Starting phenix.real_space_refine on Thu Jul 2 04:10:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y32_38866/07_2026/8y32_38866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y32_38866/07_2026/8y32_38866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y32_38866/07_2026/8y32_38866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y32_38866/07_2026/8y32_38866.map" model { file = "/net/cci-nas-00/data/ceres_data/8y32_38866/07_2026/8y32_38866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y32_38866/07_2026/8y32_38866.cif" } resolution = 4.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.070 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 38 5.16 5 Cl 1 4.86 5 C 4207 2.51 5 N 1084 2.21 5 O 1241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6571 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4906 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 571} Chain: "B" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 70 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" 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 Time building chain proxies: 1.42, per 1000 atoms: 0.22 Number of scatterers: 6571 At special positions: 0 Unit cell: (93.09, 85.6, 126.26, 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 1 17.00 S 38 16.00 O 1241 8.00 N 1084 7.00 C 4207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG A 902 " - " ASN A 53 " " NAG A 903 " - " ASN A 90 " " NAG A 905 " - " ASN A 431 " " NAG A 906 " - " ASN A 545 " " NAG B 601 " - " ASN B 343 " " NAG B 602 " - " ASN B 354 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 353.0 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 50.9% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 37 through 51 removed outlier: 3.606A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.574A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 77 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.638A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 115 through 129 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 166 through 191 removed outlier: 4.681A pdb=" N GLY A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.717A pdb=" N VAL A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 217 through 229 removed outlier: 3.547A pdb=" N LEU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.519A pdb=" N HIS A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.564A pdb=" N ILE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 364 through 384 removed outlier: 3.911A pdb=" N TYR A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.576A pdb=" N ALA A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.763A pdb=" N THR A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.646A pdb=" N TRP A 476 " --> pdb=" O TRP A 472 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 511 through 532 removed outlier: 3.974A pdb=" N TYR A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.681A pdb=" N MET A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.556A pdb=" N ALA A 568 " --> pdb=" O PRO A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.651A pdb=" N TYR A 586 " --> pdb=" O PRO A 582 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 removed outlier: 3.589A pdb=" N GLU A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.009A pdb=" N GLU B 340 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.960A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.613A pdb=" N ALA B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.508A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 262 removed outlier: 6.223A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.553A pdb=" N LYS A 358 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 356 " --> pdb=" O TRP A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.199A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.512A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.618A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 240 hydrogen bonds defined for protein. 