Starting phenix.real_space_refine on Thu Oct 10 16:57:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9em9_19814/10_2024/9em9_19814.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9em9_19814/10_2024/9em9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9em9_19814/10_2024/9em9_19814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9em9_19814/10_2024/9em9_19814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9em9_19814/10_2024/9em9_19814.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9em9_19814/10_2024/9em9_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-5477/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: 8.80, per 1000 atoms: 1.08 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: 2.16 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: 0.83 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: 2.37 Time building geometry restraints manager: 2.45 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: 0.00 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: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.330 Find NCS groups from input model: 0.210 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.000 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.008 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: 0.2853 time to fit residues: 54.5195 Evaluate side-chains 76 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 94 average time/residue: 0.2203 time to fit residues: 28.4955 Evaluate side-chains 71 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 51 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 63 optimal weight: 0.0020 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 0.0270 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 0.2980 overall best weight: 0.3046 ------------------------------------------------------------------------------- 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 10 ASN B 16 ASN B 92 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3484 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= 0.183 Angle : 0.654 10.961 11244 Z= 0.326 Chirality : 0.042 0.291 1256 Planarity : 0.004 0.042 1474 Dihedral : 8.975 47.790 1186 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.38 % Allowed : 10.63 % Favored : 86.99 % 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: 0.72 (0.26), residues: 1016 helix: 0.95 (0.20), residues: 604 sheet: -0.03 (0.44), residues: 122 loop : -0.04 (0.40), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 410 HIS 0.001 0.000 HIS A 164 PHE 0.011 0.001 PHE B 292 TYR 0.045 0.002 TYR B 201 ARG 0.005 0.000 ARG B 12 *********************** 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 91 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 80 average time/residue: 0.1866 time to fit residues: 21.5809 Evaluate side-chains 70 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 763 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 0.0020 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 82 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8310 Z= 0.202 Angle : 0.676 15.499 11244 Z= 0.328 Chirality : 0.043 0.280 1256 Planarity : 0.004 0.039 1474 Dihedral : 7.120 40.331 1186 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.38 % Allowed : 10.75 % Favored : 86.88 % 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: 0.62 (0.26), residues: 1016 helix: 0.98 (0.20), residues: 610 sheet: -0.32 (0.44), residues: 124 loop : -0.27 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 410 HIS 0.001 0.000 HIS A 164 PHE 0.014 0.001 PHE A 319 TYR 0.038 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 86 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 440 TYR cc_start: 0.6918 (t80) cc_final: 0.6609 (t80) outliers start: 21 outliers final: 17 residues processed: 78 average time/residue: 0.1751 time to fit residues: 20.3916 Evaluate side-chains 71 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 A residue 759 SER Chi-restraints excluded: chain B residue 255 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 68 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 111 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8310 Z= 0.194 Angle : 0.638 12.548 11244 Z= 0.310 Chirality : 0.044 0.337 1256 Planarity : 0.004 0.041 1474 Dihedral : 5.931 42.191 1186 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.60 % Allowed : 10.63 % Favored : 86.76 % 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: 0.77 (0.26), residues: 1016 helix: 1.11 (0.20), residues: 602 sheet: -0.40 (0.46), residues: 118 loop : -0.12 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 410 HIS 0.005 0.001 HIS B 164 PHE 0.013 0.001 PHE A 319 TYR 0.037 0.002 TYR B 201 ARG 0.004 0.000 ARG A 204 *********************** 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 87 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7608 (tm-30) outliers start: 23 outliers final: 18 residues processed: 79 average time/residue: 0.1708 time to fit residues: 20.0401 Evaluate side-chains 73 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 0.0270 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 16 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8310 Z= 0.226 Angle : 0.675 13.433 11244 Z= 0.329 Chirality : 0.045 0.367 1256 Planarity : 0.004 0.047 1474 Dihedral : 5.743 43.234 1186 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.26 % Allowed : 12.78 % 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: 0.73 (0.26), residues: 1016 helix: 1.10 (0.21), residues: 602 sheet: -0.47 (0.46), residues: 118 loop : -0.16 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 410 HIS 0.005 0.000 HIS B 164 PHE 0.015 0.001 PHE A 319 TYR 0.036 0.002 TYR B 462 ARG 0.003 0.000 ARG A 204 *********************** 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 83 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 77 average time/residue: 0.1911 time to fit residues: 21.6399 Evaluate side-chains 