Starting phenix.real_space_refine on Sat May 10 16:25:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y32_38866/05_2025/8y32_38866.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y32_38866/05_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_38866/05_2025/8y32_38866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y32_38866/05_2025/8y32_38866.map" model { file = "/net/cci-nas-00/data/ceres_data/8y32_38866/05_2025/8y32_38866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y32_38866/05_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-5687/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: 4.10, per 1000 atoms: 0.62 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: 1.64 Conformation dependent library (CDL) restraints added in 857.8 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: 0.65 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: 1.46 Time building geometry restraints manager: 1.86 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.220 Find NCS groups from input model: 0.070 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- 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 6771 Z= 0.239 Angle : 0.752 14.903 9202 Z= 0.377 Chirality : 0.046 0.530 970 Planarity : 0.010 0.269 1169 Dihedral : 21.050 124.957 2568 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.48 % Favored : 93.27 % Rotamer: Outliers : 0.72 % Allowed : 33.29 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.01782 ( 6) link_NAG-ASN : angle 6.26698 ( 18) hydrogen bonds : bond 0.15987 ( 240) hydrogen bonds : angle 5.85350 ( 672) SS BOND : bond 0.00475 ( 5) SS BOND : angle 0.91527 ( 10) covalent geometry : bond 0.00426 ( 6759) covalent geometry : angle 0.69917 ( 9174) Misc. bond : bond 0.00014 ( 1) *********************** 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 : 0.752 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: 0.1793 time to fit residues: 28.1432 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 : 0.651 ------------------------------------------------------------------------------- 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: 0.9980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.0000 chunk 61 optimal weight: 3.9990 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: 0.3572 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.129249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126296 restraints weight = 9864.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126637 restraints weight = 8200.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127162 restraints weight = 7016.253| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6771 Z= 0.114 Angle : 0.645 14.540 9202 Z= 0.306 Chirality : 0.046 0.511 970 Planarity : 0.005 0.063 1169 Dihedral : 10.958 106.722 1017 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.96 % Favored : 94.79 % 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: -1.01 (0.31), residues: 787 helix: 0.28 (0.29), residues: 361 sheet: -0.06 (0.77), residues: 47 loop : -1.72 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 167 HIS 0.003 0.001 HIS A 240 PHE 0.023 0.001 PHE A 511 TYR 0.020 0.001 TYR A 198 ARG 0.004 0.000 ARG A 176 Details of bonding type rmsd link_NAG-ASN : bond 0.01006 ( 6) link_NAG-ASN : angle 4.35610 ( 18) hydrogen bonds : bond 0.03489 ( 240) hydrogen bonds : angle 4.45457 ( 672) SS BOND : bond 0.00446 ( 5) SS BOND : angle 1.87623 ( 10) covalent geometry : bond 0.00255 ( 6759) covalent geometry : angle 0.61353 ( 9174) Misc. bond : bond 0.00034 ( 1) *********************** 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 145 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5975 (tmm) cc_final: 0.5695 (tmm) REVERT: A 151 MET cc_start: 0.7139 (tpt) cc_final: 0.6545 (tpt) REVERT: A 164 TRP cc_start: 0.5530 (m100) cc_final: 0.5102 (m100) REVERT: A 301 TRP cc_start: 0.6590 (t60) cc_final: 0.6345 (t60) REVERT: A 340 LYS cc_start: 0.8466 (mmtm) cc_final: 0.7949 (mptt) REVERT: A 362 LYS cc_start: 0.6686 (tttm) cc_final: 0.6458 (ttpp) REVERT: A 507 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6475 (mm-30) REVERT: B 346 ARG cc_start: 0.6960 (tpt-90) cc_final: 0.6742 (mtp85) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2041 time to fit residues: 38.2074 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 : 0.650 ------------------------------------------------------------------------------- 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: 0.8980 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 0.0040 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 373 HIS A 598 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119347 restraints weight = 10228.