672 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: 0.81 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2063 1.34 - 1.46: 1758 1.46 - 1.58: 2878 1.58 - 1.71: 0 1.71 - 1.83: 60 Bond restraints: 6759 Sorted by residual: bond pdb=" C TYR A 83 " pdb=" N SER A 84 " ideal model delta sigma weight residual 1.330 1.450 -0.120 1.31e-02 5.83e+03 8.41e+01 bond pdb=" C THR A 82 " pdb=" N TYR A 83 " ideal model delta sigma weight residual 1.331 1.433 -0.103 1.45e-02 4.76e+03 5.04e+01 bond pdb=" C TYR B 489 " pdb=" N PHE B 490 " ideal model delta sigma weight residual 1.331 1.417 -0.087 1.24e-02 6.50e+03 4.90e+01 bond pdb=" C CYS B 488 " pdb=" N TYR B 489 " ideal model delta sigma weight residual 1.329 1.244 0.085 1.76e-02 3.23e+03 2.35e+01 bond pdb=" C4 NAG B 602 " pdb=" C5 NAG B 602 " ideal model delta sigma weight residual 1.532 1.499 0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 6754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8988 2.00 - 4.00: 137 4.00 - 5.99: 33 5.99 - 7.99: 12 7.99 - 9.99: 4 Bond angle restraints: 9174 Sorted by residual: angle pdb=" CA TYR B 489 " pdb=" C TYR B 489 " pdb=" N PHE B 490 " ideal model delta sigma weight residual 115.90 123.10 -7.20 1.21e+00 6.83e-01 3.54e+01 angle pdb=" O TYR B 489 " pdb=" C TYR B 489 " pdb=" N PHE B 490 " ideal model delta sigma weight residual 122.59 115.19 7.40 1.35e+00 5.49e-01 3.01e+01 angle pdb=" C TYR B 489 " pdb=" N PHE B 490 " pdb=" CA PHE B 490 " ideal model delta sigma weight residual 122.65 131.50 -8.85 1.66e+00 3.63e-01 2.84e+01 angle pdb=" CA TYR A 83 " pdb=" C TYR A 83 " pdb=" N SER A 84 " ideal model delta sigma weight residual 116.24 122.20 -5.96 1.34e+00 5.57e-01 1.98e+01 angle pdb=" O TYR A 83 " pdb=" C TYR A 83 " pdb=" N SER A 84 " ideal model delta sigma weight residual 123.01 117.19 5.82 1.33e+00 5.65e-01 1.92e+01 ... (remaining 9169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.99: 3601 24.99 - 49.98: 402 49.98 - 74.97: 43 74.97 - 99.97: 16 99.97 - 124.96: 17 Dihedral angle restraints: 4079 sinusoidal: 1747 harmonic: 2332 Sorted by residual: dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 19.38 73.62 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -15.16 -70.84 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 130.34 -37.34 1 1.00e+01 1.00e-02 1.97e+01 ... (remaining 4076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 948 0.106 - 0.212: 21 0.212 - 0.318: 0 0.318 - 0.424: 0 0.424 - 0.530: 1 Chirality restraints: 970 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 354 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CB ILE A 255 " pdb=" CA ILE A 255 " pdb=" CG1 ILE A 255 " pdb=" CG2 ILE A 255 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 967 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " 0.308 2.00e-02 2.50e+03 2.69e-01 9.06e+02 pdb=" C7 NAG B 601 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " 0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.151 2.00e-02 2.50e+03 1.25e-01 1.95e+02 pdb=" C7 NAG B 602 " -0.043 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.113 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.200 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 424 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 425 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.049 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 111 2.68 - 3.23: 6195 3.23 - 3.79: 9673 3.79 - 4.34: 12784 4.34 - 4.90: 20995 Nonbonded interactions: 49758 Sorted by model distance: nonbonded pdb=" NE ARG A 339 " pdb=" O7 NAG A 902 " model vdw 2.120 2.496 nonbonded pdb=" OD2 ASP A 542 " pdb=" OG SER A 544 " model vdw 2.219 3.040 nonbonded pdb=" OE1 GLN A 238 " pdb=" ND2 ASN A 598 " model vdw 2.250 3.120 nonbonded pdb=" ND1 HIS B 339 " pdb=" OE1 GLU B 340 " model vdw 2.261 3.120 nonbonded pdb=" O ASP A 366 " pdb=" OG1 THR A 370 " model vdw 2.278 3.040 ... (remaining 49753 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.020 Set scattering table: 0.010 Process input model: 6.