Starting phenix.real_space_refine on Wed Jan 15 08:50:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9em9_19814/01_2025/9em9_19814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9em9_19814/01_2025/9em9_19814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9em9_19814/01_2025/9em9_19814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9em9_19814/01_2025/9em9_19814.map" model { file = "/net/cci-nas-00/data/ceres_data/9em9_19814/01_2025/9em9_19814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9em9_19814/01_2025/9em9_19814.cif" } resolution = 3.76 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= 0.003 sd= 0.066 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 5110 2.51 5 N 1430 2.21 5 O 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8182 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4058 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 14, 'TRANS': 497} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 8.56, per 1000 atoms: 1.05 Number of scatterers: 8182 At special positions: 0 Unit cell: (128.112, 99.552, 102.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 6 15.00 Mg 2 11.99 O 1610 8.00 N 1430 7.00 C 5110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 763 " 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=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.2 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 65.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 5 through 24 removed outlier: 4.298A pdb=" N ARG A 12 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU A 13 " --> pdb=" O GLN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 32 Processing helix chain 'A' and resid 33 through 46 removed outlier: 4.003A pdb=" N VAL A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 92 through 95 Processing helix chain 'A' and resid 104 through 120 Processing helix chain 'A' and resid 130 through 149 Processing helix chain 'A' and resid 154 through 174 Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.544A pdb=" N ARG A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.801A pdb=" N LYS A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 225' Processing helix chain 'A' and resid 239 through 252 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.614A pdb=" N ASN A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.847A pdb=" N ASP A 289 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.883A pdb=" N TRP A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 304' Processing helix chain 'A' and resid 304 through 319 Processing helix chain 'A' and resid 329 through 342 removed outlier: 3.812A pdb=" N TYR A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 4.112A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 removed outlier: 4.284A pdb=" N TYR A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 400 through 423 removed outlier: 3.719A pdb=" N ILE A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix removed outlier: 3.746A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.562A pdb=" N SER A 429 " --> pdb=" O GLU A 425 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 472 Proline residue: A 453 - end of helix Processing helix chain 'A' and resid 736 through 767 Processing helix chain 'B' and resid 5 through 24 removed outlier: 4.299A pdb=" N ARG B 12 " --> pdb=" O CYS B 8 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 33 through 46 removed outlier: 4.002A pdb=" N VAL B 37 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 92 through 95 Processing helix chain 'B' and resid 104 through 120 Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 154 through 174 Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.544A pdb=" N ARG B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.801A pdb=" N LYS B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 225' Processing helix chain 'B' and resid 239 through 252 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.614A pdb=" N ASN B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.847A pdb=" N ASP B 289 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.884A pdb=" N TRP B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 304' Processing helix chain 'B' and resid 304 through 319 Processing helix chain 'B' and resid 329 through 342 removed outlier: 3.813A pdb=" N TYR B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 4.113A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 4.285A pdb=" N TYR B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 400 through 423 removed outlier: 3.719A pdb=" N ILE B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix removed outlier: 3.746A pdb=" N ASP B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.562A pdb=" N SER B 429 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 472 Proline residue: B 453 - end of helix Processing helix chain 'B' and resid 736 through 767 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.083A pdb=" N PHE A 49 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 230 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 51 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ASN A 227 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR A 90 