Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.26, per 1000 atoms: 0.37 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.42 Conformation dependent library (CDL) restraints added in 198.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 528 0.91 - 1.16: 1115 1.16 - 1.42: 620 1.42 - 1.67: 851 1.67 - 1.93: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.524 1.772 -0.248 1.26e-02 6.30e+03 3.87e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.163 0.215 1.10e-02 8.26e+03 3.82e+02 bond pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta sigma weight residual 1.456 1.240 0.215 1.11e-02 8.12e+03 3.76e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.512 -0.191 1.00e-02 1.00e+04 3.63e+02 bond pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 1.466 1.242 0.223 1.19e-02 7.06e+03 3.52e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3338 4.85 - 9.69: 1833 9.69 - 14.54: 495 14.54 - 19.39: 105 19.39 - 24.23: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 71 " pdb=" C VAL A 71 " pdb=" N LEU A 72 " ideal model delta sigma weight residual 123.18 104.97 18.21 1.05e+00 9.07e-01 3.01e+02 angle pdb=" O SER A 47 " pdb=" C SER A 47 " pdb=" N ARG A 48 " ideal model delta sigma weight residual 122.12 138.53 -16.41 1.06e+00 8.90e-01 2.40e+02 angle pdb=" CA AGLU A 94 " pdb=" C AGLU A 94 " pdb=" O AGLU A 94 " ideal model delta sigma weight residual 119.97 104.45 15.52 1.15e+00 7.56e-01 1.82e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 133.76 -12.41 9.20e-01 1.18e+00 1.82e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.83 108.18 13.65 1.03e+00 9.43e-01 1.76e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.43: 1323 18.43 - 36.86: 115 36.86 - 55.29: 30 55.29 - 73.72: 10 73.72 - 92.15: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N LYS A 62 " pdb=" C LYS A 62 " pdb=" CA LYS A 62 " pdb=" CB LYS A 62 " ideal model delta harmonic sigma weight residual 122.80 144.01 -21.21 0 2.50e+00 1.60e-01 7.20e+01 dihedral pdb=" C LYS A 62 " pdb=" N LYS A 62 " pdb=" CA LYS A 62 " pdb=" CB LYS A 62 " ideal model delta harmonic sigma weight residual -122.60 -143.20 20.60 0 2.50e+00 1.60e-01 6.79e+01 dihedral pdb=" C BLYS A 175 " pdb=" N BLYS A 175 " pdb=" CA BLYS A 175 " pdb=" CB BLYS A 175 " ideal model delta harmonic sigma weight residual -122.60 -142.30 19.70 0 2.50e+00 1.60e-01 6.21e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.218: 109 0.218 - 0.430: 74 0.430 - 0.641: 31 0.641 - 0.853: 24 0.853 - 1.064: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -3.69 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA BLYS A 175 " pdb=" N BLYS A 175 " pdb=" C BLYS A 175 " pdb=" CB BLYS A 175 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA ILE A 117 " pdb=" N ILE A 117 " pdb=" C ILE A 117 " pdb=" CB ILE A 117 " both_signs ideal model delta sigma weight residual False 2.43 3.39 -0.95 2.00e-01 2.50e+01 2.27e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.043 2.00e-02 2.50e+03 7.35e-02 1.62e+02 pdb=" CG TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.110 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.145 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.058 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.052 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.126 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.058 2.00e-02 2.50e+03 6.04e-02 1.10e+02 pdb=" CG PHE A 119 " -0.114 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.098 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.056 