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_4426565.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4426565.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4426565.pdb" 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" 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 3 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: 1.14, per 1000 atoms: 0.34 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: 0.35 Conformation dependent library (CDL) restraints added in 148.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.60 - 0.86: 293 0.86 - 1.12: 1283 1.12 - 1.38: 539 1.38 - 1.64: 957 1.64 - 1.90: 81 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 152 " pdb=" N BLEU A 153 " ideal model delta sigma weight residual 1.331 1.591 -0.260 1.34e-02 5.57e+03 3.77e+02 bond pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 1.334 1.104 0.230 1.25e-02 6.40e+03 3.38e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.130 0.196 1.10e-02 8.26e+03 3.16e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.183 0.195 1.10e-02 8.26e+03 3.15e+02 bond pdb=" C MET A 17 " pdb=" O MET A 17 " ideal model delta sigma weight residual 1.236 1.034 0.202 1.15e-02 7.56e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 2974 4.40 - 8.80: 1886 8.80 - 13.20: 737 13.20 - 17.60: 160 17.60 - 22.00: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 105.02 14.18 9.00e-01 1.23e+00 2.48e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 137.48 -15.71 1.00e+00 1.00e+00 2.47e+02 angle pdb=" O SER A 57 " pdb=" C SER A 57 " pdb=" N LEU A 58 " ideal model delta sigma weight residual 122.96 105.96 17.00 1.13e+00 7.83e-01 2.26e+02 angle pdb=" O LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " ideal model delta sigma weight residual 122.07 106.73 15.34 1.03e+00 9.43e-01 2.22e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.32 135.38 -16.06 1.12e+00 7.97e-01 2.06e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.43: 1317 17.43 - 34.84: 110 34.84 - 52.25: 36 52.25 - 69.65: 16 69.65 - 87.06: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -139.89 17.29 0 2.50e+00 1.60e-01 4.78e+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 -139.75 17.15 0 2.50e+00 1.60e-01 4.70e+01 dihedral pdb=" C BASN A 76 " pdb=" N BASN A 76 " pdb=" CA BASN A 76 " pdb=" CB BASN A 76 " ideal model delta harmonic sigma weight residual -122.60 -139.41 16.81 0 2.50e+00 1.60e-01 4.52e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.193: 92 0.193 - 0.385: 70 0.385 - 0.577: 51 0.577 - 0.769: 23 0.769 - 0.961: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BASN A 76 " pdb=" N BASN A 76 " pdb=" C BASN A 76 " pdb=" CB BASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA BLYS A 93 " pdb=" N BLYS A 93 " pdb=" C BLYS A 93 " pdb=" CB BLYS A 93 " both_signs ideal model delta sigma weight residual False 2.51 3.43 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA ALA A 2 " pdb=" N ALA A 2 " pdb=" C ALA A 2 " pdb=" CB ALA A 2 " both_signs ideal model delta sigma weight residual False 2.48 3.40 -0.92 2.00e-01 2.50e+01 2.10e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.053 2.00e-02 2.50e+03 6.76e-02 1.37e+02 pdb=" CG PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.114 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.053 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.117 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.108 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.029 2.00e-02 2.50e+03 6.67e-02 1.33e+02 pdb=" CG BTYR A 67 " -0.097 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.142 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.065 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.045 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.107 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.007 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.015 2.00e-02 2.50e+03 6.98e-02 1.10e+02 pdb=" CG HIS A 126 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.044 