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 213 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 97 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 185 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262 removed outlier: 6.121A pdb=" N CYS A 260 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 52 removed outlier: 6.084A pdb=" N PHE B 49 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 230 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE B 51 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASN B 227 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR B 90 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 213 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 97 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 185 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 259 through 262 removed outlier: 6.121A pdb=" N CYS B 260 " --> pdb=" O VAL B 294 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1362 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: 2.77 Time building geometry restraints manager: 2.32 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: 2782 1.34 - 1.46: 1387 1.46 - 1.58: 4101 1.58 - 1.70: 6 1.70 - 1.82: 34 Bond restraints: 8310 Sorted by residual: bond pdb=" N3B GNP A 801 " pdb=" PG GNP A 801 " ideal model delta sigma weight residual 1.801 1.705 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" N3B GNP B 801 " pdb=" PG GNP B 801 " ideal model delta sigma weight residual 1.801 1.705 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O5' GNP A 801 " pdb=" PA GNP A 801 " ideal model delta sigma weight residual 1.660 1.565 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O5' GNP B 801 " pdb=" PA GNP B 801 " ideal model delta sigma weight residual 1.660 1.566 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" O3A GNP A 801 " pdb=" PB GNP A 801 " ideal model delta sigma weight residual 1.687 1.635 0.052 2.00e-02 2.50e+03 6.87e+00 ... (remaining 8305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11008 2.05 - 4.11: 180 4.11 - 6.16: 40 6.16 - 8.21: 10 8.21 - 10.27: 6 Bond angle restraints: 11244 Sorted by residual: angle pdb=" N LYS B 263 " pdb=" CA LYS B 263 " pdb=" C LYS B 263 " ideal model delta sigma weight residual 109.81 120.08 -10.27 2.21e+00 2.05e-01 2.16e+01 angle pdb=" N LYS A 263 " pdb=" CA LYS A 263 " pdb=" C LYS A 263 " ideal model delta sigma weight residual 109.81 120.06 -10.25 2.21e+00 2.05e-01 2.15e+01 angle pdb=" CA TYR B 466 " pdb=" CB TYR B 466 " pdb=" CG TYR B 466 " ideal model delta sigma weight residual 113.90 107.60 6.30 1.80e+00 3.09e-01 1.22e+01 angle pdb=" CA TYR A 466 " pdb=" CB TYR A 466 " pdb=" CG TYR A 466 " ideal model delta sigma weight residual 113.90 107.61 6.29 1.80e+00 3.09e-01 1.22e+01 angle pdb=" O1B GNP A 801 " pdb=" PB GNP A 801 " pdb=" O2B GNP A 801 " ideal model delta sigma weight residual 119.66 110.05 9.61 3.00e+00 1.11e-01 1.03e+01 ... (remaining 11239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 4569 16.10 - 32.21: 392 32.21 - 48.31: 76 48.31 - 64.41: 46 64.41 - 80.51: 22 Dihedral angle restraints: 5105 sinusoidal: 2109 harmonic: 2996 Sorted by residual: dihedral pdb=" CA SER B 256 " pdb=" C SER B 256 " pdb=" N ALA B 257 " pdb=" CA ALA B 257 " ideal model delta harmonic sigma weight residual 180.00 150.18 29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA SER A 256 " pdb=" C SER A 256 " pdb=" N ALA A 257 " pdb=" CA ALA A 257 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA THR B 255 " pdb=" C THR B 255 " pdb=" N SER B 256 " pdb=" CA SER B 256 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 5102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 926 0.044 - 0.088: 256 0.088 - 0.132: 59 0.132 - 0.176: 13 0.176 - 0.220: 2 Chirality restraints: 1256 Sorted by residual: chirality pdb=" CA TYR A 466 " pdb=" N TYR A 466 " pdb=" C TYR A 466 " pdb=" CB TYR A 466 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA TYR B 466 " pdb=" N TYR B 466 " pdb=" C TYR B 466 " pdb=" CB TYR B 466 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA LYS B 263 " pdb=" N LYS B 263 " pdb=" C LYS B 263 " pdb=" CB LYS B 263 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 1253 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 290 " -0.409 9.50e-02 1.11e+02 1.85e-01 2.58e+01 pdb=" NE ARG A 290 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 290 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A 290 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 290 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 290 " 0.409 9.50e-02 1.11e+02 1.85e-01 2.58e+01 pdb=" NE ARG B 290 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 290 " 0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG B 290 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B 290 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 372 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C SER B 372 " -0.060 2.00e-02 2.50e+03 pdb=" O SER B 372 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU B 373 " 0.020 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 29 2.46 - 3.07: 5638 3.07 - 3.68: 12218 3.68 - 4.29: 17778 4.29 - 4.90: 29257 Nonbonded interactions: 64920 Sorted by model distance: nonbonded pdb=" O2B GNP B 801 " pdb="MG MG B 802 " model vdw 1.853 2.170 nonbonded pdb=" O2B GNP A 801 " pdb="MG MG A 802 " model vdw 1.853 2.170 nonbonded pdb=" OG1 THR B 82 " pdb="MG MG B 802 " model vdw 1.883 2.170 nonbonded pdb=" OG1 THR A 82 " pdb="MG MG A 802 " model vdw 1.885 2.170 nonbonded pdb=" O1G GNP A 801 " pdb="MG MG A 802 " model vdw 1.937 2.170 ... (remaining 64915 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 9.