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " -0.002 2.00e-02 2.50e+03 7.06e-02 7.48e+01 pdb=" CG ASN A 173 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " -0.126 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " 0.010 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.101 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 717 2.27 - 2.85: 7812 2.85 - 3.43: 10581 3.43 - 4.02: 15362 4.02 - 4.60: 22067 Nonbonded interactions: 56539 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.685 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.771 2.450 x-y,-y,-z-4/3 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.773 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.798 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.801 2.450 x-y,-y,-z-4/3 ... (remaining 56534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_2963595_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.2083 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475143 | | target function (ml) not normalized (work): 22062.456019 | | target function (ml) not normalized (free): 1152.447934 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3796 0.2247 4.8531 4.9072| | 2: 3.78 - 3.00 1.00 2430 110 0.3402 0.1806 4.0863 4.142| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.92 0.83 0.13 6617.97| | 2: 3.78 - 3.00 2430 110 0.94 11.44 1.48 0.26 456.50| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 388.37 max = 12072.86 mean = 3580.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.44| |phase err.(test): min = 0.00 max = 90.00 mean = 33.60| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.248 1557 Z= 5.538 Angle : 5.254 18.207 2118 Z= 3.716 Chirality : 0.387 1.064 243 Planarity : 0.031 0.106 284 Dihedral : 14.341 92.155 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.81 % Peptide Plane: Cis-proline : 18.18 % 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: -2.73 (0.47), residues: 224 helix: -2.83 (0.34), residues: 102 sheet: -0.89 (1.00), residues: 28 loop : -0.57 (0.57), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.012 ARG A 145 TYR 0.073 0.033 TYR A 139 PHE 0.119 0.037 PHE A 119 HIS 0.065 0.031 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.2083 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.475143 | | target function (ml) not normalized (work): 22062.456019 | | target function (ml) not normalized (free): 1152.447934 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3582 0.3655 0.2200 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3582 0.3655 0.2200 n_refl.: 5182 remove outliers: r(all,work,free)=0.2537 0.2557 0.2200 n_refl.: 5178 overall B=-2.81 to atoms: r(all,work,free)=0.2430 0.2447 0.2146 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1581 0.1578 0.1642 n_refl.: 5178 remove outliers: r(all,work,free)=0.1579 0.1576 0.1642 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.3988 445.148 406.781 0.679 1.010 0.400 11.894-9.307 99.02 97 4 0.1863 714.631 690.861 0.965 1.012 0.393 9.237-7.194 100.00 213 7 0.2194 584.426 571.870 0.986 1.011 0.349 7.162-5.571 100.00 427 22 0.2260 438.541 422.783 0.943 1.009 0.346 5.546-4.326 100.00 867 58 0.1384 602.054 591.707 0.972 1.005 0.226 4.315-3.360 100.00 1859 96 0.1327 572.560 566.853 1.024 0.998 0.200 3.356-3.002 100.00 1373 60 0.1651 441.010 436.002 1.018 0.991 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.9049 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1576 r_free=0.1642 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1576 r_free=0.1642 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.239401 