 93.56 % Rotamer: Outliers : 2.66 % Allowed : 16.35 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.28), residues: 931 helix: 0.63 (0.24), residues: 498 sheet: -0.62 (0.61), residues: 67 loop : -2.15 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 227 TYR 0.010 0.001 TYR B 146 PHE 0.016 0.001 PHE B 351 TRP 0.016 0.001 TRP B 477 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7707) covalent geometry : angle 1.18204 / 0.45 (10497) SS BOND : bond 0.00041 / 0.02 ( 1) SS BOND : angle 2.25237 / 1.25 ( 2) hydrogen bonds : bond 0.04217 / 2.67 ( 334) hydrogen bonds : angle 3.96448 / 2.63 ( 972) link_BETA1-4 : bond 0.00406 / 0.21 ( 4) link_BETA1-4 : angle 2.29076 / 1.02 ( 12) link_NAG-ASN : bond 0.00452 / 0.23 ( 4) link_NAG-ASN : angle 3.40595 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 593 LYS cc_start: 0.7982 (pptt) cc_final: 0.7400 (mtpt) REVERT: B 51 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7592 (m) REVERT: B 365 MET cc_start: 0.8868 (mtt) cc_final: 0.8332 (mtt) REVERT: B 401 SER cc_start: 0.6833 (m) cc_final: 0.6317 (p) REVERT: B 438 PHE cc_start: 0.7512 (t80) cc_final: 0.7294 (t80) REVERT: B 478 TRP cc_start: 0.7745 (t-100) cc_final: 0.7476 (t-100) REVERT: B 487 GLN cc_start: 0.7655 (tp40) cc_final: 0.7288 (tm-30) outliers start: 21 outliers final: 16 residues processed: 121 average time/residue: 0.0628 time to fit residues: 11.1527 Evaluate side-chains 118 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 449 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 5.9990 chunk 80 optimal weight: 0.3980 chunk 90 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.150117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113483 restraints weight = 9720.615| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.77 r_work: 0.2958 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7716 Z= 0.191 Angle : 1.222 32.663 10523 Z= 0.471 Chirality : 0.109 1.794 1233 Planarity : 0.004 0.047 1282 Dihedral : 22.872 177.407 1357 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.63 % Favored : 92.05 % Rotamer: Outliers : 3.30 % Allowed : 16.22 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.28), residues: 931 helix: 0.61 (0.24), residues: 498 sheet: -0.54 (0.60), residues: 67 loop : -2.12 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.015 0.002 TYR A 226 PHE 0.023 0.002 PHE B 474 TRP 0.019 0.001 TRP B 477 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 7707) covalent geometry : angle 1.21536 / 0.47 (10497) SS BOND : bond 0.00106 / 0.06 ( 1) SS BOND : angle 2.91367 / 1.64 ( 2) hydrogen bonds : bond 0.05063 / 3.23 ( 334) hydrogen bonds : angle 4.13175 / 2.73 ( 972) link_BETA1-4 : bond 0.00404 / 0.20 ( 4) link_BETA1-4 : angle 2.37996 / 1.05 ( 12) link_NAG-ASN : bond 0.00433 / 0.22 ( 4) link_NAG-ASN : angle 3.35913 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 270 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7258 (tptp) REVERT: A 593 LYS cc_start: 0.8000 (pptt) cc_final: 0.7406 (mtpt) REVERT: B 51 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7595 (m) REVERT: B 234 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5312 (mp0) REVERT: B 271 TYR cc_start: 0.8884 (m-80) cc_final: 0.8562 (m-80) REVERT: B 365 MET cc_start: 0.8863 (mtt) cc_final: 0.8336 (mtt) REVERT: B 401 SER cc_start: 0.6857 (m) cc_final: 0.6331 (p) REVERT: B 438 PHE cc_start: 0.7537 (t80) cc_final: 0.7313 (t80) REVERT: B 487 GLN cc_start: 0.7670 (tp40) cc_final: 0.7286 (tm-30) outliers start: 26 outliers final: 20 residues processed: 122 average time/residue: 0.0722 time to fit residues: 12.7608 