Starting phenix.real_space_refine on Wed Mar 5 16:02:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8di5_27439/03_2025/8di5_27439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8di5_27439/03_2025/8di5_27439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8di5_27439/03_2025/8di5_27439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8di5_27439/03_2025/8di5_27439.map" model { file = "/net/cci-nas-00/data/ceres_data/8di5_27439/03_2025/8di5_27439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8di5_27439/03_2025/8di5_27439.cif" } resolution = 3.04 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= -0.000 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1573 2.51 5 N 409 2.21 5 O 473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2467 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1546 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.73, per 1000 atoms: 1.51 Number of scatterers: 2467 At special positions: 0 Unit cell: (68, 79, 73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 473 8.00 N 409 7.00 C 1573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " 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 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 311.9 milliseconds 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 5 sheets defined 15.8% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.645A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.008A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.962A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.065A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 5.268A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.296A pdb=" N GLU H 33 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 80 hydrogen bonds defined for protein. 204 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: 0.65 Time building geometry restraints manager: 0.73 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: 786 1.34 - 1.46: 698 1.46 - 1.58: 1036 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 2534 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.39e+00 bond pdb=" CB ILE C 472 " pdb=" CG2 ILE C 472 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 bond pdb=" CB ASN H 83 " pdb=" CG ASN H 83 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" CG LEU C 452 " pdb=" CD1 LEU C 452 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.67e+00 ... (remaining 2529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 3417 3.77 - 7.54: 26 7.54 - 11.31: 3 11.31 - 15.08: 0 15.08 - 18.85: 1 Bond angle restraints: 3447 Sorted by residual: angle pdb=" CA LEU C 518 " pdb=" CB LEU C 518 " pdb=" CG LEU C 518 " ideal model delta sigma weight residual 116.30 135.15 -18.85 3.50e+00 8.16e-02 2.90e+01 angle pdb=" C GLU H 33 " pdb=" N MET H 34 " pdb=" CA MET H 34 " ideal model delta sigma weight residual 122.87 118.15 4.72 1.61e+00 3.86e-01 8.60e+00 angle pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta sigma weight residual 122.68 126.77 -4.09 1.47e+00 4.63e-01 7.72e+00 angle pdb=" CA TYR C 495 " pdb=" CB TYR C 495 " pdb=" CG TYR C 495 " ideal model delta sigma weight residual 113.90 118.77 -4.87 1.80e+00 3.09e-01 7.31e+00 angle pdb=" CA TYR C 473 " pdb=" CB TYR C 473 " pdb=" CG TYR C 473 " ideal model delta sigma weight residual 113.90 118.55 -4.65 1.80e+00 3.09e-01 6.69e+00 ... (remaining 3442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 1332 15.12 - 30.23: 130 30.23 - 45.35: 23 45.35 - 60.47: 3 60.47 - 75.58: 2 Dihedral angle restraints: 1490 sinusoidal: 589 harmonic: 901 Sorted by residual: dihedral pdb=" CA ALA C 520 " pdb=" C ALA C 520 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 62.46 30.54 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 1487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 207 0.038 - 0.077: 95 0.077 - 0.115: 37 0.115 - 0.154: 22 0.154 - 0.192: 3 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA LEU C 518 " pdb=" N LEU C 518 " pdb=" C LEU C 518 " pdb=" CB LEU C 518 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CB THR H 90 " pdb=" CA THR H 90 " pdb=" OG1 THR H 90 " pdb=" CG2 THR H 90 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 361 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO C 521 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO C 463 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 362 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C VAL C 362 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL C 362 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA C 363 " -0.011 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 757 2.82 - 3.34: 1959 3.34 - 3.86: 4099 3.86 - 4.38: 4610 4.38 - 4.90: 8120 Nonbonded interactions: 19545 Sorted by model distance: nonbonded pdb=" OG SER C 359 " pdb=" OD1 ASN C 394 " model vdw 2.300 3.040 nonbonded pdb=" O ASN C 481 " pdb=" NE2 GLN H 39 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.364 3.040 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.390 3.120 nonbonded pdb=" OG SER H 117 " pdb=" N SER H 118 " model vdw 2.392 3.120 ... (remaining 19540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.660 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.180 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.006 0.049 2534 Z= 0.395 Angle : 0.951 18.847 3447 Z= 0.482 Chirality : 0.057 0.192 364 Planarity : 0.007 0.057 447 Dihedral : 12.401 75.582 907 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.38 % Allowed : 1.51 % Favored : 98.11 % 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: -2.40 (0.41), residues: 307 helix: -4.35 (0.46), residues: 33 sheet: 0.00 (0.51), residues: 90 loop : -1.97 (0.37), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 436 HIS 0.001 0.000 HIS C 519 PHE 0.032 0.004 PHE C 347 TYR 0.028 0.003 TYR C 495 ARG 0.003 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: C 386 LYS cc_start: 0.8481 (mmtp) cc_final: 0.7351 (ttpt) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2075 time to fit residues: 19.6068 Evaluate side-chains 68 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 ASN C 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.095659 restraints weight = 4265.631| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.93 r_work: 0.3136 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2534 Z= 0.257 Angle : 0.627 11.381 3447 Z= 0.321 Chirality : 0.043 0.157 364 Planarity : 0.005 0.039 447 Dihedral : 5.640 26.047 369 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.26 % Allowed : 12.08 % Favored : 85.66 % 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: -1.99 (0.43), residues: 307 helix: -3.41 (0.62), residues: 34 sheet: 0.17 (0.53), residues: 90 loop : -1.74 (0.40), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.023 0.002 PHE C 456 TYR 0.019 0.001 TYR C 495 ARG 0.003 0.000 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.268 Fit side-chains REVERT: C 386 LYS cc_start: 0.8473 (mmtp) cc_final: 0.7350 (ttpt) REVERT: C 403 ARG cc_start: 0.8730 (ptt180) cc_final: 0.8387 (ptm-80) REVERT: H 22 CYS cc_start: 0.7170 (t) cc_final: 0.6937 (t) outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 0.2134 time to fit residues: 18.7018 Evaluate side-chains 77 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.0370 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.094570 restraints weight = 4317.035| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.02 r_work: 0.3130 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2534 Z= 0.237 Angle : 0.579 9.973 3447 Z= 0.299 Chirality : 0.043 0.147 364 Planarity : 0.004 0.034 447 Dihedral : 5.148 25.175 369 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.26 % Allowed : 14.34 % Favored : 83.40 % 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: -1.70 (0.45), residues: 307 helix: -3.01 (0.80), residues: 34 sheet: 0.35 (0.52), residues: 90 loop : -1.58 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.018 