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.118 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.121 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1105 2.33 - 2.90: 8231 2.90 - 3.47: 10484 3.47 - 4.03: 15091 4.03 - 4.60: 21643 Nonbonded interactions: 56554 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.767 2.100 nonbonded pdb="HD22BASN A 76 " pdb=" HB2 PHE A 119 " model vdw sym.op. 1.802 2.270 -y,x-y-1,z+1/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.815 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.827 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.828 2.100 ... (remaining 56549 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_4426565_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= 0.3621 r_free= 0.2061 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474114 | | target function (ml) not normalized (work): 22057.383400 | | target function (ml) not normalized (free): 1149.185140 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3798 0.2258 4.8581 4.9207| | 2: 3.78 - 3.00 1.00 2430 110 0.3405 0.1728 4.0791 4.095| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.89 0.83 0.13 6617.17| | 2: 3.78 - 3.00 2430 110 0.94 11.40 1.48 0.26 454.92| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 384.91 max = 12083.14 mean = 3579.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.41| |phase err.(test): min = 0.00 max = 89.91 mean = 33.53| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.260 1557 Z= 5.645 Angle : 5.327 18.348 2118 Z= 3.706 Chirality : 0.379 0.961 243 Planarity : 0.029 0.128 284 Dihedral : 13.731 87.063 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 25.41 % 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: -2.74 (0.46), residues: 224 helix: -2.53 (0.34), residues: 109 sheet: -0.74 (0.77), residues: 40 loop : -0.85 (0.65), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.095 0.025 ARG A 28 TYR 0.079 0.025 TYR A 139 PHE 0.093 0.035 PHE A 119 HIS 0.067 0.030 HIS A 138 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= 0.3621 r_free= 0.2061 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474114 | | target function (ml) not normalized (work): 22057.383400 | | target function (ml) not normalized (free): 1149.185140 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3577 0.3652 0.2186 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3577 0.3652 0.2186 n_refl.: 5182 remove outliers: r(all,work,free)=0.2533 0.2554 0.2186 n_refl.: 5178 overall B=-2.82 to atoms: r(all,work,free)=0.2428 0.2446 0.2135 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1575 0.1572 0.1636 n_refl.: 5178 remove outliers: r(all,work,free)=0.1571 0.1568 0.1636 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 98.94 88 5 0.3942 449.653 408.904 0.665 1.074 0.404 11.894-9.307 99.02 97 4 0.1901 714.310 696.865 0.940 1.069 0.390 9.237-7.194 100.00 213 7 0.2181 584.164 575.661 0.972 1.061 0.361 7.162-5.571 100.00 427 22 0.2334 438.344 421.657 0.932 1.048 0.295 5.546-4.326 100.00 867 58 0.1379 601.784 595.159 0.974 1.025 0.215 4.315-3.360 100.00 1859 96 0.1322 572.303 565.730 1.058 0.988 0.179 3.356-3.002 100.00 1373 60 0.1602 440.812 433.237 1.070 0.951 0.058 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6066 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1568 r_free=0.1636 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1570 r_free=0.1638 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.995975 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.761724 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 0.1158 0.1828 0.0670 0.010 1.0 2.9 0.5 0.0 0 9.498 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 18.28 6.70 3.013 16.039 1.762 0.018 10.18 18.18 7.99 4.827 16.232 1.762 0.014 Individual atomic B min max mean iso aniso Overall: 2.34 112.14 17.43 5.21 1785 0 Protein: 2.34 112.14 14.72 5.20 1519 0 Water: 4.05 111.48 33.19 N/A 258 0 Other: 16.94 37.03 23.87 N/A 8 0 Chain A: 2.34 112.14 17.43 N/A 1785 0 Histogram: Values Number of atoms 2.34 - 13.32 941 13.32 - 24.30 464 24.30 - 35.28 186 35.28 - 46.26 108 46.26 - 57.24 56 57.24 - 68.22 15 68.22 - 79.20 6 79.20 - 90.18 5 90.18 - 101.16 1 101.16 - 112.14 3 =========================== Idealize ADP of riding H ========================== r_work=0.1018 r_free=0.1818 r_work=0.1011 r_free=0.1823 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1011 r_free = 0.1823 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1009 r_free = 0.1803 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1009 r_free= 0.1803 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013838 | | target function (ls_wunit_k1) not normalized (work): 68.136166 | | target function (ls_wunit_k1) not normalized (free): 10.639272 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1049 0.1009 0.1803 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2087 0.2083 0.2272 n_refl.: 5176 remove outliers: r(all,work,free)=0.2087 0.2083 0.2272 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2047 0.2041 0.2260 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1050 0.1010 0.1802 n_refl.: 5176 remove outliers: r(all,work,free)=0.1050 0.1010 0.1802 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 0.3264 330.232 312.588 0.670 1.029 0.381 11.894-9.307 99.02 97 4 0.1485 524.600 516.527 0.969 1.028 0.361 9.237-7.194 100.00 213 7 0.1708 429.018 427.887 1.005 1.025 0.319 7.162-5.571 100.00 427 22 0.1610 321.926 319.257 0.967 1.019 0.300 5.546-4.326 100.00 867 58 0.0926 441.959 439.015 0.987 1.010 0.196 4.315-3.360 100.00 1859 96 0.0756 420.308 420.200 1.048 0.995 0.183 3.356-3.002 100.00 1373 60 0.0996 323.739 322.395 1.030 0.979 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4199 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1010 r_free=0.1802 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1010 r_free=0.1802 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1802 | n_water=258 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.1025 r_free=0.1800 | n_water=252 | time (s): 20.490 (total time: 21.080) Filter (q & B) r_work=0.1024 r_free=0.1798 | n_water=249 | time (s): 1.850 (total time: 22.930) Compute maps r_work=0.1024 r_free=0.1798 | n_water=249 | time (s): 0.510 (total time: 23.440) Filter (map) r_work=0.1313 r_free=0.1851 | n_water=153 | time (s): 1.560 (total time: 25.000) Find peaks r_work=0.1313 r_free=0.1851 | n_water=153 | time (s): 0.460 (total time: 25.460) Add new water r_work=0.1665 r_free=0.2137 | n_water=239 | time (s): 1.200 (total time: 26.660) Refine new water occ: r_work=0.1157 r_free=0.1688 adp: r_work=0.1127 r_free=0.1699 occ: r_work=0.1123 r_free=0.1661 adp: r_work=0.1107 r_free=0.1671 occ: r_work=0.1107 r_free=0.1657 adp: r_work=0.1104 r_free=0.1657 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1657 r_work=0.1104 r_free=0.1657 | n_water=239 | time (s): 3.510 (total time: 30.170) Filter (q & B) r_work=0.1104 r_free=0.1657 | n_water=239 | time (s): 1.220 (total time: 31.390) Filter (dist only) r_work=0.1110 r_free=0.1637 | n_water=236 | time (s): 19.190 (total time: 50.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.608907 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.602074 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 0.1013 0.1761 0.0747 0.009 1.0 4.5 0.5 0.6 0 11.304 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.13 17.61 7.47 4.619 16.898 2.602 0.014 9.45 17.81 8.36 5.412 17.305 2.602 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 108.27 16.82 6.44 1763 0 Protein: 0.00 108.27 15.04 6.42 1519 0 Water: 0.00 62.81 27.96 N/A 236 0 Other: 12.47 42.17 27.12 N/A 8 0 Chain A: 0.00 108.27 15.85 N/A 1677 0 Chain S: 0.00 62.06 35.89 N/A 86 0 Histogram: Values Number of atoms 0.00 - 10.83 685 10.83 - 21.65 670 21.65 - 32.48 209 32.48 - 43.31 113 43.31 - 54.13 41 54.13 - 64.96 31 64.96 - 75.79 7 75.79 - 86.61 3 86.61 - 97.44 2 97.44 - 108.