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.869712 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1171 0.1795 0.0624 0.010 1.0 1.6 0.5 0.0 0 9.620 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.71 17.95 6.24 3.013 16.046 1.870 0.018 10.26 17.76 7.50 5.087 16.369 1.870 0.015 Individual atomic B min max mean iso aniso Overall: 2.27 111.62 17.69 5.42 1785 0 Protein: 2.27 111.62 15.00 5.41 1519 0 Water: 4.05 111.49 33.30 N/A 258 0 Other: 16.97 37.52 24.73 N/A 8 0 Chain A: 2.27 111.62 17.69 N/A 1785 0 Histogram: Values Number of atoms 2.27 - 13.20 892 13.20 - 24.14 504 24.14 - 35.07 194 35.07 - 46.01 106 46.01 - 56.94 57 56.94 - 67.88 15 67.88 - 78.81 8 78.81 - 89.75 5 89.75 - 100.68 1 100.68 - 111.62 3 =========================== Idealize ADP of riding H ========================== r_work=0.1026 r_free=0.1776 r_work=0.1020 r_free=0.1781 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1020 r_free = 0.1781 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1023 r_free = 0.1775 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1023 r_free= 0.1775 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.014293 | | target function (ls_wunit_k1) not normalized (work): 70.391397 | | target function (ls_wunit_k1) not normalized (free): 10.459683 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1061 0.1023 0.1775 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2136 0.2136 0.2243 n_refl.: 5177 remove outliers: r(all,work,free)=0.2136 0.2136 0.2243 n_refl.: 5177 overall B=-1.02 to atoms: r(all,work,free)=0.2091 0.2090 0.2231 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1020 0.1763 n_refl.: 5177 remove outliers: r(all,work,free)=0.1056 0.1018 0.1763 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3429 315.441 299.148 0.644 0.999 0.365 11.894-9.307 99.02 97 4 0.1516 510.760 502.175 0.962 1.002 0.361 9.237-7.194 100.00 213 7 0.1678 417.700 417.199 1.000 1.002 0.331 7.162-5.571 100.00 427 22 0.1638 313.433 310.076 0.958 1.002 0.322 5.546-4.326 100.00 867 58 0.0920 430.299 426.871 0.971 1.001 0.212 4.315-3.360 100.00 1859 96 0.0768 409.219 409.349 1.018 1.000 0.204 3.356-3.002 100.00 1373 60 0.1003 315.198 313.870 0.997 1.000 0.103 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.5551 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1018 r_free=0.1763 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1018 r_free=0.1763 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1018 r_free=0.1763 | n_water=258 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.1052 r_free=0.1762 | n_water=247 | time (s): 20.020 (total time: 20.530) Filter (q & B) r_work=0.1051 r_free=0.1768 | n_water=244 | time (s): 1.900 (total time: 22.430) Compute maps r_work=0.1051 r_free=0.1768 | n_water=244 | time (s): 0.470 (total time: 22.900) Filter (map) r_work=0.1345 r_free=0.1914 | n_water=142 | time (s): 1.680 (total time: 24.580) Find peaks r_work=0.1345 r_free=0.1914 | n_water=142 | time (s): 0.620 (total time: 25.200) Add new water r_work=0.1682 r_free=0.2212 | n_water=227 | time (s): 1.690 (total time: 26.890) Refine new water occ: r_work=0.1153 r_free=0.1728 adp: r_work=0.1133 r_free=0.1731 occ: r_work=0.1129 r_free=0.1713 adp: r_work=0.1119 r_free=0.1721 occ: r_work=0.1118 r_free=0.1706 adp: r_work=0.1115 r_free=0.1712 ADP+occupancy (water only), MIN, final r_work=0.1115 r_free=0.1712 r_work=0.1115 r_free=0.1712 | n_water=227 | time (s): 4.170 (total time: 31.060) Filter (q & B) r_work=0.1116 r_free=0.1717 | n_water=226 | time (s): 1.740 (total time: 32.800) Filter (dist only) r_work=0.1126 r_free=0.1692 | n_water=222 | time (s): 17.560 (total time: 50.