0.002 PHE C 456 TYR 0.019 0.001 TYR C 495 ARG 0.001 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.233 Fit side-chains REVERT: C 378 LYS cc_start: 0.8794 (mttm) cc_final: 0.8556 (mtpt) REVERT: C 386 LYS cc_start: 0.8473 (mmtp) cc_final: 0.7330 (ttpt) REVERT: H 22 CYS cc_start: 0.7190 (t) cc_final: 0.6921 (t) REVERT: H 79 TYR cc_start: 0.7976 (m-10) cc_final: 0.7611 (m-10) outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.2245 time to fit residues: 20.3453 Evaluate side-chains 77 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094183 restraints weight = 4334.142| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.03 r_work: 0.3115 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2534 Z= 0.228 Angle : 0.561 8.807 3447 Z= 0.291 Chirality : 0.043 0.142 364 Planarity : 0.004 0.034 447 Dihedral : 5.009 24.477 369 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.02 % Allowed : 14.72 % Favored : 82.26 % 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: -1.51 (0.46), residues: 307 helix: -3.01 (0.80), residues: 34 sheet: 0.75 (0.55), residues: 82 loop : -1.49 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.016 0.002 PHE C 456 TYR 0.018 0.001 TYR C 495 ARG 0.001 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.288 Fit side-chains REVERT: C 378 LYS cc_start: 0.8790 (mttm) cc_final: 0.8530 (mtpt) REVERT: C 386 LYS cc_start: 0.8465 (mmtp) cc_final: 0.7334 (ttpt) REVERT: C 403 ARG cc_start: 0.8669 (ptt180) cc_final: 0.8462 (ptt180) REVERT: C 481 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7775 (t0) REVERT: C 501 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8575 (m-10) REVERT: H 22 CYS cc_start: 0.7367 (t) cc_final: 0.7128 (t) REVERT: H 79 TYR cc_start: 0.7949 (m-10) cc_final: 0.7574 (m-10) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.2229 time to fit residues: 19.8424 Evaluate side-chains 78 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.093018 restraints weight = 4358.166| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.04 r_work: 0.3105 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2534 Z= 0.266 Angle : 0.574 8.195 3447 Z= 0.298 Chirality : 0.043 0.140 364 Planarity : 0.004 0.034 447 Dihedral : 5.077 24.675 369 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.64 % Allowed : 16.60 % Favored : 80.75 % 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: -1.49 (0.46), residues: 307 helix: -3.08 (0.79), residues: 34 sheet: 0.53 (0.53), residues: 88 loop : -1.38 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.014 0.002 PHE C 456 TYR 0.019 0.001 TYR C 495 ARG 0.002 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.293 Fit side-chains REVERT: C 378 LYS cc_start: 0.8794 (mttm) cc_final: 0.8543 (mtpt) REVERT: C 386 LYS cc_start: 0.8494 (mmtp) cc_final: 0.7421 (ttpt) REVERT: C 403 ARG cc_start: 0.8664 (ptt180) cc_final: 0.8443 (ptt180) REVERT: H 19 ARG cc_start: 0.8638 (ttm110) cc_final: 0.8116 (ttm110) REVERT: H 22 CYS cc_start: 0.7342 (t) cc_final: 0.7107 (t) REVERT: H 72 ASP cc_start: 0.8474 (t0) cc_final: 0.8046 (t0) REVERT: H 79 TYR cc_start: 0.7967 (m-10) cc_final: 0.7588 (m-10) REVERT: H 81 GLN cc_start: 0.8109 (tt0) cc_final: 0.7640 (tt0) outliers start: 7 outliers final: 4 residues processed: 79 average time/residue: 0.2194 time to fit residues: 19.4961 Evaluate side-chains 75 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093149 restraints weight = 4380.544| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.00 r_work: 0.3105 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2534 Z= 0.254 Angle : 0.565 7.782 3447 Z= 0.294 Chirality : 0.043 0.138 364 Planarity : 0.004 0.034 447 Dihedral : 5.058 24.826 369 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.02 % Allowed : 16.60 % Favored : 80.38 % 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: -1.46 (0.46), residues: 307 helix: -3.17 (0.76), residues: 34 sheet: 0.50 (0.52), residues: 88 loop : -1.31 