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.110 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 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 0.096 8310 Z= 0.258 Angle : 0.754 10.266 11244 Z= 0.419 Chirality : 0.044 0.220 1256 Planarity : 0.011 0.185 1474 Dihedral : 14.920 80.515 3166 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.24), residues: 1016 helix: -0.27 (0.19), residues: 600 sheet: -0.10 (0.41), residues: 118 loop : -0.68 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 302 HIS 0.004 0.001 HIS B 164 PHE 0.019 0.002 PHE B 348 TYR 0.028 0.005 TYR B 466 ARG 0.040 0.004 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.4999 (mmt) cc_final: 0.4727 (mtt) REVERT: A 444 PHE cc_start: 0.7811 (m-80) cc_final: 0.7586 (m-10) REVERT: A 447 LEU cc_start: 0.8910 (tp) cc_final: 0.8672 (tt) REVERT: B 187 MET cc_start: 0.4964 (mmt) cc_final: 0.4708 (mtt) REVERT: B 444 PHE cc_start: 0.7943 (m-80) cc_final: 0.7713 (m-10) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2483 time to fit residues: 47.6820 Evaluate side-chains 76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 10 ASN A 92 ASN A 276 GLN A 309 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 GLN B 9 GLN B 10 ASN B 276 GLN B 309 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.121088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.097373 restraints weight = 24355.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.096840 restraints weight = 20353.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097552 restraints weight = 21929.537| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8310 Z= 0.247 Angle : 0.680 9.471 11244 Z= 0.350 Chirality : 0.043 0.285 1256 Planarity : 0.005 0.062 1474 Dihedral : 10.665 61.493 1186 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.94 % Allowed : 9.05 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.26), residues: 1016 helix: 0.95 (0.20), residues: 600 sheet: 0.02 (0.44), residues: 122 loop : 0.02 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 302 HIS 0.006 0.001 HIS B 164 PHE 0.013 0.002 PHE A 319 TYR 0.039 0.003 TYR B 201 ARG 0.005 0.000 ARG B 738 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 GLU cc_start: 0.9031 (tt0) cc_final: 0.8717 (tm-30) outliers start: 26 outliers final: 18 residues processed: 94 average time/residue: 0.2211 time to fit residues: 28.6679 Evaluate side-chains 72 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 763 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 59 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN B 16 ASN B 92 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.121003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.097663 restraints weight = 25099.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.097979 restraints weight = 20743.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.098451 restraints weight = 20476.519| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8310 Z= 0.224 Angle : 0.671 11.066 11244 Z= 0.335 Chirality : 0.042 0.270 1256 Planarity : 0.004 0.048 1474 Dihedral : 9.286 50.631 1186 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.94 % Allowed : 10.63 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.26), residues: 1016 helix: 0.85 (0.20), residues: 608 sheet: -0.25 (0.44), residues: 124 loop : -0.20 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 410 HIS 0.002 0.000 HIS B 164 PHE 0.014 0.001 PHE A 319 TYR 0.044 0.002 TYR B 201 ARG 0.004 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 GLU cc_start: 0.8853 (tt0) cc_final: 0.8596 (tm-30) outliers start: 26 outliers final: 15 residues processed: 83 average time/residue: 0.1876 time to fit residues: 23.1286 Evaluate side-chains 71 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 763 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 10 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.120245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.096834 restraints weight = 26074.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.096523 restraints weight = 21188.