Starting phenix.real_space_refine on Sat May 2 16:31:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xpu_38561/05_2026/8xpu_38561_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xpu_38561/05_2026/8xpu_38561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xpu_38561/05_2026/8xpu_38561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xpu_38561/05_2026/8xpu_38561.map" model { file = "/net/cci-nas-00/data/ceres_data/8xpu_38561/05_2026/8xpu_38561_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xpu_38561/05_2026/8xpu_38561_neut.cif" } resolution = 3.3 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= -0.002 sd= 0.075 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 S 27 5.16 5 Cl 2 4.86 5 C 4830 2.51 5 N 1191 2.21 5 O 1341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7391 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3661 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 22, 'TRANS': 447} 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: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'VRW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.24 Number of scatterers: 7391 At special positions: 0 Unit cell: (86.505, 85.41, 133.59, 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) Cl 2 17.00 S 27 16.00 O 1341 8.00 N 1191 7.00 C 4830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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 382 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 507 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 387.6 milliseconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 57.2% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.912A pdb=" N LEU A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 207 removed outlier: 3.673A pdb=" N ARG A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.695A pdb=" N HIS A 221 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.582A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.757A pdb=" N LYS A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TYR A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 324 through 342 removed outlier: 4.366A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.744A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.214A pdb=" N LYS A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.234A pdb=" N PHE A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.596A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 removed outlier: 4.426A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 534 removed outlier: 3.743A pdb=" N LEU A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.521A pdb=" N ALA A 588 " --> pdb=" O PRO A 585 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 589 " --> pdb=" O ALA A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 589' Processing helix chain 'B' and resid 51 through 64 removed outlier: 3.982A pdb=" N VAL B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 removed outlier: 4.528A pdb=" N LEU B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 110 removed outlier: 3.599A pdb=" N CYS B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 140 through 157 removed outlier: 3.529A pdb=" N SER B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 189 removed outlier: 4.330A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 220 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 255 through 263 removed outlier: 3.935A pdb=" N ASN B 258 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU B 260 " --> pdb=" O TRP B 257 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN B 261 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 300 Proline residue: B 275 - end of helix Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.672A pdb=" N SER B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 319 Processing helix chain 'B' and resid 325 through 354 removed outlier: 3.677A pdb=" N PHE B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 400 through 422 removed outlier: 4.037A pdb=" N ASN B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 409 " --> pdb=" O TRP B 405 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.681A pdb=" N PHE B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.842A pdb=" N CYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 474 removed outlier: 4.080A pdb=" N TYR B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403 removed outlier: 6.539A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N GLN A 347 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU A 260 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP A 308 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LEU A 262 