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.831556 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.866612 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1007 0.1834 0.0827 0.009 1.0 4.8 0.5 0.6 0 11.916 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.07 18.34 8.27 4.756 16.984 2.867 0.014 9.37 18.54 9.17 5.731 17.512 2.867 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.04 16.98 6.80 1749 0 Protein: 0.00 107.04 15.56 6.79 1519 0 Water: 0.00 62.75 26.48 N/A 222 0 Other: 11.06 33.54 21.93 N/A 8 0 Chain A: 0.00 107.04 16.19 N/A 1666 0 Chain S: 0.36 59.27 32.73 N/A 83 0 Histogram: Values Number of atoms 0.00 - 10.70 625 10.70 - 21.41 709 21.41 - 32.11 213 32.11 - 42.81 116 42.81 - 53.52 42 53.52 - 64.22 30 64.22 - 74.93 6 74.93 - 85.63 4 85.63 - 96.33 2 96.33 - 107.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.0937 r_free=0.1854 r_work=0.0935 r_free=0.1855 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0935 r_free = 0.1855 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0932 r_free = 0.1837 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0932 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.011883 | | target function (ls_wunit_k1) not normalized (work): 58.510796 | | target function (ls_wunit_k1) not normalized (free): 10.008260 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0977 0.0932 0.1837 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2172 0.2179 0.2196 n_refl.: 5176 remove outliers: r(all,work,free)=0.2172 0.2179 0.2196 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2172 0.2179 0.2196 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0977 0.0932 0.1841 n_refl.: 5176 remove outliers: r(all,work,free)=0.0977 0.0932 0.1841 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3323 315.441 298.921 0.634 0.999 0.360 11.894-9.307 99.02 97 4 0.1472 510.760 508.782 0.962 1.002 0.340 9.237-7.194 100.00 213 7 0.1434 417.700 418.071 0.998 1.003 0.320 7.162-5.571 100.00 427 22 0.1414 313.433 311.605 0.968 1.002 0.320 5.546-4.326 100.00 867 58 0.0785 430.299 427.306 0.977 1.002 0.230 4.315-3.360 100.00 1859 96 0.0721 409.219 409.246 1.029 1.001 0.210 3.356-3.002 100.00 1373 60 0.0960 315.198 314.219 1.009 0.999 0.100 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-5.1373 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0932 r_free=0.1841 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0933 r_free=0.1841 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0933 r_free=0.1841 | n_water=222 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0955 r_free=0.1828 | n_water=216 | time (s): 18.290 (total time: 18.850) Filter (q & B) r_work=0.0995 r_free=0.1824 | n_water=214 | time (s): 1.510 (total time: 20.360) Compute maps r_work=0.0995 r_free=0.1824 | n_water=214 | time (s): 0.480 (total time: 20.840) Filter (map) r_work=0.1258 r_free=0.1867 | n_water=145 | time (s): 1.210 (total time: 22.050) Find peaks r_work=0.1258 r_free=0.1867 | n_water=145 | time (s): 0.390 (total time: 22.440) Add new water r_work=0.1625 r_free=0.2224 | n_water=228 | time (s): 1.160 (total time: 23.600) Refine new water occ: r_work=0.1043 r_free=0.1777 adp: r_work=0.1040 r_free=0.1787 occ: r_work=0.1031 r_free=0.1775 adp: r_work=0.1030 r_free=0.1779 occ: r_work=0.1024 r_free=0.1769 adp: r_work=0.1022 r_free=0.1771 ADP+occupancy (water only), MIN, final r_work=0.1022 r_free=0.1771 r_work=0.1022 r_free=0.1771 | n_water=228 | time (s): 7.780 (total time: 31.380) Filter (q & B) r_work=0.1023 r_free=0.1785 | n_water=226 | time (s): 1.730 (total time: 33.110) Filter (dist only) r_work=0.1034 r_free=0.1789 | n_water=224 | time (s): 16.380 (total time: 49.