Starting phenix.real_space_refine on Tue Mar 11 19:29:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y32_38866/03_2025/8y32_38866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y32_38866/03_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_38866/03_2025/8y32_38866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y32_38866/03_2025/8y32_38866.map" model { file = "/net/cci-nas-00/data/ceres_data/8y32_38866/03_2025/8y32_38866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y32_38866/03_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-5624/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: 4.38, per 1000 atoms: 0.67 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: 1.48 Conformation dependent library (CDL) restraints added in 829.8 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: 0.61 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: 1.61 Time building geometry restraints manager: 1.76 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.460 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.100 ------------------------------------------------------------------------------- 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 : 0.749 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: 0.1859 time to fit residues: 29.1592 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 : 0.736 ------------------------------------------------------------------------------- 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 = 75)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128728 restraints weight = 9848.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128802 restraints weight = 8443.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128853 restraints weight = 7510.750| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 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 : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6052 (tmm) cc_final: 0.5837 (tmm) REVERT: A 151 MET cc_start: 0.7092 (tpt) cc_final: 0.6656 (tpt) REVERT: A 164 TRP cc_start: 0.5479 (m100) cc_final: 0.5066 (m100) REVERT: A 254 TYR cc_start: 0.7144 (m-80) cc_final: 0.6903 (m-10) REVERT: A 340 LYS cc_start: 0.8431 (mmtm) cc_final: 0.7911 (mptt) REVERT: A 349 ASP cc_start: 0.6509 (t0) cc_final: 0.6236 (t0) REVERT: A 507 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6534 (mm-30) REVERT: B 346 ARG cc_start: 0.6930 (tpt-90) cc_final: 0.6710 (mtp85) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2041 time to fit residues: 38.7496 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 : 0.658 ------------------------------------------------------------------------------- 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: 0.7980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120746 restraints weight = 10151.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.120939 restraints weight = 8648.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121087 restraints weight = 6731.908| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6759 Z= 0.226 Angle : 0.625 9.750 9174 Z= 0.309 Chirality : 0.047 0.527 970 Planarity : 0.005 0.053 1169 Dihedral : 7.005 57.588 1017 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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 (0.31), residues: 787 helix: 0.26 (0.29), residues: 363 sheet: 0.10 (0.83), residues: 47 loop : -1.84 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 301 HIS 0.005 0.001 HIS A 240 PHE 0.012 0.001 PHE A 399 TYR 0.011 0.001 TYR A 216 ARG 0.004 0.001 ARG A 305 *********************** 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 133 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5854 (tmm) cc_final: 0.5634 (tmm) REVERT: A 151 MET cc_start: 0.7416 (tpt) cc_final: 0.6819 (tpt) REVERT: A 164 TRP cc_start: 0.5591 (m100) cc_final: 0.5120 (m100) REVERT: A 237 GLU cc_start: 0.6614 (tt0) cc_final: 0.6034 (mt-10) REVERT: A 269 MET cc_start: 0.5819 (mmm) cc_final: 0.4919 (mmm) REVERT: A 340 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8178 (mptt) REVERT: A 349 ASP cc_start: 0.6564 (t0) cc_final: 0.6287 (t0) REVERT: A 454 MET cc_start: 0.7111 (tpt) cc_final: 0.6760 (tpt) REVERT: A 479 MET cc_start: 0.7117 (ppp) cc_final: 0.6420 (ppp) REVERT: A 507 GLU cc_start: 0.6693 (mm-30) cc_final: 0.6480 (mm-30) REVERT: B 428 ASP cc_start: 0.8193 (p0) cc_final: 0.7979 (p0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2026 time to fit residues: 34.9141 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 : 0.684 ------------------------------------------------------------------------------- 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: 3.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.118949 restraints weight = 10223.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119415 restraints weight = 7716.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119467 restraints weight = 5866.176| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6759 Z= 0.205 Angle : 0.588 9.310 9174 Z= 0.294 Chirality : 0.046 0.536 970 Planarity : 0.004 0.052 1169 Dihedral : 6.485 54.406 1017 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.59 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % 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 (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 (0.31), residues: 787 helix: 0.32 (0.29), residues: 363 sheet: 0.07 (0.82), residues: 47 loop : -1.86 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 605 HIS 0.007 0.001 HIS A 377 PHE 0.014 0.001 PHE A 591 TYR 0.011 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 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5945 (tmm) cc_final: 0.5674 (tmm) REVERT: A 133 LEU cc_start: 0.8042 (tp) cc_final: 0.7752 (tt) REVERT: A 164 TRP cc_start: 0.5754 (m100) cc_final: 0.5446 (m100) REVERT: A 269 MET cc_start: 0.5946 (mmm) cc_final: 0.5140 (mmm) REVERT: A 340 LYS cc_start: 0.8594 (mmtm) cc_final: 0.8213 (mmtm) REVERT: B 428 ASP cc_start: 0.8305 (p0) cc_final: 0.8049 (p0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1945 time to fit residues: 33.3228 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 : 0.680 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.0170 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 39 optimal weight: 0.0770 chunk 14 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.124400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122788 restraints weight = 10033.