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.004 0.120 6771 Z= 0.239 Angle : 0.752 14.903 9202 Z= 0.377 Chirality : 0.046 0.530 970 Planarity : 0.010 0.269 1169 Dihedral : 21.050 124.957 2568 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.48 % Favored : 93.27 % Rotamer: Outliers : 0.72 % Allowed : 33.29 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.30), residues: 787 helix: 0.33 (0.29), residues: 346 sheet: 0.80 (0.89), residues: 36 loop : -1.87 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.009 0.001 TYR A 214 PHE 0.012 0.001 PHE B 429 TRP 0.024 0.001 TRP A 202 HIS 0.004 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.24 ( 6759) covalent geometry : angle 0.69917 / 0.37 ( 9174) SS BOND : bond 0.00475 / 0.24 ( 5) SS BOND : angle 0.91527 / 0.54 ( 10) hydrogen bonds : bond 0.15987 / 10.78 ( 240) hydrogen bonds : angle 5.85350 / 4.08 ( 672) Misc. bond : bond 0.00014 / 0.01 ( 1) link_NAG-ASN : bond 0.01782 / 0.96 ( 6) link_NAG-ASN : angle 6.26698 / 4.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.229 Fit side-chains REVERT: A 186 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: A 254 TYR cc_start: 0.7481 (m-80) cc_final: 0.7184 (m-10) REVERT: A 381 ASP cc_start: 0.6680 (t0) cc_final: 0.6170 (m-30) outliers start: 5 outliers final: 2 residues processed: 117 average time/residue: 0.0669 time to fit residues: 10.6742 Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN A 441 GLN B 422 ASN B 439 ASN B 474 GLN B 477 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121708 restraints weight = 10012.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122037 restraints weight = 8282.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122160 restraints weight = 6670.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122234 restraints weight = 6273.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122270 restraints weight = 5838.095| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6771 Z= 0.152 Angle : 0.688 15.681 9202 Z= 0.330 Chirality : 0.048 0.540 970 Planarity : 0.005 0.065 1169 Dihedral : 11.007 104.109 1017 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.03 % Rotamer: Outliers : 0.14 % Allowed : 3.03 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.19 (0.31), residues: 787 helix: 0.13 (0.29), residues: 360 sheet: -0.11 (0.78), residues: 47 loop : -1.82 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 176 TYR 0.016 0.001 TYR A 198 PHE 0.019 0.002 PHE A 511 TRP 0.020 0.002 TRP A 167 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 6759) covalent geometry : angle 0.65263 / 0.32 ( 9174) SS BOND : bond 0.00671 / 0.35 ( 5) SS BOND : angle 1.96549 / 1.06 ( 10) hydrogen bonds : bond 0.04083 / 2.65 ( 240) hydrogen bonds : angle 4.61785 / 3.25 ( 672) Misc. bond : bond 0.00028 / 0.01 ( 1) link_NAG-ASN : bond 0.01124 / 0.59 ( 6) link_NAG-ASN : angle 4.77106 / 3.75 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.7373 (tpt) cc_final: 0.6948 (tpp) REVERT: A 237 GLU cc_start: 0.6616 (tt0) cc_final: 0.6141 (tt0) REVERT: A 301 TRP cc_start: 0.6777 (t60) cc_final: 0.6261 (t60) REVERT: A 340 LYS cc_start: 0.8568 (mmtm) cc_final: 0.7984 (mptt) REVERT: A 507 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6521 (mm-30) REVERT: B 346 ARG cc_start: 0.6992 (tpt-90) cc_final: 0.6573 (mtp85) REVERT: B 378 LYS cc_start: 0.8158 (pttt) cc_final: 0.7851 (ptmm) outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.0813 time to fit residues: 15.0761 Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120846 restraints weight = 10063.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121424 restraints weight = 7571.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121683 restraints weight = 5855.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121794 restraints weight = 5092.