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.104080 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.239128 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0934 0.1814 0.0880 0.011 1.1 6.4 0.5 0.6 0 0.552 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.34 18.14 8.80 5.645 18.293 0.239 5.133 8.89 18.54 9.65 7.435 18.326 0.239 5.038 Individual atomic B min max mean iso aniso Overall: 0.00 106.97 16.78 9.20 1751 0 Protein: 0.00 106.97 15.77 9.18 1519 0 Water: 0.00 57.75 23.41 N/A 224 0 Other: 6.06 38.81 22.00 N/A 8 0 Chain A: 0.00 106.97 16.29 N/A 1651 0 Chain S: 0.00 53.39 24.79 N/A 100 0 Histogram: Values Number of atoms 0.00 - 10.70 622 10.70 - 21.39 691 21.39 - 32.09 264 32.09 - 42.79 103 42.79 - 53.49 36 53.49 - 64.18 14 64.18 - 74.88 14 74.88 - 85.58 3 85.58 - 96.27 3 96.27 - 106.97 1 =========================== Idealize ADP of riding H ========================== r_work=0.0889 r_free=0.1854 r_work=0.0894 r_free=0.1864 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0894 r_free = 0.1864 target_work(ml) = 5.041 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0886 r_free = 0.1858 target_work(ml) = 5.035 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0886 r_free= 0.1858 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.034954 | | target function (ml) not normalized (work): 24792.113204 | | target function (ml) not normalized (free): 1886.517142 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0934 0.0886 0.1858 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2195 0.2206 0.2171 n_refl.: 5176 remove outliers: r(all,work,free)=0.2195 0.2206 0.2171 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2195 0.2206 0.2171 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0926 0.0878 0.1845 n_refl.: 5176 remove outliers: r(all,work,free)=0.0924 0.0876 0.1845 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3692 317.502 286.480 0.580 0.993 0.330 11.894-9.307 99.02 97 4 0.1750 510.760 495.609 0.953 0.997 0.330 9.237-7.194 100.00 213 7 0.1815 417.700 412.937 1.010 0.999 0.330 7.162-5.571 100.00 427 22 0.1779 313.433 305.466 0.990 1.000 0.330 5.546-4.326 100.00 867 58 0.0907 430.299 424.950 1.007 1.001 0.250 4.315-3.360 100.00 1859 96 0.0587 409.219 408.828 1.068 1.003 0.220 3.356-3.002 100.00 1373 60 0.0603 315.198 315.496 1.048 1.004 0.087 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.0203 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0876 r_free=0.1845 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0876 r_free=0.1845 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0876 r_free=0.1845 | n_water=224 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0895 r_free=0.1870 | n_water=220 | time (s): 17.940 (total time: 18.450) Filter (q & B) r_work=0.0937 r_free=0.1891 | n_water=217 | time (s): 1.840 (total time: 20.290) Compute maps r_work=0.0937 r_free=0.1891 | n_water=217 | time (s): 0.640 (total time: 20.930) Filter (map) r_work=0.1203 r_free=0.1899 | n_water=151 | time (s): 1.510 (total time: 22.440) Find peaks r_work=0.1203 r_free=0.1899 | n_water=151 | time (s): 0.480 (total time: 22.920) Add new water r_work=0.1504 r_free=0.2165 | n_water=220 | time (s): 1.700 (total time: 24.620) Refine new water occ: r_work=0.1007 r_free=0.1772 adp: r_work=0.1004 r_free=0.1784 occ: r_work=0.0996 r_free=0.1765 adp: r_work=0.0995 r_free=0.1774 occ: r_work=0.0987 r_free=0.1760 adp: r_work=0.0986 r_free=0.1767 ADP+occupancy (water only), MIN, final r_work=0.0986 r_free=0.1767 r_work=0.0986 r_free=0.1767 | n_water=220 | time (s): 12.470 (total time: 37.090) Filter (q & B) r_work=0.0987 r_free=0.1767 | n_water=219 | time (s): 1.930 (total time: 39.020) Filter (dist only) r_work=0.0986 r_free=0.1771 | n_water=218 | time (s): 16.830 (total time: 55.