71 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 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 72 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 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 276 GLN ** 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** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4775 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= 0.212 Angle : 0.692 14.156 11244 Z= 0.330 Chirality : 0.044 0.335 1256 Planarity : 0.004 0.047 1474 Dihedral : 5.620 42.385 1186 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.38 % Allowed : 13.12 % Favored : 84.50 % 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: 0.67 (0.26), residues: 1016 helix: 1.07 (0.21), residues: 602 sheet: -0.62 (0.47), residues: 118 loop : -0.19 (0.38), residues: 296 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 0.014 0.001 PHE A 319 TYR 0.042 0.002 TYR A 201 ARG 0.004 0.000 ARG A 390 *********************** 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 80 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 20 residues processed: 75 average time/residue: 0.1765 time to fit residues: 19.9141 Evaluate side-chains 71 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE 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 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 753 TYR 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 19 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8310 Z= 0.213 Angle : 0.681 12.088 11244 Z= 0.330 Chirality : 0.045 0.344 1256 Planarity : 0.004 0.046 1474 Dihedral : 5.544 41.187 1186 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.71 % Allowed : 13.80 % Favored : 83.48 % 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: 0.92 (0.21), residues: 616 sheet: -0.62 (0.48), residues: 118 loop : -0.38 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 410 HIS 0.003 0.000 HIS B 164 PHE 0.014 0.001 PHE A 319 TYR 0.039 0.002 TYR A 201 ARG 0.003 0.000 ARG A 390 *********************** 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 81 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 57 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 21 residues processed: 76 average time/residue: 0.1737 time to fit residues: 19.8030 Evaluate side-chains 75 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 54 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.0050 chunk 82 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8310 Z= 0.187 Angle : 0.679 13.031 11244 Z= 0.324 Chirality : 0.044 0.342 1256 Planarity : 0.004 0.038 1474 Dihedral : 5.419 41.758 1186 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.04 % Allowed : 14.03 % Favored : 83.94 % 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 (0.27), residues: 1016 helix: 1.10 (0.21), residues: 600 sheet: -0.57 (0.49), residues: 118 loop : -0.30 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 410 HIS 0.003 0.000 HIS B 164 PHE 0.012 0.001 PHE A 319 TYR 0.034 0.002 TYR A 201 ARG 0.003 0.000 ARG A 390 *********************** 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 77 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 16 residues processed: 72 average time/residue: 0.1632 time to fit residues: 18.0324 Evaluate side-chains 71 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 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 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 101 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 80 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 chunk 11 optimal weight: 0.6980 overall best weight: 0.2804 ------------------------------------------------------------------------------- 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 ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8310 Z= 0.148 Angle : 0.667 13.505 11244 Z= 0.321 Chirality : 0.044 0.359 1256 Planarity : 0.003 0.036 1474 Dihedral : 5.227 42.408 1186 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.47 % Allowed : 15.38 % Favored : 83.14 % 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: 0.72 (0.27), residues: 1016 helix: 1.13 (0.21), residues: 604 sheet: -0.48 (0.48), residues: 122 loop : -0.27 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 302 HIS 0.003 0.000 HIS B 164 PHE 0.013 0.001 PHE B 444 TYR 0.033 0.002 TYR A 201 ARG 0.003 0.000 ARG A 390 ********************** 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 74 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 0.2200 time to fit residues: 21.6276 Evaluate side-chains 68 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU 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 367 THR Chi-restraints excluded: chain B residue 380 ASN 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 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 54 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 369 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.118608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.094686 restraints weight = 24587.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094097 restraints weight = 21117.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.094865 restraints weight = 19597.343| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8310 Z= 0.242 Angle : 0.697 13.237 11244 Z= 0.336 Chirality : 0.045 0.354 1256 Planarity : 0.004 0.048 1474 Dihedral : 5.447 43.469 1186 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.36 % Allowed : 15.16 % Favored : 83.48 % 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: 0.41 (0.26), residues: 1016 helix: 0.93 (0.21), residues: 614 sheet: -0.62 (0.48), residues: 122 loop : -0.57 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 410 HIS 0.004 0.000 HIS B 164 PHE 0.016 0.001 PHE B 319 TYR 0.035 0.002 TYR A 462 ARG 0.003 0.000 ARG A 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.41 seconds wall clock time: 35 minutes 34.74 seconds (2134.74 seconds total)