Starting phenix.real_space_refine on Tue Jan 14 11:42:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y32_38866/01_2025/8y32_38866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y32_38866/01_2025/8y32_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_38866/01_2025/8y32_38866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y32_38866/01_2025/8y32_38866.map" model { file = "/net/cci-nas-00/data/ceres_data/8y32_38866/01_2025/8y32_38866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y32_38866/01_2025/8y32_38866.cif" } resolution = 4.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.070 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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, 71 Unusual residues: {' CL': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 4.23, per 1000 atoms: 0.64 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: 1.66 Conformation dependent library (CDL) restraints added in 925.1 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: 0.48 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: 1.59 Time building geometry restraints manager: 1.90 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: 0.950 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.990 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 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 6759 Z= 0.301 Angle : 0.699 9.989 9174 Z= 0.365 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.30), 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 TRP 0.024 0.001 TRP A 202 HIS 0.004 0.001 HIS A 102 PHE 0.012 0.001 PHE B 429 TYR 0.009 0.001 TYR A 214 ARG 0.003 0.000 ARG A 66 *********************** 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 : 0.700 Fit side-chains REVERT: A 186 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: A 254 TYR cc_start: 0.7481 (m-80) cc_final: 0.7182 (m-10) REVERT: A 381 ASP cc_start: 0.6680 (t0) cc_final: 0.6434 (m-30) outliers start: 5 outliers final: 2 residues processed: 117 average time/residue: 0.1865 time to fit residues: 29.1099 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 : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.0570 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.0070 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.0030 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 overall best weight: 0.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 441 GLN B 439 ASN B 474 GLN B 477 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128880 restraints weight = 9848.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129215 restraints weight = 8035.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129259 restraints weight = 6569.438| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6759 Z= 0.162 Angle : 0.602 10.285 9174 Z= 0.293 Chirality : 0.045 0.493 970 Planarity : 0.005 0.063 1169 Dihedral : 10.459 104.392 1017 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.45 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.31), residues: 787 helix: 0.35 (0.29), residues: 356 sheet: -0.04 (0.77), residues: 47 loop : -1.72 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 167 HIS 0.002 0.001 HIS A 377 PHE 0.022 0.001 PHE A 511 TYR 0.018 0.001 TYR A 198 ARG 0.004 0.000 ARG A 176 *********************** 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 147 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6045 (tmm) cc_final: 0.5830 (tmm) REVERT: A 151 MET cc_start: 0.7084 (tpt) cc_final: 0.6647 (tpt) REVERT: A 164 TRP cc_start: 0.5474 (m100) cc_final: 0.5075 (m100) REVERT: A 254 TYR cc_start: 0.7134 (m-80) cc_final: 0.6894 (m-10) REVERT: A 340 LYS cc_start: 0.8431 (mmtm) cc_final: 0.7913 (mptt) REVERT: A 349 ASP cc_start: 0.6507 (t0) cc_final: 0.6234 (t0) REVERT: A 507 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6537 (mm-30) REVERT: B 346 ARG cc_start: 0.6929 (tpt-90) cc_final: 0.6713 (mtp85) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2192 time to fit residues: 41.4132 Evaluate side-chains 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122377 restraints weight = 10134.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122426 restraints weight = 10779.