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121814 restraints weight = 4528.170| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6771 Z= 0.128 Angle : 0.637 14.485 9202 Z= 0.307 Chirality : 0.046 0.528 970 Planarity : 0.004 0.054 1169 Dihedral : 7.280 61.849 1017 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.14 (0.30), residues: 787 helix: 0.21 (0.29), residues: 359 sheet: -0.05 (0.79), residues: 47 loop : -1.84 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 339 TYR 0.010 0.001 TYR A 216 PHE 0.032 0.001 PHE A 437 TRP 0.016 0.002 TRP A 164 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 6759) covalent geometry : angle 0.60449 / 0.30 ( 9174) SS BOND : bond 0.00500 / 0.25 ( 5) SS BOND : angle 1.47672 / 0.83 ( 10) hydrogen bonds : bond 0.03553 / 2.32 ( 240) hydrogen bonds : angle 4.25042 / 3.01 ( 672) Misc. bond : bond 0.00051 / 0.03 ( 1) link_NAG-ASN : bond 0.00945 / 0.49 ( 6) link_NAG-ASN : angle 4.48468 / 3.50 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8581 (mmtm) cc_final: 0.8225 (mptt) REVERT: A 454 MET cc_start: 0.7155 (tpt) cc_final: 0.6784 (tpt) REVERT: A 479 MET cc_start: 0.7148 (ppp) cc_final: 0.6589 (ppp) REVERT: B 437 ASN cc_start: 0.8796 (t0) cc_final: 0.8511 (t0) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0764 time to fit residues: 13.1508 Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.0770 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 GLN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122076 restraints weight = 10234.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122075 restraints weight = 10154.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122073 restraints weight = 9786.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122073 restraints weight = 8447.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122073 restraints weight = 8447.252| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6771 Z= 0.106 Angle : 0.578 13.368 9202 Z= 0.280 Chirality : 0.044 0.493 970 Planarity : 0.004 0.050 1169 Dihedral : 6.137 49.793 1017 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.34 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.97 (0.31), residues: 787 helix: 0.35 (0.29), residues: 360 sheet: 0.02 (0.78), residues: 47 loop : -1.74 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.009 0.001 TYR A 216 PHE 0.021 0.001 PHE A 437 TRP 0.016 0.001 TRP A 472 HIS 0.007 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 ( 6759) covalent geometry : angle 0.54908 / 0.27 ( 9174) SS BOND : bond 0.00378 / 0.19 ( 5) SS BOND : angle 1.18602 / 0.67 ( 10) hydrogen bonds : bond 0.03162 / 2.04 ( 240) hydrogen bonds : angle 4.03962 / 2.85 ( 672) Misc. bond : bond 0.00016 / 0.01 ( 1) link_NAG-ASN : bond 0.00905 / 0.47 ( 6) link_NAG-ASN : angle 4.05541 / 3.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5925 (tmm) cc_final: 0.5645 (tmm) REVERT: A 133 LEU cc_start: 0.8011 (tp) cc_final: 0.7644 (tt) REVERT: A 340 LYS cc_start: 0.8622 (mmtm) cc_final: 0.8215 (mmtm) REVERT: A 349 ASP cc_start: 0.6781 (t0) cc_final: 0.6356 (t0) REVERT: A 454 MET cc_start: 0.7084 (tpt) cc_final: 0.6682 (tpp) REVERT: A 479 MET cc_start: 0.7028 (ppp) cc_final: 0.6276 (ppp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0634 time to fit residues: 10.7154 Evaluate side-chains 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111487 restraints weight = 10548.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111814 restraints weight = 8736.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111822 restraints weight = 8036.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112014 restraints weight = 7277.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112003 restraints weight = 6963.452| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 6771 Z= 0.288 Angle : 0.820 16.148 9202 Z= 0.410 Chirality : 0.055 0.603 970 Planarity : 0.005 0.054 1169 Dihedral : 7.828 65.633 1017 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.37 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.89 (0.29), residues: 787 helix: -0.49 (0.27), residues: 372 sheet: -0.13 (0.81), residues: 45 loop : -2.23 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 552 TYR 0.016 0.002 TYR B 453 PHE 0.023 0.002 PHE A 399 TRP 0.036 0.003 TRP A 605 HIS 0.012 0.002 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.29 ( 6759) covalent geometry : angle 0.78578 / 0.40 ( 9174) SS BOND : bond 0.00549 / 0.29 ( 5) SS BOND : angle 1.41519 / 0.82 ( 10) hydrogen bonds : bond 0.05604 / 3.70 ( 240) hydrogen bonds : angle 4.73531 / 3.38 ( 672) Misc. bond : bond 0.00040 / 0.02 ( 1) link_NAG-ASN : bond 0.01404 / 0.74 ( 6) link_NAG-ASN : angle 5.30137 / 4.