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.119428 restraints weight = 10233.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119893 restraints weight = 8136.884| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 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 : 0.003 0.066 6771 Z= 0.152 Angle : 0.657 14.688 9202 Z= 0.317 Chirality : 0.047 0.534 970 Planarity : 0.005 0.059 1169 Dihedral : 7.344 60.556 1017 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.77 % Rotamer: Outliers : 0.29 % Allowed : 2.88 % 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: -1.12 (0.31), residues: 787 helix: 0.29 (0.29), residues: 361 sheet: 0.03 (0.82), residues: 47 loop : -1.92 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 167 HIS 0.006 0.001 HIS A 373 PHE 0.011 0.001 PHE A 399 TYR 0.011 0.001 TYR A 216 ARG 0.003 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.01056 ( 6) link_NAG-ASN : angle 4.66120 ( 18) hydrogen bonds : bond 0.03911 ( 240) hydrogen bonds : angle 4.34548 ( 672) SS BOND : bond 0.00540 ( 5) SS BOND : angle 1.52494 ( 10) covalent geometry : bond 0.00348 ( 6759) covalent geometry : angle 0.62295 ( 9174) Misc. bond : bond 0.00063 ( 1) *********************** 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 134 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.5802 (tmm) cc_final: 0.5564 (tmm) REVERT: A 164 TRP cc_start: 0.5677 (m100) cc_final: 0.5462 (m100) REVERT: A 237 GLU cc_start: 0.6564 (tt0) cc_final: 0.6077 (mt-10) REVERT: A 269 MET cc_start: 0.5741 (mmm) cc_final: 0.4723 (mmm) REVERT: A 340 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8179 (mptt) REVERT: A 454 MET cc_start: 0.7075 (tpt) cc_final: 0.6669 (tpp) REVERT: A 479 MET cc_start: 0.7160 (ppp) cc_final: 0.6416 (ppp) REVERT: A 488 GLU cc_start: 0.5638 (pp20) cc_final: 0.5422 (pp20) REVERT: B 366 SER cc_start: 0.6861 (m) cc_final: 0.6618 (m) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.2069 time to fit residues: 35.5140 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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: 0.4980 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 31 optimal weight: 0.0270 chunk 1 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS B 409 GLN B 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123578 restraints weight = 10194.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123566 restraints weight = 6306.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123564 restraints weight = 7018.511| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6771 Z= 0.106 Angle : 0.580 13.387 9202 Z= 0.281 Chirality : 0.045 0.503 970 Planarity : 0.004 0.051 1169 Dihedral : 6.225 51.479 1017 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 0.14 % Allowed : 2.74 % Favored : 97.12 % 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: 0.23 (0.28), residues: 373 sheet: -0.06 (0.80), residues: 47 loop : -1.78 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 472 HIS 0.006 0.001 HIS A 377 PHE 0.013 0.001 PHE A 591 TYR 0.010 0.001 TYR B 380 ARG 0.002 0.000 ARG A 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00877 ( 6) link_NAG-ASN : angle 4.04658 ( 18) hydrogen bonds : bond 0.03154 ( 240) hydrogen bonds : angle 4.06164 ( 672) SS BOND : bond 0.00413 ( 5) SS BOND : angle 1.19055 ( 10) covalent geometry : bond 0.00242 ( 6759) covalent geometry : angle 0.55110 ( 9174) Misc. bond : bond 0.00039 ( 1) *********************** 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: 1 poor density : 128 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.5897 (tmm) cc_final: 0.5644 (tmm) REVERT: A 133 LEU cc_start: 0.7975 (tp) cc_final: 0.7580 (tt) REVERT: A 164 TRP cc_start: 0.5695 (m100) cc_final: 0.5391 (m100) REVERT: A 301 TRP cc_start: 0.6904 (t60) cc_final: 0.6307 (t60) REVERT: A 340 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8236 (mmtm) REVERT: A 454 MET cc_start: 0.6992 (tpt) cc_final: 0.6612 (tpp) REVERT: A 479 MET cc_start: 0.7160 (ppp) cc_final: 0.6471 (ppp) REVERT: A 488 GLU cc_start: 0.5548 (pp20) cc_final: 0.5342 (pp20) REVERT: B 428 ASP cc_start: 0.8281 (p0) cc_final: 0.7978 (p0) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.1861 time to fit residues: 31.4794 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 : 0.719 ------------------------------------------------------------------------------- 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: 0.5980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS ** A 377 HIS ** 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 = 0.3348 r_free = 0.3348 target = 0.122046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115010 restraints weight = 101478.