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122717 restraints weight = 7894.751| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6759 Z= 0.202 Angle : 0.603 9.451 9174 Z= 0.296 Chirality : 0.046 0.519 970 Planarity : 0.005 0.053 1169 Dihedral : 6.773 55.022 1017 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.21 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.31), residues: 787 helix: 0.32 (0.29), residues: 363 sheet: 0.08 (0.82), residues: 47 loop : -1.80 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 167 HIS 0.004 0.001 HIS A 240 PHE 0.011 0.001 PHE A 437 TYR 0.010 0.001 TYR A 198 ARG 0.002 0.000 ARG A 160 *********************** 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 136 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.5884 (tmm) cc_final: 0.5678 (tmm) REVERT: A 151 MET cc_start: 0.7374 (tpt) cc_final: 0.6786 (tpt) REVERT: A 164 TRP cc_start: 0.5534 (m100) cc_final: 0.5123 (m100) REVERT: A 237 GLU cc_start: 0.6534 (tt0) cc_final: 0.5968 (mt-10) REVERT: A 269 MET cc_start: 0.5740 (mmm) cc_final: 0.4865 (mmm) REVERT: A 340 LYS cc_start: 0.8530 (mmtm) cc_final: 0.8173 (mptt) REVERT: A 349 ASP cc_start: 0.6584 (t0) cc_final: 0.6333 (t0) REVERT: A 454 MET cc_start: 0.7155 (tpt) cc_final: 0.6837 (tpt) REVERT: A 479 MET cc_start: 0.7113 (ppp) cc_final: 0.6421 (ppp) REVERT: A 507 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6543 (mm-30) REVERT: B 366 SER cc_start: 0.6889 (m) cc_final: 0.6569 (m) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2087 time to fit residues: 37.0830 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 : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121095 restraints weight = 10229.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121100 restraints weight = 10273.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121294 restraints weight = 9021.742| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6759 Z= 0.187 Angle : 0.571 8.777 9174 Z= 0.285 Chirality : 0.045 0.515 970 Planarity : 0.004 0.050 1169 Dihedral : 6.214 50.551 1017 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.31), residues: 787 helix: 0.45 (0.29), residues: 363 sheet: 0.12 (0.83), residues: 47 loop : -1.80 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 605 HIS 0.007 0.001 HIS A 377 PHE 0.013 0.001 PHE A 591 TYR 0.010 0.001 TYR A 216 ARG 0.002 0.000 ARG A 66 *********************** 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 : 0.708 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.5924 (tmm) cc_final: 0.5690 (tmm) REVERT: A 133 LEU cc_start: 0.8034 (tp) cc_final: 0.7693 (tt) REVERT: A 164 TRP cc_start: 0.5759 (m100) cc_final: 0.5466 (m100) REVERT: A 269 MET cc_start: 0.5925 (mmm) cc_final: 0.5092 (mmm) REVERT: A 340 LYS cc_start: 0.8583 (mmtm) cc_final: 0.8186 (mmtm) REVERT: A 454 MET cc_start: 0.7084 (tpt) cc_final: 0.6561 (tpp) REVERT: A 479 MET cc_start: 0.7227 (ppp) cc_final: 0.6544 (ppp) REVERT: B 428 ASP cc_start: 0.8231 (p0) cc_final: 0.7977 (p0) REVERT: B 437 ASN cc_start: 0.8730 (t0) cc_final: 0.8416 (t0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1890 time to fit residues: 31.7368 Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121284 restraints weight = 10240.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121242 restraints weight = 13125.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121266 restraints weight = 10707.848| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6759 Z= 0.195 Angle : 0.596 10.856 9174 Z= 0.296 Chirality : 0.046 0.524 970 Planarity : 0.004 0.047 1169 Dihedral : 6.133 48.029 1017 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.59 % Favored : 94.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.31), residues: 787 helix: 0.47 (0.29), residues: 357 sheet: 0.18 (0.84), residues: 45 loop : -1.74 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 472 HIS 0.004 0.001 HIS A 240 PHE 0.018 0.001 PHE A 399 TYR 0.010 0.001 TYR A 216 ARG 0.003 0.000 ARG A 66 *********************** 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 128 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5893 (tmm) cc_final: 0.5672 (tmm) REVERT: A 133 LEU cc_start: 0.8048 (tp) cc_final: 0.7721 (tt) REVERT: A 152 GLU cc_start: 0.5881 (mt-10) cc_final: 0.5651 (mt-10) REVERT: A 269 MET cc_start: 0.5718 (mmm) cc_final: 0.5481 (mmm) REVERT: A 297 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6396 (mt-10) REVERT: A 300 SER cc_start: 0.8363 (m) cc_final: 0.8012 (p) REVERT: A 340 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8194 (mmtm) REVERT: A 349 ASP cc_start: 0.6566 (t0) cc_final: 0.6169 (t0) REVERT: A 473 MET cc_start: 0.7210 (mmt) cc_final: 0.6631 (mmt) REVERT: B 428 ASP cc_start: 0.8365 (p0) cc_final: 0.8029 (p0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1955 time to fit residues: 33.1384 Evaluate side-chains 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119422 restraints weight = 10096.