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR A 226 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A 225 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N CYS A 432 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL A 466 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP A 434 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N SER A 468 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 541 through 544 removed outlier: 3.775A pdb=" N GLU A 621 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 576 Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 594 357 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1158 1.29 - 1.42: 1958 1.42 - 1.55: 4409 1.55 - 1.68: 8 1.68 - 1.81: 42 Bond restraints: 7575 Sorted by residual: bond pdb=" C12 VRW B 601 " pdb=" C13 VRW B 601 " ideal model delta sigma weight residual 1.383 1.572 -0.189 2.00e-02 2.50e+03 8.95e+01 bond pdb=" C8 VRW B 601 " pdb=" C9 VRW B 601 " ideal model delta sigma weight residual 1.389 1.560 -0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" C19 VRW B 601 " pdb=" C20 VRW B 601 " ideal model delta sigma weight residual 1.384 1.533 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C15 VRW B 601 " pdb=" C16 VRW B 601 " ideal model delta sigma weight residual 1.391 1.539 -0.148 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C16 VRW B 601 " pdb=" C17 VRW B 601 " ideal model delta sigma weight residual 1.385 1.530 -0.145 2.00e-02 2.50e+03 5.23e+01 ... (remaining 7570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 9936 1.75 - 3.50: 289 3.50 - 5.26: 69 5.26 - 7.01: 19 7.01 - 8.76: 6 Bond angle restraints: 10319 Sorted by residual: angle pdb=" N TRP B 257 " pdb=" CA TRP B 257 " pdb=" C TRP B 257 " ideal model delta sigma weight residual 112.38 104.78 7.60 1.22e+00 6.72e-01 3.88e+01 angle pdb=" N VAL B 240 " pdb=" CA VAL B 240 " pdb=" C VAL B 240 " ideal model delta sigma weight residual 113.71 108.32 5.39 9.50e-01 1.11e+00 3.22e+01 angle pdb=" N ASN B 54 " pdb=" CA ASN B 54 " pdb=" C ASN B 54 " ideal model delta sigma weight residual 112.72 105.73 6.99 1.28e+00 6.10e-01 2.98e+01 angle pdb=" N ILE A 473 " pdb=" CA ILE A 473 " pdb=" C ILE A 473 " ideal model delta sigma weight residual 112.29 108.46 3.83 9.40e-01 1.13e+00 1.66e+01 angle pdb=" N VAL B 190 " pdb=" CA VAL B 190 " pdb=" C VAL B 190 " ideal model delta sigma weight residual 112.96 109.00 3.96 1.00e+00 1.00e+00 1.57e+01 ... (remaining 10314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3808 17.95 - 35.91: 545 35.91 - 53.86: 149 53.86 - 71.81: 17 71.81 - 89.76: 13 Dihedral angle restraints: 4532 sinusoidal: 1855 harmonic: 2677 Sorted by residual: dihedral pdb=" CA SER B 281 " pdb=" C SER B 281 " pdb=" N LEU B 282 " pdb=" CA LEU B 282 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+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 -162.51 -17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP A 471 " pdb=" CB ASP A 471 " pdb=" CG ASP A 471 " pdb=" OD1 ASP A 471 " ideal model delta sinusoidal sigma weight residual -30.00 -88.20 58.20 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 4529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 1210 0.158 - 0.317: 2 0.317 - 0.475: 1 0.475 - 0.634: 1 0.634 - 0.792: 1 Chirality restraints: 1215 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-02 2.50e+03 5.26e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.01e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.57e+01 ... (remaining 1212 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.353 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG F 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.541 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.307 2.00e-02 2.50e+03 2.62e-01 8.55e+02 pdb=" C7 NAG E 1 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.309 2.00e-02 2.50e+03 2.61e-01 8.53e+02 pdb=" C7 NAG C 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.451 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.037 2.00e-02 2.50e+03 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1064 2.75 - 3.29: 7289 3.29 - 3.83: 12182 3.83 - 4.36: 12949 4.36 - 4.90: 23309 Nonbonded interactions: 56793 Sorted by model distance: nonbonded pdb=" O ILE B 268 " pdb=" ND2 ASN B 273 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASN A 317 " pdb=" OG SER A 321 " model vdw 2.216 3.040 nonbonded pdb=" NH1 ARG A 452 " pdb=" O THR A 600 " model vdw 2.269 3.120 nonbonded pdb=" OG SER B 354 " pdb=" O PRO B 360 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASP A 250 " pdb=" N TYR A 251 " model vdw 2.288 3.120 ... (remaining 56788 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: 