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 TRP cc_start: 0.5901 (m100) cc_final: 0.5520 (m100) REVERT: A 340 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8362 (mmtm) REVERT: A 409 LEU cc_start: 0.8548 (tt) cc_final: 0.8190 (tp) REVERT: A 428 HIS cc_start: 0.5842 (p-80) cc_final: 0.5615 (p-80) REVERT: A 479 MET cc_start: 0.7330 (ppp) cc_final: 0.7081 (ppp) REVERT: B 439 ASN cc_start: 0.7126 (t0) cc_final: 0.6894 (t0) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0649 time to fit residues: 11.7060 Evaluate side-chains 112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 HIS A 400 HIS A 441 GLN A 585 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117445 restraints weight = 10377.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117287 restraints weight = 12665.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117807 restraints weight = 10058.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117946 restraints weight = 5741.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118301 restraints weight = 4318.759| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6771 Z= 0.129 Angle : 0.662 14.977 9202 Z= 0.323 Chirality : 0.047 0.553 970 Planarity : 0.004 0.042 1169 Dihedral : 6.793 57.580 1017 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.59 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.52 (0.30), residues: 787 helix: -0.20 (0.28), residues: 377 sheet: 0.10 (0.82), residues: 44 loop : -2.04 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.011 0.001 TYR B 380 PHE 0.028 0.002 PHE A 511 TRP 0.020 0.002 TRP A 167 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6759) covalent geometry : angle 0.62908 / 0.31 ( 9174) SS BOND : bond 0.00488 / 0.25 ( 5) SS BOND : angle 2.07689 / 1.14 ( 10) hydrogen bonds : bond 0.03757 / 2.41 ( 240) hydrogen bonds : angle 4.26897 / 3.06 ( 672) Misc. bond : bond 0.00007 / 0.00 ( 1) link_NAG-ASN : bond 0.00990 / 0.52 ( 6) link_NAG-ASN : angle 4.49416 / 3.53 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.7550 (tpt) cc_final: 0.7276 (tpt) REVERT: A 164 TRP cc_start: 0.6008 (m100) cc_final: 0.5403 (m100) REVERT: A 304 GLU cc_start: 0.6935 (pm20) cc_final: 0.6713 (pm20) REVERT: A 340 LYS cc_start: 0.8574 (mmtm) cc_final: 0.8265 (mmtm) REVERT: A 409 LEU cc_start: 0.8540 (tt) cc_final: 0.8279 (tp) REVERT: A 428 HIS cc_start: 0.5669 (p-80) cc_final: 0.5464 (p-80) REVERT: B 367 VAL cc_start: 0.8307 (p) cc_final: 0.7907 (p) REVERT: B 428 ASP cc_start: 0.8384 (p0) cc_final: 0.8161 (p0) REVERT: B 481 LYS cc_start: 0.7229 (mmtp) cc_final: 0.7024 (tmmt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0726 time to fit residues: 12.5213 Evaluate side-chains 116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117828 restraints weight = 10183.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116434 restraints weight = 11287.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116475 restraints weight = 8817.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116761 restraints weight = 8568.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.116910 restraints weight = 6336.859| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6771 Z= 0.160 Angle : 0.685 14.861 9202 Z= 0.336 Chirality : 0.049 0.569 970 Planarity : 0.004 0.043 1169 Dihedral : 6.751 55.108 1017 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.61 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.57 (0.30), residues: 787 helix: -0.20 (0.28), residues: 377 sheet: 0.10 (0.81), residues: 46 loop : -2.12 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.015 0.001 TYR A 182 PHE 0.021 0.002 PHE A 399 TRP 0.023 0.002 TRP A 167 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 6759) covalent geometry : angle 0.65228 / 0.33 ( 9174) SS BOND : bond 0.00592 / 0.30 ( 5) SS BOND : angle 2.03330 / 1.10 ( 10) hydrogen bonds : bond 0.04072 / 2.63 ( 240) hydrogen bonds : angle 4.29355 / 3.06 ( 672) Misc. bond : bond 0.00024 / 0.01 ( 1) link_NAG-ASN : bond 0.01065 / 0.56 ( 6) link_NAG-ASN : angle 4.57105 / 3.