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.0945 r_free=0.1781 r_work=0.0942 r_free=0.1781 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0942 r_free = 0.1781 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0939 r_free = 0.1784 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 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= 0.0939 r_free= 0.1784 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ls_wunit_k1) (work): 0.012274 | | target function (ls_wunit_k1) not normalized (work): 60.434962 | | target function (ls_wunit_k1) not normalized (free): 9.736305 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0982 0.0939 0.1784 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2125 0.2128 0.2213 n_refl.: 5176 remove outliers: r(all,work,free)=0.2125 0.2128 0.2213 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2125 0.2128 0.2213 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0982 0.0939 0.1783 n_refl.: 5176 remove outliers: r(all,work,free)=0.0980 0.0937 0.1783 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 0.3407 327.451 312.384 0.646 1.029 0.360 11.894-9.307 99.02 97 4 0.1523 524.600 518.510 0.963 1.029 0.330 9.237-7.194 100.00 213 7 0.1438 429.018 429.909 1.010 1.026 0.310 7.162-5.571 100.00 427 22 0.1421 321.926 320.118 0.979 1.021 0.300 5.546-4.326 100.00 867 58 0.0794 441.959 439.632 1.000 1.011 0.213 4.315-3.360 100.00 1859 96 0.0723 420.308 419.739 1.063 0.996 0.197 3.356-3.002 100.00 1373 60 0.0954 323.739 322.888 1.050 0.981 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.3044 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0937 r_free=0.1783 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.0940 r_free=0.1781 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0940 r_free=0.1781 | n_water=236 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.0959 r_free=0.1793 | n_water=231 | time (s): 20.430 (total time: 21.100) Filter (q & B) r_work=0.1047 r_free=0.1778 | n_water=227 | time (s): 1.310 (total time: 22.410) Compute maps r_work=0.1047 r_free=0.1778 | n_water=227 | time (s): 0.470 (total time: 22.880) Filter (map) r_work=0.1305 r_free=0.1921 | n_water=151 | time (s): 1.310 (total time: 24.190) Find peaks r_work=0.1305 r_free=0.1921 | n_water=151 | time (s): 0.390 (total time: 24.580) Add new water r_work=0.1683 r_free=0.2339 | n_water=237 | time (s): 1.230 (total time: 25.810) Refine new water occ: r_work=0.1078 r_free=0.1815 adp: r_work=0.1072 r_free=0.1840 occ: r_work=0.1058 r_free=0.1811 adp: r_work=0.1059 r_free=0.1822 occ: r_work=0.1045 r_free=0.1794 adp: r_work=0.1045 r_free=0.1805 ADP+occupancy (water only), MIN, final r_work=0.1045 r_free=0.1805 r_work=0.1045 r_free=0.1805 | n_water=237 | time (s): 11.280 (total time: 37.090) Filter (q & B) r_work=0.1045 r_free=0.1805 | n_water=237 | time (s): 0.770 (total time: 37.860) Filter (dist only) r_work=0.1056 r_free=0.1805 | n_water=232 | time (s): 17.000 (total time: 54.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.114079 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.241274 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 0.0955 0.1831 0.0876 0.011 1.1 3.5 0.5 0.6 0 0.557 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.55 18.31 8.76 5.397 17.882 0.241 5.179 9.09 18.37 9.27 6.973 17.852 0.241 5.084 Individual atomic B min max mean iso aniso Overall: 0.00 107.53 16.44 8.54 1759 0 Protein: 0.00 107.53 15.10 8.52 1519 0 Water: 0.00 58.04 24.87 N/A 232 0 Other: 7.90 42.49 26.38 N/A 8 0 Chain A: 0.00 107.53 15.81 N/A 1660 0 Chain S: 0.00 58.04 26.98 N/A 99 0 Histogram: Values Number of atoms 0.00 - 10.75 674 10.75 - 21.51 658 21.51 - 32.26 241 32.26 - 43.01 112 43.01 - 53.76 35 53.76 - 64.52 20 64.52 - 75.27 11 75.27 - 86.02 3 86.02 - 96.78 4 96.78 - 107.53 1 =========================== Idealize ADP of riding H ========================== r_work=0.0909 r_free=0.1837 r_work=0.0914 r_free=0.1843 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0914 r_free = 0.1843 target_work(ml) = 5.087 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0905 r_free = 0.1816 target_work(ml) = 5.082 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0905 