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.116510 restraints weight = 74352.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.117195 restraints weight = 55730.283| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6771 Z= 0.136 Angle : 0.620 13.499 9202 Z= 0.301 Chirality : 0.046 0.531 970 Planarity : 0.004 0.049 1169 Dihedral : 6.203 49.568 1017 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.41 % Rotamer: Outliers : 0.14 % Allowed : 3.17 % Favored : 96.69 % 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: -1.09 (0.31), residues: 787 helix: 0.18 (0.28), residues: 373 sheet: 0.06 (0.82), residues: 45 loop : -1.79 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 472 HIS 0.005 0.001 HIS A 240 PHE 0.017 0.001 PHE A 399 TYR 0.010 0.001 TYR A 216 ARG 0.003 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00964 ( 6) link_NAG-ASN : angle 4.18219 ( 18) hydrogen bonds : bond 0.03733 ( 240) hydrogen bonds : angle 4.09323 ( 672) SS BOND : bond 0.00452 ( 5) SS BOND : angle 1.11345 ( 10) covalent geometry : bond 0.00311 ( 6759) covalent geometry : angle 0.59130 ( 9174) Misc. bond : bond 0.00009 ( 1) *********************** 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 125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6120 (tmm) cc_final: 0.5829 (tmm) REVERT: A 151 MET cc_start: 0.7427 (tpt) cc_final: 0.7002 (tpt) REVERT: A 152 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5852 (mt-10) REVERT: A 340 LYS cc_start: 0.8740 (mmtm) cc_final: 0.8297 (mmtm) REVERT: A 349 ASP cc_start: 0.7256 (t0) cc_final: 0.6832 (t0) REVERT: A 479 MET cc_start: 0.7427 (ppp) cc_final: 0.7174 (ppp) REVERT: B 428 ASP cc_start: 0.8414 (p0) cc_final: 0.8128 (p0) REVERT: B 481 LYS cc_start: 0.7138 (mmtp) cc_final: 0.6877 (tmmt) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1865 time to fit residues: 30.5608 Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 74 optimal weight: 0.4980 chunk 52 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 55 optimal weight: 0.0170 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS ** A 377 HIS ** 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 = 0.3384 r_free = 0.3384 target = 0.124600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122399 restraints weight = 10142.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122345 restraints weight = 11230.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122756 restraints weight = 8614.673| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6771 Z= 0.103 Angle : 0.586 12.119 9202 Z= 0.283 Chirality : 0.044 0.474 970 Planarity : 0.004 0.036 1169 Dihedral : 5.713 42.759 1017 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.08 % Favored : 94.66 % Rotamer: Outliers : 0.14 % Allowed : 2.45 % 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: -0.91 (0.31), residues: 787 helix: 0.38 (0.29), residues: 364 sheet: 0.10 (0.81), residues: 47 loop : -1.73 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.004 0.001 HIS A 377 PHE 0.012 0.001 PHE A 591 TYR 0.011 0.001 TYR B 380 ARG 0.002 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 6) link_NAG-ASN : angle 3.67914 ( 18) hydrogen bonds : bond 0.03169 ( 240) hydrogen bonds : angle 3.95597 ( 672) SS BOND : bond 0.00689 ( 5) SS BOND : angle 1.66929 ( 10) covalent geometry : bond 0.00231 ( 6759) covalent geometry : angle 0.56066 ( 9174) Misc. bond : bond 0.00017 ( 1) *********************** 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 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6024 (tmm) cc_final: 0.5716 (tmm) REVERT: A 164 TRP cc_start: 0.5763 (m100) cc_final: 0.5337 (m100) REVERT: A 340 LYS cc_start: 0.8679 (mmtm) cc_final: 0.8208 (mmtm) REVERT: A 349 ASP cc_start: 0.6867 (t0) cc_final: 0.6493 (t0) REVERT: A 454 MET cc_start: 0.7475 (tpp) cc_final: 0.7189 (tpp) REVERT: B 428 ASP cc_start: 0.8399 (p0) cc_final: 0.8091 (p0) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1910 time to fit residues: 30.6985 Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.0470 chunk 65 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 0.0040 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3374 r_free = 0.3374 target = 0.123363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120635 restraints weight = 10002.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120828 restraints weight = 8254.