1.100 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.240 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.009 0.189 7583 Z= 0.430 Angle : 0.877 27.232 10343 Z= 0.408 Chirality : 0.051 0.792 1215 Planarity : 0.018 0.304 1275 Dihedral : 18.042 89.764 2812 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 33.76 % Favored : 66.24 % 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: -0.43 (0.28), residues: 930 helix: 1.03 (0.25), residues: 483 sheet: -0.26 (0.62), residues: 57 loop : -2.05 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 440 TYR 0.019 0.001 TYR B 259 PHE 0.021 0.001 PHE A 291 TRP 0.012 0.001 TRP A 220 HIS 0.002 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00826 ( 7575) covalent geometry : angle 0.75551 (10319) hydrogen bonds : bond 0.14352 ( 357) hydrogen bonds : angle 5.57427 ( 1047) link_BETA1-4 : bond 0.00419 ( 4) link_BETA1-4 : angle 3.16995 ( 12) link_NAG-ASN : bond 0.09818 ( 4) link_NAG-ASN : angle 12.72315 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.307 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0800 time to fit residues: 11.5817 Evaluate side-chains 101 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN B 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.224231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.166734 restraints weight = 8474.026| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.69 r_work: 0.3546 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7583 Z= 0.140 Angle : 0.700 13.899 10343 Z= 0.322 Chirality : 0.042 0.312 1215 Planarity : 0.004 0.062 1275 Dihedral : 8.891 82.862 1170 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 3.30 % Allowed : 30.08 % Favored : 66.62 % 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: 0.12 (0.28), residues: 930 helix: 1.50 (0.25), residues: 477 sheet: -0.14 (0.63), residues: 57 loop : -1.73 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.012 0.001 TYR B 259 PHE 0.017 0.001 PHE A 542 TRP 0.010 0.001 TRP A 219 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7575) covalent geometry : angle 0.66004 (10319) hydrogen bonds : bond 0.05186 ( 357) hydrogen bonds : angle 4.22714 ( 1047) link_BETA1-4 : bond 0.00524 ( 4) link_BETA1-4 : angle 2.78448 ( 12) link_NAG-ASN : bond 0.00655 ( 4) link_NAG-ASN : angle 6.30682 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 440 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7223 (mmt90) REVERT: B 54 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.7191 (t0) outliers start: 26 outliers final: 15 residues processed: 126 average time/residue: 0.0792 time to fit residues: 13.8600 Evaluate side-chains 116 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.222457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166392 restraints weight = 8315.601| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.62 r_work: 0.3534 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7583 Z= 0.125 Angle : 0.650 13.352 10343 Z= 0.303 Chirality : 0.041 0.396 1215 Planarity : 0.004 0.062 1275 Dihedral : 8.115 79.750 1170 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.31 % Allowed : 29.82 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.29), residues: 930 helix: 1.62 (0.25), residues: 479 sheet: 0.11 (0.63), residues: 63 loop : -1.71 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.008 0.001 TYR B 259 PHE 0.016 0.001 PHE A 542 TRP 0.009 0.001 TRP A 220 HIS 0.004 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7575) covalent geometry : angle 0.61604 (10319) hydrogen bonds : bond 0.04407 ( 357) hydrogen bonds : angle 3.98424 ( 1047) link_BETA1-4 : bond 0.00616 ( 4) link_BETA1-4 : angle 2.24171 ( 12) link_NAG-ASN : bond 0.00835 ( 4) link_NAG-ASN : angle 5.70901 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.8103 (t80) REVERT: B 330 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6443 (t80) outliers start: 34 outliers final: 22 residues processed: 127 average time/residue: 0.0647 time to fit residues: 11.7793 Evaluate side-chains 123 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.0170 chunk 84 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 73 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.220867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.164392 restraints weight = 8515.039| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.82 r_work: 0.3502 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7583 Z= 0.144 Angle : 0.669 14.322 10343 Z= 0.309 Chirality : 0.041 0.273 1215 Planarity : 0.004 0.062 1275 Dihedral : 7.800 77.417 1170 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 5.58 % Allowed : 29.70 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 930 helix: 1.64 (0.25), residues: 479 sheet: -0.21 (0.62), residues: 57 loop : -1.74 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.010 0.001 TYR A 554 PHE 0.019 0.001 PHE A 542 TRP 0.012 0.001 TRP A 219 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7575) covalent geometry : angle 0.64312 (10319) hydrogen bonds : bond 0.04284 ( 357) hydrogen bonds : angle 3.92778 ( 1047) link_BETA1-4 : bond 0.00622 ( 4) link_BETA1-4 : angle 2.29436 ( 12) link_NAG-ASN : bond 0.00755 ( 4) link_NAG-ASN : angle 5.02751 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.5975 (OUTLIER) cc_final: 0.5671 (mt) REVERT: B 103 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.8069 (t80) REVERT: B 251 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7138 (mp) REVERT: B 330 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6116 (t80) REVERT: B 446 LEU cc_start: 0.5399 (OUTLIER) cc_final: 0.5162 (mt) outliers start: 44 outliers final: 25 residues processed: 133 average time/residue: 0.0720 time to fit residues: 13.6839 Evaluate side-chains 127 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 31 optimal weight: 0.0870 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.219854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158821 restraints weight = 8519.556| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.93 r_work: 0.3527 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7583 Z= 0.142 Angle : 0.658 11.901 10343 Z= 0.307 Chirality : 0.041 0.276 1215 Planarity : 0.004 0.062 1275 Dihedral : 7.620 76.553 1170 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 5.71 % Allowed : 30.71 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.29), residues: 930 helix: 1.63 (0.25), residues: 481 sheet: -0.00 (0.62), residues: 63 loop : -1.72 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 440 TYR 0.009 0.001 TYR A 554 PHE 0.019 0.001 PHE A 542 TRP 0.012 0.001 TRP A 219 HIS 0.003 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7575) covalent geometry : angle 0.63310 (10319) hydrogen bonds : bond 0.04162 ( 357) hydrogen bonds : angle 3.88422 ( 1047) link_BETA1-4 : bond 0.00627 ( 4) link_BETA1-4 : angle 2.28919 ( 12) link_NAG-ASN : bond 0.00763 ( 4) link_NAG-ASN : angle 4.79467 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5793 (pm20) REVERT: B 103 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.8057 (t80) REVERT: B 251 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7041 (mp) REVERT: B 330 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6205 (t80) REVERT: B 387 TYR cc_start: 0.6816 (m-10) cc_final: 0.6334 (m-80) outliers start: 45 outliers final: 30 residues processed: 133 average time/residue: 0.0774 time to fit residues: 14.5368 Evaluate side-chains 132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.218938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157723 restraints weight = 8508.762| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.93 r_work: 0.3475 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7583 Z= 0.151 Angle : 0.661 11.493 10343 Z= 0.311 Chirality : 0.041 0.276 1215 Planarity : 0.004 0.062 1275 Dihedral : 7.462 76.351 1170 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 5.96 % Allowed : 30.58 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.28), residues: 930 helix: 1.52 (0.25), residues: 485 sheet: -0.10 (0.62), residues: 63 loop : -1.84 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 440 TYR 0.010 0.001 TYR A 554 PHE 0.019 0.001 PHE A 542 TRP 0.014 0.001 TRP A 219 HIS 0.003 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7575) covalent geometry : angle 0.63841 (10319) hydrogen bonds : bond 0.04252 ( 357) hydrogen bonds : angle 3.87937 ( 1047) link_BETA1-4 : bond 0.00639 ( 4) link_BETA1-4 : angle 2.27388 ( 12) link_NAG-ASN : bond 0.00745 ( 4) link_NAG-ASN : angle 4.57254 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 102 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: A 515 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5828 (pm20) REVERT: B 103 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7914 (t80) REVERT: B 251 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7016 (mp) REVERT: B 259 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.5017 (t80) REVERT: B 330 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6321 (t80) REVERT: B 387 TYR cc_start: 0.6846 (m-10) cc_final: 0.6366 (m-80) REVERT: B 446 LEU cc_start: 0.5091 (OUTLIER) cc_final: 0.4881 (mt) outliers start: 47 outliers final: 31 residues processed: 132 average time/residue: 0.0780 time to fit residues: 