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.009 0.001 PHE C 347 TYR 0.019 0.001 TYR C 495 ARG 0.002 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.289 Fit side-chains REVERT: C 378 LYS cc_start: 0.8806 (mttm) cc_final: 0.8537 (mtpt) REVERT: C 386 LYS cc_start: 0.8523 (mmtp) cc_final: 0.7471 (ttpt) REVERT: C 403 ARG cc_start: 0.8650 (ptt180) cc_final: 0.8405 (ptt180) REVERT: C 405 ASP cc_start: 0.8288 (p0) cc_final: 0.8079 (p0) REVERT: H 19 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8082 (ttm110) REVERT: H 22 CYS cc_start: 0.7250 (t) cc_final: 0.7023 (t) REVERT: H 72 ASP cc_start: 0.8434 (t0) cc_final: 0.8012 (t0) REVERT: H 79 TYR cc_start: 0.7962 (m-10) cc_final: 0.7588 (m-10) REVERT: H 81 GLN cc_start: 0.8148 (tt0) cc_final: 0.7553 (tt0) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.2218 time to fit residues: 19.6717 Evaluate side-chains 77 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092853 restraints weight = 4479.414| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.03 r_work: 0.3104 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2534 Z= 0.253 Angle : 0.557 7.593 3447 Z= 0.292 Chirality : 0.043 0.137 364 Planarity : 0.004 0.035 447 Dihedral : 5.066 24.860 369 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.77 % Allowed : 15.85 % Favored : 80.38 % 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: -1.42 (0.46), residues: 307 helix: -3.16 (0.77), residues: 34 sheet: 0.52 (0.52), residues: 88 loop : -1.28 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.012 0.002 PHE C 456 TYR 0.019 0.002 TYR C 473 ARG 0.002 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8800 (mttm) cc_final: 0.8522 (mtpt) REVERT: C 386 LYS cc_start: 0.8515 (mmtp) cc_final: 0.7463 (ttpt) REVERT: C 403 ARG cc_start: 0.8645 (ptt180) cc_final: 0.8385 (ptt180) REVERT: C 405 ASP cc_start: 0.8334 (p0) cc_final: 0.8121 (p0) REVERT: H 19 ARG cc_start: 0.8688 (ttm110) cc_final: 0.8347 (ttm110) REVERT: H 22 CYS cc_start: 0.7237 (t) cc_final: 0.7007 (t) REVERT: H 72 ASP cc_start: 0.8409 (t0) cc_final: 0.8013 (t0) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.2198 time to fit residues: 18.9831 Evaluate side-chains 80 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 13 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.093442 restraints weight = 4392.367| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.03 r_work: 0.3112 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2534 Z= 0.221 Angle : 0.553 7.490 3447 Z= 0.289 Chirality : 0.043 0.136 364 Planarity : 0.004 0.035 447 Dihedral : 4.963 24.552 369 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.02 % Allowed : 17.36 % Favored : 79.62 % 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: -1.34 (0.47), residues: 307 helix: -3.04 (0.94), residues: 27 sheet: 0.55 (0.52), residues: 88 loop : -1.31 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.008 0.001 PHE C 347 TYR 0.018 0.001 TYR C 473 ARG 0.002 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8793 (mttm) cc_final: 0.8509 (mtpt) REVERT: C 386 LYS cc_start: 0.8513 (mmtp) cc_final: 0.7462 (ttpt) REVERT: C 403 ARG cc_start: 0.8647 (ptt180) cc_final: 0.8392 (ptt180) REVERT: C 405 ASP cc_start: 0.8388 (p0) cc_final: 0.8170 (p0) REVERT: H 19 ARG cc_start: 0.8692 (ttm110) cc_final: 0.8370 (ttm110) REVERT: H 22 CYS cc_start: 0.7221 (t) cc_final: 0.6994 (t) REVERT: H 66 ARG cc_start: 0.8616 (mtm110) cc_final: 0.8413 (mtm110) REVERT: H 72 ASP cc_start: 0.8374 (t0) cc_final: 0.7976 (t0) outliers start: 8 outliers final: 7 residues processed: 78 average time/residue: 0.2335 time to fit residues: 20.3870 Evaluate side-chains 81 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN ** C 506 GLN ** 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 = 0.3495 r_free = 0.3495 target = 0.111506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093948 restraints weight = 4343.674| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.03 r_work: 0.3122 