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119467 restraints weight = 9699.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119540 restraints weight = 7631.358| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6759 Z= 0.194 Angle : 0.603 10.012 9174 Z= 0.298 Chirality : 0.046 0.516 970 Planarity : 0.004 0.042 1169 Dihedral : 6.018 46.153 1017 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.34 % Favored : 94.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.31), residues: 787 helix: 0.36 (0.29), residues: 364 sheet: 0.25 (0.83), residues: 45 loop : -1.87 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 605 HIS 0.004 0.001 HIS A 240 PHE 0.014 0.001 PHE A 591 TYR 0.010 0.001 TYR A 254 ARG 0.003 0.000 ARG A 66 *********************** 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 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.5973 (tmm) cc_final: 0.5669 (tmm) REVERT: A 152 GLU cc_start: 0.5929 (mt-10) cc_final: 0.5711 (mt-10) REVERT: A 164 TRP cc_start: 0.5533 (m100) cc_final: 0.5303 (m100) REVERT: A 237 GLU cc_start: 0.6575 (tt0) cc_final: 0.6120 (mt-10) REVERT: A 297 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6491 (mt-10) REVERT: A 340 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8200 (mmtm) REVERT: A 349 ASP cc_start: 0.6697 (t0) cc_final: 0.6260 (t0) REVERT: A 473 MET cc_start: 0.7233 (mmt) cc_final: 0.6549 (mmt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1821 time to fit residues: 30.4054 Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112784 restraints weight = 101927.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.114283 restraints weight = 74608.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114783 restraints weight = 56721.396| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6759 Z= 0.273 Angle : 0.676 11.859 9174 Z= 0.338 Chirality : 0.050 0.575 970 Planarity : 0.004 0.042 1169 Dihedral : 6.581 51.123 1017 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.35 % Favored : 93.39 % Rotamer: Outliers : 0.14 % Allowed : 1.73 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.30), residues: 787 helix: 0.14 (0.28), residues: 364 sheet: 0.04 (0.83), residues: 46 loop : -1.97 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 167 HIS 0.007 0.001 HIS A 240 PHE 0.019 0.002 PHE A 511 TYR 0.010 0.001 TYR B 453 ARG 0.003 0.000 ARG A 552 *********************** 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 128 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.6127 (tmm) cc_final: 0.5860 (tmm) REVERT: A 148 ASP cc_start: 0.6280 (t0) cc_final: 0.5365 (t0) REVERT: A 152 GLU cc_start: 0.6248 (mt-10) cc_final: 0.4954 (mt-10) REVERT: A 164 TRP cc_start: 0.5706 (m100) cc_final: 0.5051 (m100) REVERT: A 237 GLU cc_start: 0.6660 (tt0) cc_final: 0.6380 (mt-10) REVERT: A 269 MET cc_start: 0.5786 (mmm) cc_final: 0.5457 (tpp) REVERT: A 340 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8295 (mmtm) REVERT: A 428 HIS cc_start: 0.5951 (p-80) cc_final: 0.5711 (p-80) REVERT: A 473 MET cc_start: 0.7236 (mmt) cc_final: 0.6546 (mmt) REVERT: A 486 VAL cc_start: 0.8138 (t) cc_final: 0.7892 (m) REVERT: B 428 ASP cc_start: 0.8476 (p0) cc_final: 0.8238 (p0) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2008 time to fit residues: 33.6538 Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119577 restraints weight = 10098.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119561 restraints weight = 11028.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119901 restraints weight = 8664.875| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6759 Z= 0.201 Angle : 0.618 11.399 9174 Z= 0.305 Chirality : 0.047 0.537 970 Planarity : 0.004 0.039 1169 Dihedral : 6.292 48.477 1017 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.08 % Favored : 94.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.30), residues: 787 helix: 0.14 (0.28), residues: 365 sheet: 0.01 (0.82), residues: 46 loop : -1.88 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 167 HIS 0.004 0.001 HIS A 240 PHE 0.013 0.001 PHE A 591 TYR 0.012 0.001 TYR B 380 ARG 0.003 0.000 ARG A 66 *********************** 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 : 0.752 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.5934 (tmm) cc_final: 0.5632 (tmm) REVERT: A 148 ASP cc_start: 0.6281 (t0) cc_final: 0.5369 (t0) REVERT: A 152 GLU cc_start: 0.5709 (mt-10) cc_final: 0.4503 (mt-10) REVERT: A 237 GLU cc_start: 0.6459 (tt0) cc_final: 0.6122 (mt-10) REVERT: A 269 MET cc_start: 0.5866 (mmm) cc_final: 0.5583 (mmm) REVERT: A 340 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8218 (mmtm) REVERT: A 349 ASP cc_start: 0.6981 (t0) cc_final: 0.6713 (t0) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.1917 time to fit residues: 31.8987 Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.0010 chunk 59 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3358 r_free = 0.3358 target = 0.122555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120660 restraints weight = 10108.