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.030908 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.218527 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0892 0.1821 0.0929 0.011 1.1 5.4 0.5 0.6 0 0.515 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.92 18.21 9.29 7.162 18.507 0.219 5.008 8.67 18.36 9.69 8.477 18.639 0.219 4.943 Individual atomic B min max mean iso aniso Overall: 0.00 108.49 17.13 11.08 1745 0 Protein: 0.00 108.49 16.22 11.06 1519 0 Water: 0.00 60.43 23.30 N/A 218 0 Other: 5.99 37.93 21.47 N/A 8 0 Chain A: 0.00 108.49 16.63 N/A 1644 0 Chain S: 0.00 60.43 25.19 N/A 101 0 Histogram: Values Number of atoms 0.00 - 10.85 621 10.85 - 21.70 673 21.70 - 32.55 273 32.55 - 43.39 96 43.39 - 54.24 45 54.24 - 65.09 15 65.09 - 75.94 11 75.94 - 86.79 6 86.79 - 97.64 3 97.64 - 108.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.0867 r_free=0.1836 r_work=0.0871 r_free=0.1840 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0871 r_free = 0.1840 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0861 r_free = 0.1827 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0861 r_free= 0.1827 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.941810 | | target function (ml) not normalized (work): 24328.528443 | | target function (ml) not normalized (free): 2168.485119 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0908 0.0861 0.1827 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2172 0.2176 0.2225 n_refl.: 5175 remove outliers: r(all,work,free)=0.2172 0.2176 0.2225 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2172 0.2176 0.2225 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0908 0.0861 0.1829 n_refl.: 5175 remove outliers: r(all,work,free)=0.0908 0.0861 0.1829 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3703 317.502 293.326 0.584 0.989 0.320 11.894-9.307 99.02 97 4 0.1873 510.760 495.611 0.960 0.993 0.323 9.237-7.194 100.00 213 7 0.1949 417.700 411.363 1.009 0.996 0.311 7.162-5.571 100.00 427 22 0.1911 313.433 304.439 0.993 0.997 0.300 5.546-4.326 100.00 867 58 0.0968 430.299 424.839 1.015 0.999 0.254 4.315-3.360 100.00 1859 96 0.0557 409.219 409.109 1.080 1.002 0.238 3.356-3.002 100.00 1373 60 0.0458 315.198 315.635 1.061 1.004 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.5752 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0861 r_free=0.1829 After: r_work=0.0863 r_free=0.1828 ================================== NQH flips ================================== r_work=0.0863 r_free=0.1828 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0863 r_free=0.1828 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0863 r_free=0.1828 | n_water=218 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0869 r_free=0.1840 | n_water=216 | time (s): 17.100 (total time: 17.650) Filter (q & B) r_work=0.0984 r_free=0.1874 | n_water=212 | time (s): 1.800 (total time: 19.450) Compute maps r_work=0.0984 r_free=0.1874 | n_water=212 | time (s): 0.560 (total time: 20.010) Filter (map) r_work=0.1240 r_free=0.1966 | n_water=152 | time (s): 1.450 (total time: 21.460) Find peaks r_work=0.1240 