r_free= 0.1816 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.081815 | | target function (ml) not normalized (work): 25017.777178 | | target function (ml) not normalized (free): 1726.079439 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0951 0.0905 0.1816 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2121 0.2134 0.2077 n_refl.: 5175 remove outliers: r(all,work,free)=0.2121 0.2134 0.2077 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2121 0.2134 0.2077 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0946 0.0902 0.1805 n_refl.: 5175 remove outliers: r(all,work,free)=0.0944 0.0899 0.1805 n_refl.: 5174 ======================== 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 94.79 86 5 0.3643 329.628 295.881 0.573 1.005 0.330 11.894-9.307 99.02 97 4 0.1927 524.600 511.001 0.942 1.008 0.323 9.237-7.194 100.00 213 7 0.1920 429.018 424.457 1.001 1.008 0.290 7.162-5.571 100.00 427 22 0.1836 321.926 314.920 0.972 1.007 0.280 5.546-4.326 100.00 867 58 0.0897 441.959 437.722 1.001 1.005 0.220 4.315-3.360 100.00 1859 96 0.0600 420.308 419.641 1.064 1.001 0.210 3.356-3.002 100.00 1373 60 0.0633 323.739 322.732 1.046 0.996 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.6475 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0899 r_free=0.1805 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=0.0900 r_free=0.1809 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0900 r_free=0.1809 | n_water=232 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0913 r_free=0.1819 | n_water=228 | time (s): 17.460 (total time: 18.120) Filter (q & B) r_work=0.0950 r_free=0.1828 | n_water=227 | time (s): 1.650 (total time: 19.770) Compute maps r_work=0.0950 r_free=0.1828 | n_water=227 | time (s): 0.580 (total time: 20.350) Filter (map) r_work=0.1226 r_free=0.1883 | n_water=157 | time (s): 1.390 (total time: 21.740) Find peaks r_work=0.1226 r_free=0.1883 | n_water=157 | time (s): 0.420 (total time: 22.160) Add new water r_work=0.1565 r_free=0.2191 | n_water=234 | time (s): 1.310 (total time: 23.470) Refine new water occ: r_work=0.1002 r_free=0.1828 adp: r_work=0.0998 r_free=0.1840 occ: r_work=0.0987 r_free=0.1814 adp: r_work=0.0987 r_free=0.1823 occ: r_work=0.0978 r_free=0.1796 adp: r_work=0.0977 r_free=0.1807 ADP+occupancy (water only), MIN, final r_work=0.0977 r_free=0.1807 r_work=0.0977 r_free=0.1807 | n_water=234 | time (s): 11.090 (total time: 34.560) Filter (q & B) r_work=0.0977 r_free=0.1807 | n_water=234 | time (s): 0.940 (total time: 35.500) Filter (dist only) r_work=0.0976 r_free=0.1805 | n_water=233 | time (s): 17.090 (total time: 52.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.015004 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.239923 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 0.0897 0.1871 0.0975 0.011 1.1 5.1 0.5 0.6 0 0.508 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.97 18.71 9.75 6.706 17.931 0.240 5.026 8.74 18.84 10.10 7.817 18.013 0.240 4.962 Individual atomic B min max mean iso aniso Overall: 0.00 107.64 16.63 10.09 1760 0 Protein: 0.00 107.64 15.43 10.08 1519 0 Water: 0.00 57.28 24.06 N/A 233 0 Other: 9.23 42.86 26.61 N/A 8 0 Chain A: 0.00 107.64 16.02 N/A 1649 0 Chain S: 0.00 57.28 25.65 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.76 671 10.76 - 21.53 657 21.53 - 32.29 248 32.29 - 43.05 109 43.05 - 53.82 39 53.82 - 64.58 15 64.58 - 75.35 12 75.35 - 86.11 5 86.11 - 96.87 3 96.87 - 107.64 1 =========================== Idealize ADP of riding H ========================== r_work=0.0874 r_free=0.1884 r_work=0.0879 r_free=0.1888 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0879 r_free = 0.1888 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0868 r_free = 0.1862 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0868 r_free= 0.1862 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.958874 | | target function (ml) not normalized (work): 24407.579642 | | target function (ml) not normalized (free): 2029.288112 