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5695 (tmm) cc_final: 0.5067 (tmm) REVERT: A 133 LEU cc_start: 0.8203 (tp) cc_final: 0.7928 (tt) REVERT: A 151 MET cc_start: 0.7626 (tpt) cc_final: 0.7308 (tpt) REVERT: A 164 TRP cc_start: 0.6058 (m100) cc_final: 0.5359 (m100) REVERT: A 297 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6592 (mt-10) REVERT: A 340 LYS cc_start: 0.8569 (mmtm) cc_final: 0.8277 (mmtm) REVERT: A 349 ASP cc_start: 0.7415 (m-30) cc_final: 0.6853 (t0) REVERT: A 409 LEU cc_start: 0.8571 (tt) cc_final: 0.8307 (tp) REVERT: B 481 LYS cc_start: 0.7198 (mmtp) cc_final: 0.6993 (tmmt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0784 time to fit residues: 13.6185 Evaluate side-chains 119 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 0.0170 chunk 73 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 HIS B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119789 restraints weight = 10090.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119789 restraints weight = 7977.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119789 restraints weight = 7970.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119789 restraints weight = 7970.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119789 restraints weight = 7970.292| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6771 Z= 0.117 Angle : 0.628 13.534 9202 Z= 0.307 Chirality : 0.046 0.512 970 Planarity : 0.004 0.040 1169 Dihedral : 6.098 46.863 1017 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.03 % Rotamer: Outliers : 0.14 % Allowed : 0.72 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.27 (0.31), residues: 787 helix: 0.07 (0.29), residues: 367 sheet: 0.02 (0.80), residues: 47 loop : -1.93 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.011 0.001 TYR B 380 PHE 0.013 0.001 PHE A 437 TRP 0.019 0.001 TRP A 605 HIS 0.005 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6759) covalent geometry : angle 0.59932 / 0.30 ( 9174) SS BOND : bond 0.00459 / 0.23 ( 5) SS BOND : angle 2.01247 / 1.09 ( 10) hydrogen bonds : bond 0.03297 / 2.13 ( 240) hydrogen bonds : angle 4.10990 / 2.93 ( 672) Misc. bond : bond 0.00013 / 0.01 ( 1) link_NAG-ASN : bond 0.00900 / 0.47 ( 6) link_NAG-ASN : angle 4.05713 / 3.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5793 (tmm) cc_final: 0.5130 (tmm) REVERT: A 151 MET cc_start: 0.7587 (tpt) cc_final: 0.7331 (tpt) REVERT: A 164 TRP cc_start: 0.6042 (m100) cc_final: 0.5415 (m100) REVERT: A 340 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8251 (mmtm) REVERT: A 349 ASP cc_start: 0.7325 (m-30) cc_final: 0.6813 (t0) REVERT: B 481 LYS cc_start: 0.7167 (mmtp) cc_final: 0.6956 (tmmt) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.0756 time to fit residues: 12.6447 Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 HIS B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121224 restraints weight = 10254.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119241 restraints weight = 17239.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.119458 restraints weight = 13381.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119559 restraints weight = 10320.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119595 restraints weight = 8913.168| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6771 Z= 0.115 Angle : 0.619 12.950 9202 Z= 0.304 Chirality : 0.045 0.500 970 Planarity : 0.004 0.046 1169 Dihedral : 5.811 42.348 1017 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.03 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.16 (0.31), residues: 787 helix: 0.12 (0.29), residues: 368 sheet: 0.09 (0.80), residues: 47 loop : -1.83 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.009 0.001 TYR B 380 PHE 0.036 0.001 PHE A 511 TRP 0.017 0.001 TRP A 605 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 6759) covalent geometry : angle 0.59219 / 0.30 ( 9174) SS BOND : bond 0.00405 / 0.21 ( 5) SS BOND : angle 1.95472 / 1.06 ( 10) hydrogen bonds : bond 0.03314 / 2.13 ( 240) hydrogen bonds : angle 4.06622 / 2.92 ( 672) Misc. bond : bond 0.00019 / 0.01 ( 1) link_NAG-ASN : bond 0.00871 / 0.45 ( 6) link_NAG-ASN : angle 3.89177 / 3.