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.097085 restraints weight = 20636.190| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8310 Z= 0.268 Angle : 0.692 10.945 11244 Z= 0.345 Chirality : 0.043 0.286 1256 Planarity : 0.005 0.058 1474 Dihedral : 7.414 43.183 1186 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.71 % Allowed : 11.09 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.26), residues: 1016 helix: 0.88 (0.20), residues: 598 sheet: -0.61 (0.44), residues: 122 loop : -0.19 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 410 HIS 0.001 0.000 HIS B 164 PHE 0.014 0.002 PHE B 319 TYR 0.040 0.002 TYR A 201 ARG 0.004 0.000 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8531 (mmm) cc_final: 0.8290 (mtt) REVERT: B 38 GLU cc_start: 0.9094 (tt0) cc_final: 0.8679 (tm-30) REVERT: B 115 LEU cc_start: 0.8938 (mm) cc_final: 0.8683 (mm) REVERT: B 197 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7529 (tm-30) REVERT: B 270 MET cc_start: 0.8551 (mmm) cc_final: 0.8261 (mtt) outliers start: 24 outliers final: 19 residues processed: 83 average time/residue: 0.1655 time to fit residues: 20.9278 Evaluate side-chains 76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 763 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 0.0870 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.120920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.097485 restraints weight = 24703.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.097235 restraints weight = 20655.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.097696 restraints weight = 20525.517| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8310 Z= 0.187 Angle : 0.654 12.991 11244 Z= 0.316 Chirality : 0.044 0.345 1256 Planarity : 0.004 0.044 1474 Dihedral : 6.065 41.743 1186 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.38 % Allowed : 11.54 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.26), residues: 1016 helix: 1.04 (0.20), residues: 598 sheet: -0.47 (0.45), residues: 122 loop : -0.26 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 410 HIS 0.003 0.000 HIS B 164 PHE 0.010 0.001 PHE A 292 TYR 0.033 0.002 TYR B 201 ARG 0.003 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 TYR cc_start: 0.7944 (t80) cc_final: 0.7658 (t80) REVERT: B 38 GLU cc_start: 0.8915 (tt0) cc_final: 0.8544 (tm-30) REVERT: B 115 LEU cc_start: 0.8865 (mm) cc_final: 0.8613 (mm) REVERT: B 197 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7647 (tm-30) REVERT: B 270 MET cc_start: 0.8441 (mmm) cc_final: 0.8232 (mtt) outliers start: 21 outliers final: 17 residues processed: 82 average time/residue: 0.2049 time to fit residues: 23.7148 Evaluate side-chains 77 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 763 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 99 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 220 HIS ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.119423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.095887 restraints weight = 24684.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.095466 restraints weight = 20721.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.096019 restraints weight = 20201.722| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8310 Z= 0.210 Angle : 0.679 14.467 11244 Z= 0.323 Chirality : 0.045 0.341 1256 Planarity : 0.004 0.047 1474 Dihedral : 5.743 40.754 1186 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.26 % Allowed : 13.01 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1016 helix: 1.08 (0.21), residues: 598 sheet: -0.62 (0.46), residues: 118 loop : -0.23 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 410 HIS 0.003 0.000 HIS B 164 PHE 0.015 0.001 PHE A 319 TYR 0.037 0.002 TYR B 462 ARG 0.009 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 LEU cc_start: 0.7856 (mt) cc_final: 0.7527 (tp) REVERT: B 115 LEU cc_start: 0.8870 (mm) cc_final: 0.8627 (mm) REVERT: B 440 TYR cc_start: 0.7116 (t80) cc_final: 0.6593 (t80) outliers start: 20 outliers final: 19 residues processed: 78 average time/residue: 0.1995 time to fit residues: 22.4559 Evaluate side-chains 77 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 763 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.0000 chunk 33 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.119575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.095745 restraints weight = 24422.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.095754 restraints weight = 19368.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.096374 restraints weight = 19533.278| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8310 Z= 0.174 Angle : 0.672 13.321 11244 Z= 0.323 Chirality : 0.044 0.351 1256 Planarity : 0.003 0.039 1474 Dihedral : 5.519 37.440 1186 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.49 % Allowed : 12.56 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.26), residues: 1016 helix: 1.05 (0.21), residues: 602 sheet: -0.61 (0.48), residues: 118 loop : -0.20 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 410 HIS 0.003 0.000 HIS B 164 PHE 0.011 0.001 PHE A 319 TYR 0.038 0.002 TYR B 201 ARG 0.003 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 LEU cc_start: 0.7883 (mt) cc_final: 0.7605 (tp) REVERT: B 115 LEU cc_start: 0.8966 (mm) cc_final: 0.8700 (mm) REVERT: B 440 TYR cc_start: 0.7043 (t80) cc_final: 0.6718 (t80) outliers start: 22 outliers final: 18 residues processed: 76 average time/residue: 0.1802 time to fit residues: 19.9024 Evaluate side-chains 76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 763 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 55 optimal weight: 0.0470 chunk 88 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.118694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.094860 restraints weight = 24572.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.095404 restraints weight = 19233.