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0918 0.0868 0.1862 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2059 0.2061 0.2213 n_refl.: 5174 remove outliers: r(all,work,free)=0.2059 0.2061 0.2213 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2059 0.2061 0.2213 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0917 0.0867 0.1864 n_refl.: 5174 remove outliers: r(all,work,free)=0.0917 0.0867 0.1864 n_refl.: 5174 ======================== 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 94.79 86 5 0.3809 329.628 299.134 0.603 0.990 0.340 11.894-9.307 99.02 97 4 0.1831 524.600 509.536 0.953 0.995 0.340 9.237-7.194 100.00 213 7 0.2110 429.018 418.013 1.002 0.997 0.304 7.162-5.571 100.00 427 22 0.2067 321.926 312.228 0.978 0.999 0.270 5.546-4.326 100.00 867 58 0.0956 441.959 436.527 1.013 1.001 0.215 4.315-3.360 100.00 1859 96 0.0546 420.308 420.163 1.077 1.003 0.210 3.356-3.002 100.00 1373 60 0.0434 323.739 323.737 1.054 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.3638 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0867 r_free=0.1864 After: r_work=0.0870 r_free=0.1862 ================================== NQH flips ================================== r_work=0.0870 r_free=0.1862 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0870 r_free=0.1862 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0870 r_free=0.1862 | n_water=233 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.0896 r_free=0.1864 | n_water=226 | time (s): 18.310 (total time: 18.810) Filter (q & B) r_work=0.1003 r_free=0.1906 | n_water=223 | time (s): 1.630 (total time: 20.440) Compute maps r_work=0.1003 r_free=0.1906 | n_water=223 | time (s): 0.520 (total time: 20.960) Filter (map) r_work=0.1296 r_free=0.1979 | n_water=155 | time (s): 1.250 (total time: 22.210) Find peaks r_work=0.1296 r_free=0.1979 | n_water=155 | time (s): 0.420 (total time: 22.630) Add new water r_work=0.1599 r_free=0.2233 | n_water=231 | time (s): 1.490 (total time: 24.120) Refine new water occ: r_work=0.0996 r_free=0.1859 adp: r_work=0.0989 r_free=0.1860 occ: r_work=0.0983 r_free=0.1845 adp: r_work=0.0982 r_free=0.1850 occ: r_work=0.0977 r_free=0.1837 adp: r_work=0.0976 r_free=0.1842 ADP+occupancy (water only), MIN, final r_work=0.0976 r_free=0.1842 r_work=0.0976 r_free=0.1842 | n_water=231 | time (s): 13.520 (total time: 37.640) Filter (q & B) r_work=0.0976 r_free=0.1847 | n_water=228 | time (s): 1.850 (total time: 39.490) Filter (dist only) r_work=0.0983 r_free=0.1850 | n_water=227 | time (s): 17.770 (total time: 57.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.004248 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.176207 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 0.0918 0.1866 0.0948 0.010 1.1 5.8 0.5 0.0 0 0.502 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.18 18.66 9.48 7.725 18.174 0.176 5.021 9.01 18.73 9.73 8.561 18.275 0.176 4.966 Individual atomic B min max mean iso aniso Overall: 0.00 111.11 16.80 11.25 1754 0 Protein: 0.00 111.11 15.79 11.24 1519 0 Water: 0.00 58.85 23.28 N/A 227 0 Other: 11.17 41.28 24.97 N/A 8 0 Chain A: 0.00 111.11 16.27 N/A 1635 0 Chain S: 0.00 58.85 24.15 N/A 119 0 Histogram: Values Number of atoms 0.00 - 11.11 682 11.11 - 22.22 648 22.22 - 33.33 248 33.33 - 44.45 102 44.45 - 55.56 39 55.56 - 66.67 16 66.67 - 77.78 10 77.78 - 88.89 4 88.89 - 100.00 3 100.00 - 111.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1873 r_work=0.0904 r_free=0.1876 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0904 r_free = 0.1876 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0897 r_free = 0.1875 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0897 r_free= 0.1875 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.966577 | | target function (ml) not normalized (work): 24445.490402 | | target function (ml) not normalized (free): 2032.923986 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1276 0.1943 5.5458 6.2808| | 2: 3.78 - 3.00 1.00 2430 110 0.0434 0.1759 4.3726 10.373| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2492 142 0.91 12.21 1.00 0.98 13411.06| | 2: 3.78 - 3.00 2430 110 0.99 1.91 1.00 1.00 942.73| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 602.84 max = 22410.70 mean = 7255.