Evaluate side-chains 123 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 449 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.0870 chunk 15 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.158323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121611 restraints weight = 9486.641| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.78 r_work: 0.2987 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7716 Z= 0.125 Angle : 1.191 32.602 10523 Z= 0.452 Chirality : 0.109 1.812 1233 Planarity : 0.004 0.047 1282 Dihedral : 22.804 176.890 1357 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.34 % Favored : 93.34 % Rotamer: Outliers : 2.79 % Allowed : 16.98 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.28), residues: 931 helix: 0.79 (0.24), residues: 498 sheet: -0.47 (0.61), residues: 67 loop : -2.04 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 440 TYR 0.010 0.001 TYR B 146 PHE 0.015 0.001 PHE B 351 TRP 0.019 0.001 TRP B 477 HIS 0.005 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7707) covalent geometry : angle 1.18400 / 0.45 (10497) SS BOND : bond 0.00340 / 0.18 ( 1) SS BOND : angle 2.26340 / 1.27 ( 2) hydrogen bonds : bond 0.04147 / 2.63 ( 334) hydrogen bonds : angle 3.95901 / 2.62 ( 972) link_BETA1-4 : bond 0.00374 / 0.19 ( 4) link_BETA1-4 : angle 2.30260 / 1.02 ( 12) link_NAG-ASN : bond 0.00438 / 0.22 ( 4) link_NAG-ASN : angle 3.29574 / 1.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 270 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7185 (tptp) REVERT: A 593 LYS cc_start: 0.7950 (pptt) cc_final: 0.7381 (mtpt) REVERT: B 51 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7537 (m) REVERT: B 271 TYR cc_start: 0.8850 (m-80) cc_final: 0.8606 (m-80) REVERT: B 401 SER cc_start: 0.6657 (m) cc_final: 0.6220 (p) REVERT: B 433 LEU cc_start: 0.6827 (tp) cc_final: 0.6567 (tp) REVERT: B 438 PHE cc_start: 0.7552 (t80) cc_final: 0.7325 (t80) REVERT: B 487 GLN cc_start: 0.7737 (tp40) cc_final: 0.7328 (tm-30) outliers start: 22 outliers final: 17 residues processed: 111 average time/residue: 0.0691 time to fit residues: 11.3191 Evaluate side-chains 115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 449 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122371 restraints weight = 9442.984| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.71 r_work: 0.3026 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7716 Z= 0.120 Angle : 1.184 32.333 10523 Z= 0.449 Chirality : 0.109 1.819 1233 Planarity : 0.004 0.047 1282 Dihedral : 22.745 177.850 1357 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.23 % Favored : 93.45 % Rotamer: Outliers : 2.28 % Allowed : 17.62 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.28), residues: 931 helix: 0.94 (0.24), residues: 496 sheet: -0.51 (0.61), residues: 67 loop : -1.98 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 440 TYR 0.010 0.001 TYR B 146 PHE 0.023 0.001 PHE B 474 TRP 0.021 0.001 TRP B 477 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 7707) covalent geometry : angle 1.17763 / 0.45 (10497) SS BOND : bond 0.00057 / 0.03 ( 1) SS BOND : angle 2.05273 / 1.15 ( 2) hydrogen bonds : bond 0.03941 / 2.50 ( 334) hydrogen bonds : angle 3.88928 / 2.57 ( 972) link_BETA1-4 : bond 0.00380 / 0.19 ( 4) link_BETA1-4 : angle 2.29829 / 1.03 ( 12) link_NAG-ASN : bond 0.00426 / 0.22 ( 4) link_NAG-ASN : angle 3.28697 / 1.