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122571 restraints weight = 12545.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122675 restraints weight = 10650.154| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6759 Z= 0.160 Angle : 0.572 10.449 9174 Z= 0.282 Chirality : 0.044 0.493 970 Planarity : 0.004 0.047 1169 Dihedral : 5.982 46.980 1017 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.08 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: -1.03 (0.31), residues: 787 helix: 0.31 (0.28), residues: 371 sheet: -0.00 (0.80), residues: 47 loop : -1.85 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 476 HIS 0.003 0.001 HIS A 377 PHE 0.017 0.001 PHE A 511 TYR 0.008 0.001 TYR A 216 ARG 0.003 0.000 ARG A 160 *********************** 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 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5890 (tmm) cc_final: 0.5582 (tmm) REVERT: A 133 LEU cc_start: 0.8060 (tp) cc_final: 0.7748 (tt) REVERT: A 304 GLU cc_start: 0.7116 (pm20) cc_final: 0.6813 (pm20) REVERT: A 340 LYS cc_start: 0.8630 (mmtm) cc_final: 0.8272 (mmtm) REVERT: A 454 MET cc_start: 0.7427 (tpp) cc_final: 0.6808 (tpp) REVERT: A 479 MET cc_start: 0.7544 (ppp) cc_final: 0.6849 (ppp) REVERT: B 428 ASP cc_start: 0.8319 (p0) cc_final: 0.7967 (p0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2233 time to fit residues: 37.6182 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 : 0.741 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.120142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117100 restraints weight = 10244.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117066 restraints weight = 10885.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117564 restraints weight = 8996.757| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6759 Z= 0.223 Angle : 0.620 10.269 9174 Z= 0.308 Chirality : 0.047 0.542 970 Planarity : 0.004 0.046 1169 Dihedral : 6.173 47.741 1017 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -1.11 (0.31), residues: 787 helix: 0.26 (0.28), residues: 369 sheet: 0.09 (0.82), residues: 45 loop : -1.91 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 167 HIS 0.006 0.001 HIS A 240 PHE 0.013 0.001 PHE A 399 TYR 0.011 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 125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.5946 (tmm) cc_final: 0.5657 (tmm) REVERT: A 152 GLU cc_start: 0.5836 (mt-10) cc_final: 0.5622 (mt-10) REVERT: A 164 TRP cc_start: 0.5591 (m100) cc_final: 0.5381 (m100) REVERT: A 237 GLU cc_start: 0.6676 (tt0) cc_final: 0.6189 (mt-10) REVERT: A 340 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8260 (mmtm) REVERT: A 473 MET cc_start: 0.7119 (mmt) cc_final: 0.6763 (mmt) REVERT: B 428 ASP cc_start: 0.8382 (p0) cc_final: 0.8073 (p0) REVERT: B 437 ASN cc_start: 0.8724 (t0) cc_final: 0.8502 (t0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1989 time to fit residues: 33.0486 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 : 0.795 ------------------------------------------------------------------------------- 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: 0.8980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 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 = 0.3348 r_free = 0.3348 target = 0.121695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114743 restraints weight = 101389.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.116528 restraints weight = 72992.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116749 restraints weight = 54493.041| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6759 Z= 0.198 Angle : 0.617 12.312 9174 Z= 0.305 Chirality : 0.046 0.528 970 Planarity : 0.004 0.042 1169 Dihedral : 6.096 46.806 1017 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.59 % Favored : 94.16 % 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: -1.12 (0.31), residues: 787 helix: 0.21 (0.28), residues: 370 sheet: -0.02 (0.81), residues: 46 loop : -1.86 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 167 HIS 0.004 0.001 HIS A 240 PHE 0.025 0.001 PHE A 511 TYR 0.013 0.001 TYR B 380 ARG 0.003 0.000 ARG A 160 *********************** 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 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.6052 (tmm) cc_final: 0.5791 (tmm) REVERT: A 164 TRP cc_start: 0.5594 (m100) cc_final: 0.3915 (m100) REVERT: A 237 GLU cc_start: 0.6686 (tt0) cc_final: 0.6340 (mt-10) REVERT: A 297 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6489 (mt-10) REVERT: A 340 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8256 (mmtm) REVERT: A 454 MET cc_start: 0.7405 (tpp) cc_final: 0.7032 (tpp) REVERT: A 473 MET cc_start: 0.7211 (mmt) cc_final: 0.6857 (mmt) REVERT: B 428 ASP cc_start: 0.8382 (p0) cc_final: 0.8180 (p0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1980 time to fit residues: 32.5773 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 : 0.788 ------------------------------------------------------------------------------- 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: 0.7980 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120141 restraints weight = 10237.