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2534 Z= 0.210 Angle : 0.556 7.304 3447 Z= 0.288 Chirality : 0.043 0.135 364 Planarity : 0.004 0.036 447 Dihedral : 4.892 23.880 369 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.40 % Allowed : 17.74 % Favored : 78.87 % 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: -1.27 (0.46), residues: 307 helix: -3.02 (0.94), residues: 27 sheet: 0.67 (0.54), residues: 82 loop : -1.24 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.012 0.001 PHE C 456 TYR 0.017 0.001 TYR C 473 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8801 (mttm) cc_final: 0.8515 (mtpt) REVERT: C 386 LYS cc_start: 0.8487 (mmtp) cc_final: 0.7464 (ttpt) REVERT: C 403 ARG cc_start: 0.8645 (ptt180) cc_final: 0.8394 (ptt180) REVERT: C 405 ASP cc_start: 0.8417 (p0) cc_final: 0.8204 (p0) REVERT: H 17 SER cc_start: 0.8387 (p) cc_final: 0.7850 (m) REVERT: H 19 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8405 (ttm110) REVERT: H 22 CYS cc_start: 0.7200 (t) cc_final: 0.6967 (t) REVERT: H 66 ARG cc_start: 0.8628 (mtm110) cc_final: 0.8424 (mtm110) REVERT: H 72 ASP cc_start: 0.8387 (t0) cc_final: 0.8010 (t0) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.2273 time to fit residues: 19.5731 Evaluate side-chains 80 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094072 restraints weight = 4322.942| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.03 r_work: 0.3117 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2534 Z= 0.226 Angle : 0.562 7.265 3447 Z= 0.293 Chirality : 0.044 0.135 364 Planarity : 0.004 0.036 447 Dihedral : 4.900 23.605 369 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.02 % Allowed : 18.87 % Favored : 78.11 % 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: -1.22 (0.47), residues: 307 helix: -3.00 (0.96), residues: 27 sheet: 0.71 (0.55), residues: 82 loop : -1.20 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.000 0.000 HIS C 519 PHE 0.008 0.001 PHE C 347 TYR 0.017 0.001 TYR C 495 ARG 0.002 0.000 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 614 Ramachandran restraints generated. 307 Oldfield, 0 Emsley, 307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: C 378 LYS cc_start: 0.8794 (mttm) cc_final: 0.8509 (mtpt) REVERT: C 386 LYS cc_start: 0.8510 (mmtp) cc_final: 0.7449 (ttpt) REVERT: C 403 ARG cc_start: 0.8653 (ptt180) cc_final: 0.8393 (ptt180) REVERT: C 405 ASP cc_start: 0.8415 (p0) cc_final: 0.8197 (p0) REVERT: H 17 SER cc_start: 0.8382 (p) cc_final: 0.7877 (m) REVERT: H 19 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8387 (ttm110) REVERT: H 22 CYS cc_start: 0.7214 (t) cc_final: 0.6978 (t) REVERT: H 66 ARG cc_start: 0.8624 (mtm110) cc_final: 0.8388 (mtm110) REVERT: H 72 ASP cc_start: 0.8359 (t0) cc_final: 0.7986 (t0) REVERT: H 113 LEU cc_start: 0.8847 (tt) cc_final: 0.8596 (mp) outliers start: 8 outliers final: 7 residues processed: 78 average time/residue: 0.2464 time to fit residues: 21.7305 Evaluate side-chains 79 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 0.0010 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 481 ASN C 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.095006 restraints weight = 4371.541| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.08 r_work: 0.3129 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2534 Z= 0.212 Angle : 0.556 7.246 3447 Z= 0.290 Chirality : 0.043 0.136 364 Planarity : 0.004 0.036 447 Dihedral : 4.876 23.415 369 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.02 % Allowed : 19.25 % Favored : 77.74 % 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: -1.21 (0.47), residues: 307 helix: -3.00 (0.96), residues: 27 sheet: 0.72 (0.56), residues: 82 loop : -1.20 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 PHE 0.011 0.001 PHE C 456 TYR 0.017 0.001 TYR C 495 ARG 0.002 0.000 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1894.06 seconds wall clock time: 33 minutes 4.57 seconds (1984.57 seconds total)