r_free=0.1966 | n_water=152 | time (s): 0.440 (total time: 21.900) Add new water r_work=0.1525 r_free=0.2218 | n_water=221 | time (s): 1.340 (total time: 23.240) Refine new water occ: r_work=0.0979 r_free=0.1792 adp: r_work=0.0967 r_free=0.1805 occ: r_work=0.0961 r_free=0.1786 adp: r_work=0.0960 r_free=0.1798 occ: r_work=0.0954 r_free=0.1780 adp: r_work=0.0953 r_free=0.1791 ADP+occupancy (water only), MIN, final r_work=0.0953 r_free=0.1791 r_work=0.0953 r_free=0.1791 | n_water=221 | time (s): 10.240 (total time: 33.480) Filter (q & B) r_work=0.0953 r_free=0.1794 | n_water=220 | time (s): 1.760 (total time: 35.240) Filter (dist only) r_work=0.0953 r_free=0.1799 | n_water=219 | time (s): 18.090 (total time: 53.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.892936 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.220413 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0904 0.1837 0.0934 0.010 1.1 9.0 0.5 0.6 0 0.446 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.04 18.37 9.34 8.413 18.968 0.220 4.983 8.87 18.43 9.55 9.024 19.053 0.220 4.934 Individual atomic B min max mean iso aniso Overall: 0.00 109.76 17.36 11.97 1746 0 Protein: 0.00 109.76 16.51 11.95 1519 0 Water: 0.00 60.11 23.18 N/A 219 0 Other: 4.23 39.31 19.97 N/A 8 0 Chain A: 0.00 109.76 16.88 N/A 1639 0 Chain S: 0.00 60.11 24.83 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.98 611 10.98 - 21.95 676 21.95 - 32.93 276 32.93 - 43.90 108 43.90 - 54.88 38 54.88 - 65.86 16 65.86 - 76.83 9 76.83 - 87.81 8 87.81 - 98.78 2 98.78 - 109.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.0887 r_free=0.1843 r_work=0.0890 r_free=0.1848 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0890 r_free = 0.1848 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1837 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.932473 | | target function (ml) not normalized (work): 24282.566644 | | target function (ml) not normalized (free): 2283.940523 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1244 0.1776 5.4964 6.2032| | 2: 3.78 - 3.00 1.00 2430 110 0.0439 0.1939 4.3539 12.755| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.92 11.77 1.00 0.96 11823.07| | 2: 3.78 - 3.00 2430 110 0.99 1.90 1.00 0.98 894.37| |alpha: min = 0.95 max = 0.98 mean = 0.97| |beta: min = 574.64 max = 19581.02 mean = 6428.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.58 mean = 6.90| |phase err.(test): min = 0.00 max = 87.15 mean = 7.08| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0929 0.0881 0.1837 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2213 0.2220 0.2180 n_refl.: 5175 remove outliers: r(all,work,free)=0.2213 0.2220 0.2180 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2213 0.2220 0.2180 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0930 0.0882 0.1844 n_refl.: 5175 remove outliers: r(all,work,free)=0.0930 0.0882 0.1844 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3843 317.502 289.758 0.593 0.989 0.324 11.894-9.307 99.02 97 4 0.1870 510.760 497.713 0.961 0.995 0.320 9.237-7.194 100.00 213 7 0.1993 417.700 411.260 1.008 0.998 0.313 7.162-5.571 100.00 427 22 0.1984 313.433 304.943 0.993 0.999 0.297 5.546-4.326 100.00 867 58 0.1042 430.299 425.089 1.019 1.000 0.249 4.315-3.360 100.00 1859 96 0.0575 409.219 409.012 1.095 1.001 0.230 3.356-3.002 100.00 1373 60 0.0414 315.198 315.255 1.080 1.002 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.2149 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3619 0.2083 0.082 5.254 8.8 119.3 19.9 258 0.000 1_bss: 0.1576 0.1642 0.082 5.254 