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120136 restraints weight = 10161.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120143 restraints weight = 8497.204| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6759 Z= 0.183 Angle : 0.611 11.053 9174 Z= 0.298 Chirality : 0.045 0.509 970 Planarity : 0.004 0.047 1169 Dihedral : 5.922 43.593 1017 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -1.03 (0.30), residues: 787 helix: 0.32 (0.29), residues: 357 sheet: -0.02 (0.81), residues: 46 loop : -1.78 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 164 HIS 0.004 0.001 HIS A 377 PHE 0.013 0.001 PHE A 591 TYR 0.009 0.001 TYR A 157 ARG 0.004 0.000 ARG A 160 *********************** 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 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.5936 (tmm) cc_final: 0.5652 (tmm) REVERT: A 152 GLU cc_start: 0.6181 (mt-10) cc_final: 0.5976 (mt-10) REVERT: A 297 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6379 (mt-10) REVERT: A 340 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8224 (mmtm) REVERT: A 473 MET cc_start: 0.6882 (mmt) cc_final: 0.6582 (mmt) REVERT: B 437 ASN cc_start: 0.8711 (t0) cc_final: 0.8501 (t0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2063 time to fit residues: 35.3074 Evaluate side-chains 117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 chunk 59 optimal weight: 0.0770 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 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 = 0.3389 r_free = 0.3389 target = 0.124446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122303 restraints weight = 10048.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122287 restraints weight = 10524.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122293 restraints weight = 9131.672| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6759 Z= 0.165 Angle : 0.592 10.689 9174 Z= 0.291 Chirality : 0.044 0.466 970 Planarity : 0.004 0.039 1169 Dihedral : 5.568 38.038 1017 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.34 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -0.92 (0.31), residues: 787 helix: 0.38 (0.29), residues: 360 sheet: 0.05 (0.82), residues: 46 loop : -1.70 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 167 HIS 0.004 0.001 HIS A 377 PHE 0.012 0.001 PHE A 229 TYR 0.021 0.001 TYR A 453 ARG 0.004 0.000 ARG A 66 *********************** 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 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5990 (tmm) cc_final: 0.5683 (tmm) REVERT: A 340 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8206 (mmtm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2056 time to fit residues: 34.4019 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 : 0.738 ------------------------------------------------------------------------------- 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: 0.7980 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.0170 chunk 17 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121544 restraints weight = 10336.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121510 restraints weight = 11566.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121954 restraints weight = 8547.419| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6759 Z= 0.162 Angle : 0.578 11.149 9174 Z= 0.284 Chirality : 0.044 0.457 970 Planarity : 0.004 0.041 1169 Dihedral : 5.450 35.252 1017 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % 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: -0.81 (0.31), residues: 787 helix: 0.51 (0.29), residues: 352 sheet: 0.09 (0.81), residues: 48 loop : -1.65 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 167 HIS 0.004 0.001 HIS A 373 PHE 0.010 0.001 PHE A 591 TYR 0.017 0.001 TYR A 496 ARG 0.004 0.000 ARG A 481 ********************** 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 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.6134 (tmm) cc_final: 0.5903 (tmm) REVERT: A 164 TRP cc_start: 0.5262 (m100) cc_final: 0.4633 (m100) REVERT: A 237 GLU cc_start: 0.6382 (tt0) cc_final: 0.6110 (mt-10) REVERT: A 340 LYS cc_start: 0.8537 (mmtm) cc_final: 0.8171 (mmtm) REVERT: A 349 ASP cc_start: 0.6691 (t0) cc_final: 0.6218 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1826 time to fit residues: 31.6129 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 : 0.705 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 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 = 0.3339 r_free = 0.3339 target = 0.121137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120585 restraints weight = 10250.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120600 restraints weight = 10356.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.120536 restraints weight = 9248.050| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6759 Z= 0.205 Angle : 0.627 10.786 9174 Z= 0.311 Chirality : 0.046 0.485 970 Planarity : 0.004 0.043 1169 Dihedral : 5.659 36.731 1017 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -0.87 (0.31), residues: 787 helix: 0.41 (0.29), residues: 352 sheet: 0.15 (0.83), residues: 46 loop : -1.63 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 167 HIS 0.005 0.001 HIS A 377 PHE 0.018 0.001 PHE A 399 TYR 0.009 0.001 TYR B 495 ARG 0.004 0.000 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.57 seconds wall clock time: 39 minutes 20.96 seconds (2360.96 seconds total)