14.5250 Evaluate side-chains 137 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 120 MET 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 251 LEU Chi-restraints excluded: chain B residue 259 TYR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.217124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155740 restraints weight = 8544.530| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.92 r_work: 0.3466 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7583 Z= 0.178 Angle : 0.692 11.506 10343 Z= 0.327 Chirality : 0.042 0.276 1215 Planarity : 0.004 0.062 1275 Dihedral : 7.441 76.331 1170 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.96 % Allowed : 31.22 % Favored : 62.82 % 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: -0.04 (0.28), residues: 930 helix: 1.38 (0.25), residues: 485 sheet: -0.56 (0.58), residues: 64 loop : -1.87 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.011 0.002 TYR A 554 PHE 0.022 0.002 PHE A 542 TRP 0.016 0.001 TRP A 219 HIS 0.004 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 7575) covalent geometry : angle 0.67213 (10319) hydrogen bonds : bond 0.04595 ( 357) hydrogen bonds : angle 3.97696 ( 1047) link_BETA1-4 : bond 0.00678 ( 4) link_BETA1-4 : angle 2.27194 ( 12) link_NAG-ASN : bond 0.00700 ( 4) link_NAG-ASN : angle 4.41506 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 ASP cc_start: 0.7577 (m-30) cc_final: 0.7180 (t0) REVERT: A 515 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5830 (pm20) REVERT: B 92 CYS cc_start: 0.7269 (m) cc_final: 0.7016 (m) REVERT: B 103 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7988 (t80) REVERT: B 251 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7069 (mp) REVERT: B 271 TYR cc_start: 0.8053 (m-80) cc_final: 0.7507 (m-80) REVERT: B 387 TYR cc_start: 0.7053 (m-10) cc_final: 0.6590 (m-80) REVERT: B 446 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.5051 (mt) outliers start: 47 outliers final: 37 residues processed: 135 average time/residue: 0.0744 time to fit residues: 14.3946 Evaluate side-chains 146 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 259 TYR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 28 optimal weight: 0.0670 chunk 1 optimal weight: 10.0000 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.219001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.158135 restraints weight = 8526.743| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.90 r_work: 0.3475 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7583 Z= 0.142 Angle : 0.655 11.020 10343 Z= 0.310 Chirality : 0.041 0.274 1215 Planarity : 0.004 0.061 1275 Dihedral : 7.358 76.483 1170 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.46 % Allowed : 31.22 % Favored : 63.32 % 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: 0.07 (0.28), residues: 930 helix: 1.48 (0.25), residues: 485 sheet: -0.30 (0.60), residues: 63 loop : -1.85 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 440 TYR 0.009 0.001 TYR A 554 PHE 0.017 0.001 PHE A 542 TRP 0.012 0.001 TRP A 219 HIS 0.002 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7575) covalent geometry : angle 0.63557 (10319) hydrogen bonds : bond 0.04125 ( 357) hydrogen bonds : angle 3.87994 ( 1047) link_BETA1-4 : bond 0.00651 ( 4) link_BETA1-4 : angle 2.18845 ( 12) link_NAG-ASN : bond 0.00671 ( 4) link_NAG-ASN : angle 4.22724 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 385 ASP cc_start: 0.7437 (m-30) cc_final: 0.7082 (t0) REVERT: A 422 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: A 515 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5854 (pm20) REVERT: B 103 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7939 (t80) REVERT: B 251 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6987 (mp) REVERT: B 271 TYR cc_start: 0.8020 (m-80) cc_final: 0.7555 (m-80) REVERT: B 387 TYR cc_start: 0.6970 (m-10) cc_final: 0.6523 (m-80) outliers start: 43 outliers final: 34 residues processed: 132 average time/residue: 0.0763 time to fit residues: 14.2483 Evaluate side-chains 137 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 259 TYR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.219386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.158119 restraints weight = 8412.341| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.90 r_work: 0.3476 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7583 Z= 0.146 Angle : 0.663 11.212 10343 Z= 0.313 Chirality : 0.041 0.273 1215 Planarity : 0.004 0.061 1275 Dihedral : 7.272 76.464 1170 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 5.71 % Allowed : 31.60 % Favored : 62.69 % 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: 