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5872 (tmm) cc_final: 0.5136 (tmm) REVERT: A 148 ASP cc_start: 0.7384 (t0) cc_final: 0.5529 (t0) REVERT: A 151 MET cc_start: 0.7659 (tpt) cc_final: 0.7384 (tpt) REVERT: A 164 TRP cc_start: 0.5901 (m100) cc_final: 0.5373 (m100) REVERT: A 340 LYS cc_start: 0.8579 (mmtm) cc_final: 0.8246 (mmtm) REVERT: A 349 ASP cc_start: 0.7247 (m-30) cc_final: 0.6728 (t0) REVERT: B 481 LYS cc_start: 0.7141 (mmtp) cc_final: 0.6924 (tmmt) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.0743 time to fit residues: 12.1440 Evaluate side-chains 114 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 HIS A 585 ASN B 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119724 restraints weight = 10177.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118324 restraints weight = 12777.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.118710 restraints weight = 9351.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118792 restraints weight = 7851.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118954 restraints weight = 6574.480| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6771 Z= 0.132 Angle : 0.643 13.166 9202 Z= 0.314 Chirality : 0.047 0.522 970 Planarity : 0.004 0.046 1169 Dihedral : 5.867 42.927 1017 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.21 % Favored : 94.54 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.20 (0.31), residues: 787 helix: 0.11 (0.29), residues: 370 sheet: 0.09 (0.81), residues: 47 loop : -1.89 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.008 0.001 TYR B 495 PHE 0.012 0.001 PHE A 399 TRP 0.023 0.002 TRP A 605 HIS 0.005 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 6759) covalent geometry : angle 0.61717 / 0.31 ( 9174) SS BOND : bond 0.00435 / 0.22 ( 5) SS BOND : angle 1.51564 / 0.82 ( 10) hydrogen bonds : bond 0.03533 / 2.29 ( 240) hydrogen bonds : angle 4.11493 / 2.94 ( 672) Misc. bond : bond 0.00023 / 0.01 ( 1) link_NAG-ASN : bond 0.00923 / 0.48 ( 6) link_NAG-ASN : angle 3.99054 / 3.12 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5814 (tmm) cc_final: 0.5088 (tmm) REVERT: A 153 ASN cc_start: 0.5995 (p0) cc_final: 0.5786 (p0) REVERT: A 179 TYR cc_start: 0.7273 (t80) cc_final: 0.7065 (t80) REVERT: A 340 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8314 (mmtm) REVERT: A 507 GLU cc_start: 0.6698 (tp30) cc_final: 0.6457 (mm-30) REVERT: B 481 LYS cc_start: 0.7179 (mmtp) cc_final: 0.6953 (tmmt) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.0633 time to fit residues: 10.5024 Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 15 optimal weight: 0.0370 chunk 39 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 400 HIS A 585 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123958 restraints weight = 10069.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123954 restraints weight = 10851.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123950 restraints weight = 11011.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123949 restraints weight = 10343.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123947 restraints weight = 10169.858| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6771 Z= 0.099 Angle : 0.575 11.124 9202 Z= 0.283 Chirality : 0.043 0.440 970 Planarity : 0.004 0.043 1169 Dihedral : 5.322 34.799 1017 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.34 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.99 (0.31), residues: 787 helix: 0.27 (0.29), residues: 370 sheet: 0.49 (0.80), residues: 44 loop : -1.80 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 66 TYR 0.016 0.001 TYR A 496 PHE 0.012 0.001 PHE A 437 TRP 0.038 0.002 TRP A 164 HIS 0.006 0.001 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 6759) covalent geometry : angle 0.55471 / 0.28 ( 9174) SS BOND : bond 0.00317 / 0.16 ( 5) SS BOND : angle 1.29458 / 0.71 ( 10) hydrogen bonds : bond 0.02799 / 1.79 ( 240) hydrogen bonds : angle 3.93404 / 2.81 ( 672) Misc. bond : bond 0.00015 / 0.01 ( 1) link_NAG-ASN : bond 0.00734 / 0.38 ( 6) link_NAG-ASN : angle 3.34478 / 2.63 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 996.14 seconds wall clock time: 17 minutes 54.26 seconds (1074.26 seconds total)