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.095872 restraints weight = 17432.996| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8310 Z= 0.176 Angle : 0.661 12.534 11244 Z= 0.315 Chirality : 0.044 0.346 1256 Planarity : 0.004 0.036 1474 Dihedral : 5.424 39.566 1186 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.49 % Allowed : 12.78 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1016 helix: 1.10 (0.21), residues: 602 sheet: -0.55 (0.47), residues: 122 loop : -0.25 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 410 HIS 0.003 0.000 HIS B 164 PHE 0.012 0.001 PHE B 444 TYR 0.043 0.002 TYR B 201 ARG 0.013 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 TYR cc_start: 0.8017 (t80) cc_final: 0.7777 (t80) REVERT: A 742 LEU cc_start: 0.7908 (mt) cc_final: 0.7601 (tp) REVERT: B 440 TYR cc_start: 0.7049 (t80) cc_final: 0.6639 (t80) REVERT: B 749 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8125 (tttt) outliers start: 22 outliers final: 19 residues processed: 80 average time/residue: 0.1879 time to fit residues: 22.1259 Evaluate side-chains 78 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 749 LYS Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 763 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.117416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.087521 restraints weight = 24947.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.089663 restraints weight = 15407.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.091102 restraints weight = 11346.214| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8310 Z= 0.251 Angle : 0.700 12.739 11244 Z= 0.333 Chirality : 0.046 0.379 1256 Planarity : 0.004 0.047 1474 Dihedral : 5.529 41.228 1186 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.49 % Allowed : 13.24 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.26), residues: 1016 helix: 0.93 (0.21), residues: 614 sheet: -0.63 (0.47), residues: 122 loop : -0.45 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 410 HIS 0.004 0.000 HIS B 164 PHE 0.015 0.001 PHE B 319 TYR 0.038 0.002 TYR B 201 ARG 0.010 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 TYR cc_start: 0.8618 (t80) cc_final: 0.8327 (t80) REVERT: A 742 LEU cc_start: 0.8045 (mt) cc_final: 0.7742 (tp) REVERT: B 140 TYR cc_start: 0.8849 (m-80) cc_final: 0.8557 (m-80) REVERT: B 440 TYR cc_start: 0.6911 (t80) cc_final: 0.6606 (t80) REVERT: B 452 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8784 (mm-40) outliers start: 22 outliers final: 21 residues processed: 76 average time/residue: 0.1763 time to fit residues: 19.8594 Evaluate side-chains 78 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 763 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.117480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.093669 restraints weight = 24819.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.093516 restraints weight = 20196.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.094118 restraints weight = 18862.509| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8310 Z= 0.235 Angle : 0.704 13.129 11244 Z= 0.336 Chirality : 0.045 0.377 1256 Planarity : 0.004 0.047 1474 Dihedral : 5.528 42.026 1186 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.49 % Allowed : 13.46 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.26), residues: 1016 helix: 0.89 (0.21), residues: 614 sheet: -0.78 (0.49), residues: 118 loop : -0.40 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 410 HIS 0.004 0.000 HIS B 164 PHE 0.015 0.001 PHE B 319 TYR 0.056 0.002 TYR B 462 ARG 0.008 0.000 ARG B 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 LEU cc_start: 0.7713 (mt) cc_final: 0.7447 (tp) REVERT: B 440 TYR cc_start: 0.7008 (t80) cc_final: 0.6690 (t80) REVERT: B 452 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8368 (mm-40) outliers start: 22 outliers final: 21 residues processed: 76 average time/residue: 0.1773 time to fit residues: 20.1999 Evaluate side-chains 79 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 763 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 92 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 120 ASN A 276 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.119690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.095757 restraints weight = 24829.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.095577 restraints weight = 20154.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.096166 restraints weight = 19418.168| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8310 Z= 0.169 Angle : 0.687 13.494 11244 Z= 0.329 Chirality : 0.044 0.358 1256 Planarity : 0.003 0.035 1474 Dihedral : 5.347 42.994 1186 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.38 % Allowed : 14.03 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.26), residues: 1016 helix: 1.00 (0.21), residues: 614 sheet: -0.76 (0.47), residues: 122 loop : -0.44 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 410 HIS 0.003 0.000 HIS B 164 PHE 0.009 0.001 PHE B 319 TYR 0.041 0.002 TYR B 462 ARG 0.007 0.000 ARG B 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2679.62 seconds wall clock time: 49 minutes 29.96 seconds (2969.96 seconds total)