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.8572 (mt) cc_final: 0.8343 (mt) REVERT: A 593 LYS cc_start: 0.7996 (pptt) cc_final: 0.7389 (mtpt) REVERT: B 51 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7521 (m) REVERT: B 304 GLN cc_start: 0.7229 (pt0) cc_final: 0.6620 (pm20) REVERT: B 433 LEU cc_start: 0.6835 (tp) cc_final: 0.6534 (tp) REVERT: B 438 PHE cc_start: 0.7510 (t80) cc_final: 0.7293 (t80) REVERT: B 487 GLN cc_start: 0.7849 (tp40) cc_final: 0.7426 (tm-30) outliers start: 18 outliers final: 14 residues processed: 115 average time/residue: 0.0778 time to fit residues: 12.7735 Evaluate side-chains 114 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 449 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 501 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.121357 restraints weight = 9483.989| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.71 r_work: 0.2998 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7716 Z= 0.134 Angle : 1.190 32.222 10523 Z= 0.452 Chirality : 0.109 1.815 1233 Planarity : 0.004 0.047 1282 Dihedral : 22.717 177.735 1357 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.23 % Favored : 93.45 % Rotamer: Outliers : 2.03 % Allowed : 18.12 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.28), residues: 931 helix: 0.92 (0.24), residues: 496 sheet: -0.45 (0.62), residues: 67 loop : -1.95 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.011 0.001 TYR A 226 PHE 0.017 0.001 PHE B 351 TRP 0.024 0.001 TRP B 477 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 7707) covalent geometry : angle 1.18299 / 0.45 (10497) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 2.20011 / 1.24 ( 2) hydrogen bonds : bond 0.04166 / 2.66 ( 334) hydrogen bonds : angle 3.90812 / 2.59 ( 972) link_BETA1-4 : bond 0.00370 / 0.19 ( 4) link_BETA1-4 : angle 2.30679 / 1.03 ( 12) link_NAG-ASN : bond 0.00415 / 0.21 ( 4) link_NAG-ASN : angle 3.24735 / 1.56 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.8571 (mt) cc_final: 0.8339 (mt) REVERT: A 593 LYS cc_start: 0.8000 (pptt) cc_final: 0.7388 (mtpt) REVERT: B 433 LEU cc_start: 0.6739 (tp) cc_final: 0.6430 (tp) REVERT: B 438 PHE cc_start: 0.7489 (t80) cc_final: 0.7269 (t80) outliers start: 16 outliers final: 14 residues processed: 109 average time/residue: 0.0736 time to fit residues: 11.5844 Evaluate side-chains 112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 449 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 80 optimal weight: 0.0870 chunk 33 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118663 restraints weight = 9495.248| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.82 r_work: 0.3006 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7716 Z= 0.115 Angle : 1.179 32.050 10523 Z= 0.445 Chirality : 0.109 1.820 1233 Planarity : 0.004 0.047 1282 Dihedral : 22.657 178.199 1357 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.23 % Favored : 93.45 % Rotamer: Outliers : 1.90 % Allowed : 18.00 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.28), residues: 931 helix: 1.07 (0.24), residues: 490 sheet: -0.43 (0.62), residues: 67 loop : -1.83 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.009 0.001 TYR A 226 PHE 0.023 0.001 PHE B 474 TRP 0.024 0.001 TRP B 477 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7707) covalent geometry : angle 1.17252 / 0.44 (10497) SS BOND : bond 0.00013 / 0.01 ( 1) SS BOND : angle 1.91557 / 1.08 ( 2) hydrogen bonds : bond 0.03817 / 2.42 ( 334) hydrogen bonds : angle 3.83945 / 2.54 ( 972) link_BETA1-4 : bond 0.00368 / 0.19 ( 4) link_BETA1-4 : angle 2.26728 / 1.01 ( 12) link_NAG-ASN : bond 0.00415 / 0.21 ( 4) link_NAG-ASN : angle 3.20914 / 1.54 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1738.86 seconds wall clock time: 30 minutes 28.24 seconds (1828.24 seconds total)