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120754 restraints weight = 10267.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.121044 restraints weight = 8469.712| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6759 Z= 0.179 Angle : 0.601 10.821 9174 Z= 0.297 Chirality : 0.045 0.505 970 Planarity : 0.004 0.046 1169 Dihedral : 5.904 42.577 1017 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.84 % Favored : 93.90 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.31), residues: 787 helix: 0.31 (0.29), residues: 360 sheet: 0.13 (0.82), residues: 46 loop : -1.81 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 301 HIS 0.004 0.001 HIS A 377 PHE 0.009 0.001 PHE A 539 TYR 0.015 0.001 TYR A 496 ARG 0.005 0.000 ARG A 160 *********************** 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 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6013 (tmm) cc_final: 0.5732 (tmm) REVERT: A 148 ASP cc_start: 0.6230 (t0) cc_final: 0.5758 (t0) REVERT: A 340 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8223 (mmtm) REVERT: A 472 TRP cc_start: 0.8585 (m-10) cc_final: 0.8035 (m-10) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1910 time to fit residues: 32.5724 Evaluate side-chains 120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS A 600 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 = 0.3369 r_free = 0.3369 target = 0.123318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122815 restraints weight = 10269.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122804 restraints weight = 11128.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122761 restraints weight = 8746.796| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6759 Z= 0.172 Angle : 0.602 11.028 9174 Z= 0.295 Chirality : 0.045 0.489 970 Planarity : 0.004 0.045 1169 Dihedral : 5.724 39.710 1017 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.21 % Favored : 94.54 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.30), residues: 787 helix: 0.28 (0.29), residues: 362 sheet: 0.15 (0.81), residues: 48 loop : -1.82 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 301 HIS 0.004 0.001 HIS A 377 PHE 0.013 0.001 PHE A 591 TYR 0.013 0.001 TYR A 496 ARG 0.004 0.000 ARG A 66 ********************** 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 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5987 (tmm) cc_final: 0.5690 (tmm) REVERT: A 133 LEU cc_start: 0.8138 (tp) cc_final: 0.7901 (tp) REVERT: A 148 ASP cc_start: 0.6379 (t0) cc_final: 0.5906 (t0) REVERT: A 164 TRP cc_start: 0.5542 (m100) cc_final: 0.4800 (m100) REVERT: A 340 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8241 (mmtm) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1965 time to fit residues: 33.3551 Evaluate side-chains 120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 60 optimal weight: 0.0270 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS A 600 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 = 0.3366 r_free = 0.3366 target = 0.123098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120681 restraints weight = 10294.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120918 restraints weight = 8980.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120944 restraints weight = 8075.190| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6759 Z= 0.173 Angle : 0.597 10.750 9174 Z= 0.295 Chirality : 0.045 0.473 970 Planarity : 0.004 0.046 1169 Dihedral : 5.551 36.651 1017 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.77 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.31), residues: 787 helix: 0.46 (0.29), residues: 354 sheet: 0.18 (0.81), residues: 48 loop : -1.75 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 301 HIS 0.004 0.001 HIS A 377 PHE 0.014 0.001 PHE A 399 TYR 0.009 0.001 TYR A 509 ARG 0.004 0.000 ARG A 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2099.29 seconds wall clock time: 38 minutes 49.57 seconds (2329.57 seconds total)