0.04 (0.28), residues: 930 helix: 1.48 (0.25), residues: 485 sheet: -0.65 (0.58), residues: 57 loop : -1.83 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.009 0.001 TYR A 554 PHE 0.018 0.001 PHE A 542 TRP 0.013 0.001 TRP A 219 HIS 0.009 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7575) covalent geometry : angle 0.64515 (10319) hydrogen bonds : bond 0.04148 ( 357) hydrogen bonds : angle 3.87345 ( 1047) link_BETA1-4 : bond 0.00670 ( 4) link_BETA1-4 : angle 2.10180 ( 12) link_NAG-ASN : bond 0.00657 ( 4) link_NAG-ASN : angle 4.04966 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 ASP cc_start: 0.7458 (m-30) cc_final: 0.7094 (t0) REVERT: A 515 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5854 (pm20) REVERT: B 92 CYS cc_start: 0.7250 (m) cc_final: 0.7020 (m) REVERT: B 103 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7913 (t80) REVERT: B 251 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6959 (mp) REVERT: B 271 TYR cc_start: 0.7994 (m-80) cc_final: 0.7547 (m-80) REVERT: B 387 TYR cc_start: 0.6984 (m-10) cc_final: 0.6531 (m-80) outliers start: 45 outliers final: 36 residues processed: 138 average time/residue: 0.0705 time to fit residues: 14.1993 Evaluate side-chains 142 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 259 TYR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 78 optimal weight: 0.0050 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.219930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158976 restraints weight = 8444.967| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.89 r_work: 0.3490 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7583 Z= 0.137 Angle : 0.659 10.890 10343 Z= 0.311 Chirality : 0.041 0.272 1215 Planarity : 0.004 0.061 1275 Dihedral : 7.236 76.496 1170 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 5.08 % Allowed : 31.98 % Favored : 62.94 % 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: 0.11 (0.28), residues: 930 helix: 1.51 (0.25), residues: 485 sheet: -0.47 (0.59), residues: 63 loop : -1.81 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.009 0.001 TYR A 554 PHE 0.026 0.001 PHE A 291 TRP 0.012 0.001 TRP A 219 HIS 0.008 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7575) covalent geometry : angle 0.64266 (10319) hydrogen bonds : bond 0.03959 ( 357) hydrogen bonds : angle 3.84842 ( 1047) link_BETA1-4 : bond 0.00659 ( 4) link_BETA1-4 : angle 2.08301 ( 12) link_NAG-ASN : bond 0.00621 ( 4) link_NAG-ASN : angle 3.91628 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 PHE cc_start: 0.7652 (m-80) cc_final: 0.7435 (m-80) REVERT: A 385 ASP cc_start: 0.7370 (m-30) cc_final: 0.6989 (t0) REVERT: A 515 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5815 (pm20) REVERT: B 103 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7906 (t80) REVERT: B 251 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7039 (mp) REVERT: B 271 TYR cc_start: 0.8010 (m-80) cc_final: 0.7518 (m-80) REVERT: B 387 TYR cc_start: 0.6927 (m-10) cc_final: 0.6616 (m-80) outliers start: 40 outliers final: 34 residues processed: 132 average time/residue: 0.0703 time to fit residues: 13.3916 Evaluate side-chains 139 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 259 TYR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 330 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 500 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 54 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.220848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.159731 restraints weight = 8466.954| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.94 r_work: 0.3566 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7583 Z= 0.129 Angle : 0.648 11.130 10343 Z= 0.306 Chirality : 0.041 0.270 1215 Planarity : 0.004 0.061 1275 Dihedral : 7.158 76.520 1170 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 5.08 % Allowed : 31.98 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.29), residues: 930 helix: 1.57 (0.25), residues: 485 sheet: -0.42 (0.61), residues: 63 loop : -1.79 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 440 TYR 0.009 0.001 TYR A 554 PHE 0.016 0.001 PHE A 542 TRP 0.011 0.001 TRP A 219 HIS 0.007 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7575) covalent geometry : angle 0.63237 (10319) hydrogen bonds : bond 0.03778 ( 357) hydrogen bonds : angle 3.78917 ( 1047) link_BETA1-4 : bond 0.00646 ( 4) link_BETA1-4 : angle 2.04298 ( 12) link_NAG-ASN : bond 0.00605 ( 4) link_NAG-ASN : angle 3.76744 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2016.60 seconds wall clock time: 35 minutes 12.62 seconds (2112.62 seconds total)