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120828 restraints weight = 6898.978| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6771 Z= 0.115 Angle : 0.600 11.781 9202 Z= 0.293 Chirality : 0.044 0.473 970 Planarity : 0.004 0.038 1169 Dihedral : 5.568 38.784 1017 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.08 % Favored : 94.66 % 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: -0.89 (0.31), residues: 787 helix: 0.42 (0.29), residues: 365 sheet: 0.15 (0.81), residues: 47 loop : -1.75 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 605 HIS 0.005 0.001 HIS A 377 PHE 0.022 0.001 PHE A 511 TYR 0.011 0.001 TYR A 254 ARG 0.002 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00819 ( 6) link_NAG-ASN : angle 3.65767 ( 18) hydrogen bonds : bond 0.03339 ( 240) hydrogen bonds : angle 3.98464 ( 672) SS BOND : bond 0.00453 ( 5) SS BOND : angle 1.86361 ( 10) covalent geometry : bond 0.00259 ( 6759) covalent geometry : angle 0.57585 ( 9174) Misc. bond : bond 0.00001 ( 1) *********************** 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 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6135 (tmm) cc_final: 0.5908 (tmm) REVERT: A 340 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8223 (mmtm) REVERT: A 349 ASP cc_start: 0.6888 (t0) cc_final: 0.6619 (t0) REVERT: A 473 MET cc_start: 0.7273 (mmt) cc_final: 0.7037 (mmm) REVERT: B 428 ASP cc_start: 0.8452 (p0) cc_final: 0.8189 (p0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1771 time to fit residues: 29.0015 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 0.6980 chunk 68 optimal weight: 0.0170 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 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 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3375 r_free = 0.3375 target = 0.123824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123350 restraints weight = 10086.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122289 restraints weight = 11757.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121565 restraints weight = 15607.771| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6771 Z= 0.107 Angle : 0.577 11.182 9202 Z= 0.280 Chirality : 0.044 0.454 970 Planarity : 0.004 0.035 1169 Dihedral : 5.440 35.983 1017 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.21 % Favored : 94.54 % Rotamer: Outliers : 0.14 % Allowed : 0.86 % Favored : 98.99 % 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: -0.85 (0.31), residues: 787 helix: 0.47 (0.29), residues: 359 sheet: 0.05 (0.82), residues: 48 loop : -1.70 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 605 HIS 0.005 0.001 HIS A 377 PHE 0.013 0.001 PHE A 591 TYR 0.012 0.001 TYR A 453 ARG 0.003 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 6) link_NAG-ASN : angle 3.46675 ( 18) hydrogen bonds : bond 0.03148 ( 240) hydrogen bonds : angle 3.93565 ( 672) SS BOND : bond 0.00426 ( 5) SS BOND : angle 1.83174 ( 10) covalent geometry : bond 0.00245 ( 6759) covalent geometry : angle 0.55334 ( 9174) Misc. bond : bond 0.00001 ( 1) *********************** 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 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6108 (tmm) cc_final: 0.5802 (tmm) REVERT: A 269 MET cc_start: 0.5304 (mmm) cc_final: 0.3662 (mmm) REVERT: A 340 LYS cc_start: 0.8586 (mmtm) cc_final: 0.8216 (mmtm) REVERT: A 349 ASP cc_start: 0.6882 (t0) cc_final: 0.6553 (t0) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.1979 time to fit residues: 32.6262 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 : 0.640 ------------------------------------------------------------------------------- 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: 0.0270 chunk 21 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3383 r_free = 0.3383 target = 0.124526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124045 restraints weight = 10112.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124040 restraints weight = 9996.