6.0 116.5 17.1 258 0.000 1_settarget: 0.1576 0.1642 0.082 5.254 6.0 116.5 17.1 258 0.000 1_nqh: 0.1576 0.1642 0.082 5.254 6.0 116.5 17.1 258 0.000 1_weight: 0.1576 0.1642 0.082 5.254 6.0 116.5 17.1 258 0.000 1_xyzrec: 0.1171 0.1795 0.010 0.978 6.0 116.5 17.1 258 0.195 1_adp: 0.1026 0.1776 0.010 0.978 2.3 111.6 17.7 258 0.195 1_regHadp: 0.1020 0.1781 0.010 0.978 2.3 111.6 17.7 258 0.195 1_occ: 0.1023 0.1775 0.010 0.978 2.3 111.6 17.7 258 0.195 2_bss: 0.1018 0.1763 0.010 0.978 1.3 110.6 16.7 258 0.195 2_settarget: 0.1018 0.1763 0.010 0.978 1.3 110.6 16.7 258 0.195 2_updatecdl: 0.1018 0.1763 0.010 0.996 1.3 110.6 16.7 258 0.195 2_nqh: 0.1018 0.1763 0.010 0.996 1.3 110.6 16.7 258 0.195 2_sol: 0.1126 0.1692 0.010 0.996 1.0 110.6 16.0 222 n/a 2_weight: 0.1126 0.1692 0.010 0.996 1.0 110.6 16.0 222 n/a 2_xyzrec: 0.1007 0.1834 0.009 0.993 1.0 110.6 16.0 222 n/a 2_adp: 0.0937 0.1854 0.009 0.993 0.0 107.0 17.0 222 n/a 2_regHadp: 0.0935 0.1855 0.009 0.993 0.0 107.0 17.0 222 n/a 2_occ: 0.0932 0.1837 0.009 0.993 0.0 107.0 17.0 222 n/a 3_bss: 0.0932 0.1841 0.009 0.993 0.0 107.0 17.0 222 n/a 3_settarget: 0.0932 0.1841 0.009 0.993 0.0 107.0 17.0 222 n/a 3_updatecdl: 0.0932 0.1841 0.009 1.004 0.0 107.0 17.0 222 n/a 3_nqh: 0.0933 0.1841 0.009 1.004 0.0 107.0 17.0 222 n/a 3_sol: 0.1034 0.1789 0.009 1.004 0.0 107.0 16.7 224 n/a 3_weight: 0.1034 0.1789 0.009 1.004 0.0 107.0 16.7 224 n/a 3_xyzrec: 0.0934 0.1814 0.011 1.086 0.0 107.0 16.7 224 n/a 3_adp: 0.0889 0.1854 0.011 1.086 0.0 107.0 16.8 224 n/a 3_regHadp: 0.0894 0.1864 0.011 1.086 0.0 107.0 16.8 224 n/a 3_occ: 0.0886 0.1858 0.011 1.086 0.0 107.0 16.8 224 n/a 4_bss: 0.0876 0.1845 0.011 1.086 0.0 107.0 16.8 224 n/a 4_settarget: 0.0876 0.1845 0.011 1.086 0.0 107.0 16.8 224 n/a 4_updatecdl: 0.0876 0.1845 0.011 1.090 0.0 107.0 16.8 224 n/a 4_nqh: 0.0876 0.1845 0.011 1.090 0.0 107.0 16.8 224 n/a 4_sol: 0.0986 0.1771 0.011 1.090 0.0 107.0 16.9 218 n/a 4_weight: 0.0986 0.1771 0.011 1.090 0.0 107.0 16.9 218 n/a 4_xyzrec: 0.0892 0.1821 0.011 1.060 0.0 107.0 16.9 218 n/a 4_adp: 0.0867 0.1836 0.011 1.060 0.0 108.5 17.1 218 n/a 4_regHadp: 0.0871 0.1840 0.011 1.060 0.0 108.5 17.1 218 n/a 4_occ: 0.0861 0.1827 0.011 1.060 0.0 108.5 17.1 218 n/a 5_bss: 0.0861 0.1829 0.011 1.060 0.0 108.5 17.1 218 n/a 5_settarget: 0.0861 0.1829 0.011 1.060 0.0 108.5 17.1 218 n/a 5_updatecdl: 0.0861 0.1829 0.011 1.058 0.0 108.5 17.1 218 n/a 5_setrh: 0.0863 0.1828 0.011 1.058 0.0 108.5 17.1 218 n/a 5_nqh: 0.0863 0.1828 0.011 1.058 0.0 108.5 17.1 218 n/a 5_sol: 0.0953 0.1799 0.011 1.058 0.0 108.5 17.2 219 n/a 5_weight: 0.0953 0.1799 0.011 1.058 0.0 108.5 17.2 219 n/a 5_xyzrec: 0.0904 0.1837 0.010 1.084 0.0 108.5 17.2 219 n/a 5_adp: 0.0887 0.1843 0.010 1.084 0.0 109.8 17.4 219 n/a 5_regHadp: 0.0890 0.1848 0.010 1.084 0.0 109.8 17.4 219 n/a 5_occ: 0.0881 0.1837 0.010 1.084 0.0 109.8 17.4 219 n/a end: 0.0882 0.1844 0.010 1.084 0.0 109.8 17.4 219 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2963595_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2963595_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7200 Refinement macro-cycles (run) : 481.4200 Write final files (write_after_run_outputs) : 10.8200 Total : 495.9600 Total CPU time: 8.63 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:00 PST -0800 (1735492740.04 s) Start R-work = 0.1576, R-free = 0.1642 Final R-work = 0.0882, R-free = 0.1844 =============================================================================== Job complete usr+sys time: 525.83 seconds wall clock time: 9 minutes 8.58 seconds (548.58 seconds total)