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124000 restraints weight = 8786.884| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6771 Z= 0.105 Angle : 0.583 11.117 9202 Z= 0.283 Chirality : 0.043 0.431 970 Planarity : 0.004 0.039 1169 Dihedral : 5.264 31.932 1017 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.46 % Favored : 94.28 % 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: -0.73 (0.31), residues: 787 helix: 0.57 (0.29), residues: 365 sheet: 0.05 (0.82), residues: 48 loop : -1.67 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 605 HIS 0.005 0.001 HIS A 377 PHE 0.009 0.001 PHE A 307 TYR 0.010 0.001 TYR A 453 ARG 0.002 0.000 ARG A 305 Details of bonding type rmsd link_NAG-ASN : bond 0.00735 ( 6) link_NAG-ASN : angle 3.30439 ( 18) hydrogen bonds : bond 0.03023 ( 240) hydrogen bonds : angle 3.90422 ( 672) SS BOND : bond 0.00425 ( 5) SS BOND : angle 1.76487 ( 10) covalent geometry : bond 0.00242 ( 6759) covalent geometry : angle 0.56204 ( 9174) Misc. bond : bond 0.00001 ( 1) *********************** 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 119 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6135 (tmm) cc_final: 0.5881 (tmm) REVERT: A 269 MET cc_start: 0.4830 (mmm) cc_final: 0.3563 (mmm) REVERT: A 340 LYS cc_start: 0.8471 (mmtm) cc_final: 0.8092 (mmtm) REVERT: A 349 ASP cc_start: 0.6835 (t0) cc_final: 0.6545 (t0) REVERT: B 428 ASP cc_start: 0.8376 (p0) cc_final: 0.8174 (p0) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.1968 time to fit residues: 31.2275 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 : 0.731 ------------------------------------------------------------------------------- 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: 0.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 62 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** 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 = 0.3375 r_free = 0.3375 target = 0.124043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123365 restraints weight = 10339.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.123222 restraints weight = 16317.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.123172 restraints weight = 12843.761| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6771 Z= 0.105 Angle : 0.573 10.778 9202 Z= 0.278 Chirality : 0.043 0.418 970 Planarity : 0.004 0.037 1169 Dihedral : 5.112 33.621 1017 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.08 % Favored : 94.66 % 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: -0.66 (0.31), residues: 787 helix: 0.71 (0.29), residues: 350 sheet: 0.14 (0.83), residues: 46 loop : -1.63 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 605 HIS 0.005 0.001 HIS A 377 PHE 0.014 0.001 PHE A 591 TYR 0.006 0.001 TYR A 254 ARG 0.002 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 6) link_NAG-ASN : angle 3.19479 ( 18) hydrogen bonds : bond 0.03016 ( 240) hydrogen bonds : angle 3.90699 ( 672) SS BOND : bond 0.00427 ( 5) SS BOND : angle 1.75537 ( 10) covalent geometry : bond 0.00241 ( 6759) covalent geometry : angle 0.55361 ( 9174) Misc. bond : bond 0.00002 ( 1) ********************** 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 121 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6134 (tmm) cc_final: 0.5864 (tmm) REVERT: A 269 MET cc_start: 0.5036 (mmm) cc_final: 0.3571 (mmm) REVERT: A 340 LYS cc_start: 0.8472 (mmtm) cc_final: 0.8114 (mmtm) REVERT: A 349 ASP cc_start: 0.6821 (t0) cc_final: 0.6504 (t0) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1937 time to fit residues: 30.9136 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 : 0.706 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.0040 chunk 4 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** 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 = 0.3363 r_free = 0.3363 target = 0.122725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122371 restraints weight = 10220.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121193 restraints weight = 15032.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120870 restraints weight = 11379.609| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.003 0.030 6771 Z= 0.118 Angle : 0.598 10.848 9202 Z= 0.294 Chirality : 0.044 0.421 970 Planarity : 0.004 0.037 1169 Dihedral : 5.147 34.227 1017 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.34 % Favored : 94.41 % 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: -0.68 (0.31), residues: 787 helix: 0.65 (0.29), residues: 358 sheet: 0.12 (0.80), residues: 48 loop : -1.65 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 605 HIS 0.005 0.001 HIS A 377 PHE 0.015 0.001 PHE A 399 TYR 0.008 0.001 TYR A 254 ARG 0.004 0.000 ARG A 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 6) link_NAG-ASN : angle 3.26094 ( 18) hydrogen bonds : bond 0.03215 ( 240) hydrogen bonds : angle 3.92301 ( 672) SS BOND : bond 0.00476 ( 5) SS BOND : angle 1.78627 ( 10) covalent geometry : bond 0.00269 ( 6759) covalent geometry : angle 0.57848 ( 9174) Misc. bond : bond 0.00017 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.75 seconds wall clock time: 39 minutes 29.77 seconds (2369.77 seconds total)