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.84 mean = 7.13| |phase err.(test): min = 0.00 max = 87.66 mean = 7.09| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0947 0.0897 0.1875 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2133 0.2134 0.2281 n_refl.: 5174 remove outliers: r(all,work,free)=0.2133 0.2134 0.2281 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2133 0.2134 0.2281 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0945 0.0896 0.1870 n_refl.: 5174 remove outliers: r(all,work,free)=0.0945 0.0896 0.1870 n_refl.: 5174 ======================== 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 94.79 86 5 0.3917 329.628 296.348 0.605 0.985 0.320 11.894-9.307 99.02 97 4 0.1861 524.600 509.078 0.999 0.991 0.310 9.237-7.194 100.00 213 7 0.2178 429.018 417.621 1.053 0.995 0.295 7.162-5.571 100.00 427 22 0.2083 321.926 313.853 1.031 0.997 0.290 5.546-4.326 100.00 867 58 0.1037 441.959 435.889 1.070 1.000 0.220 4.315-3.360 100.00 1859 96 0.0569 420.308 420.182 1.147 1.003 0.210 3.356-3.002 100.00 1373 60 0.0416 323.739 323.866 1.126 1.007 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.4999 ================= 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 : 0.3621 0.2061 0.083 5.327 8.8 119.3 19.9 258 0.000 1_bss: 0.1568 0.1636 0.083 5.327 6.0 116.5 17.1 258 0.000 1_settarget: 0.1568 0.1636 0.083 5.327 6.0 116.5 17.1 258 0.000 1_nqh: 0.1570 0.1638 0.083 5.327 6.0 116.5 17.1 258 0.006 1_weight: 0.1570 0.1638 0.083 5.327 6.0 116.5 17.1 258 0.006 1_xyzrec: 0.1158 0.1828 0.010 0.963 6.0 116.5 17.1 258 0.210 1_adp: 0.1018 0.1818 0.010 0.963 2.3 112.1 17.4 258 0.210 1_regHadp: 0.1011 0.1823 0.010 0.963 2.3 112.1 17.4 258 0.210 1_occ: 0.1009 0.1803 0.010 0.963 2.3 112.1 17.4 258 0.210 2_bss: 0.1010 0.1802 0.010 0.963 1.4 111.2 16.5 258 0.210 2_settarget: 0.1010 0.1802 0.010 0.963 1.4 111.2 16.5 258 0.210 2_updatecdl: 0.1010 0.1802 0.010 0.993 1.4 111.2 16.5 258 0.210 2_nqh: 0.1010 0.1802 0.010 0.993 1.4 111.2 16.5 258 0.210 2_sol: 0.1110 0.1637 0.010 0.993 1.0 111.2 16.0 236 n/a 2_weight: 0.1110 0.1637 0.010 0.993 1.0 111.2 16.0 236 n/a 2_xyzrec: 0.1013 0.1761 0.009 0.967 1.0 111.2 16.0 236 n/a 2_adp: 0.0945 0.1781 0.009 0.967 0.0 108.3 16.8 236 n/a 2_regHadp: 0.0942 0.1781 0.009 0.967 0.0 108.3 16.8 236 n/a 2_occ: 0.0939 0.1784 0.009 0.967 0.0 108.3 16.8 236 n/a 3_bss: 0.0937 0.1783 0.009 0.967 0.0 108.3 16.8 236 n/a 3_settarget: 0.0937 0.1783 0.009 0.967 0.0 108.3 16.8 236 n/a 3_updatecdl: 0.0937 0.1783 0.009 0.971 0.0 108.3 16.8 236 n/a 3_nqh: 0.0940 0.1781 0.009 0.971 0.0 108.3 16.8 236 n/a 3_sol: 0.1056 0.1805 0.009 0.971 0.0 108.3 16.5 232 n/a 3_weight: 0.1056 0.1805 0.009 0.971 0.0 108.3 16.5 232 n/a 3_xyzrec: 0.0955 0.1831 0.011 1.050 0.0 108.3 16.5 232 n/a 3_adp: 0.0909 0.1837 0.011 1.050 0.0 107.5 16.4 232 n/a 3_regHadp: 0.0914 0.1843 0.011 1.050 0.0 107.5 16.4 232 n/a 3_occ: 0.0905 0.1816 0.011 1.050 0.0 107.5 16.4 232 n/a 4_bss: 0.0899 0.1805 0.011 1.050 0.0 107.5 16.4 232 n/a 4_settarget: 0.0899 0.1805 0.011 1.050 0.0 107.5 16.4 232 n/a 4_updatecdl: 0.0899 0.1805 0.011 1.053 0.0 107.5 16.4 232 n/a 4_nqh: 0.0900 0.1809 0.011 1.053 0.0 107.5 16.4 232 n/a 4_sol: 0.0976 0.1805 0.011 1.053 0.0 107.5 16.5 233 n/a 4_weight: 0.0976 0.1805 0.011 1.053 0.0 107.5 16.5 233 n/a 4_xyzrec: 0.0897 0.1871 0.011 1.057 0.0 107.5 16.5 233 n/a 4_adp: 0.0874 0.1884 0.011 1.057 0.0 107.6 16.6 233 n/a 4_regHadp: 0.0879 0.1888 0.011 1.057 0.0 107.6 16.6 233 n/a 4_occ: 0.0868 0.1862 0.011 1.057 0.0 107.6 16.6 233 n/a 5_bss: 0.0867 0.1864 0.011 1.057 0.0 107.6 16.6 233 n/a 5_settarget: 0.0867 0.1864 0.011 1.057 0.0 107.6 16.6 233 n/a 5_updatecdl: 0.0867 0.1864 0.011 1.066 0.0 107.6 16.6 233 n/a 5_setrh: 0.0870 0.1862 0.011 1.066 0.0 107.6 16.6 233 n/a 5_nqh: 0.0870 0.1862 0.011 1.066 0.0 107.6 16.6 233 n/a 5_sol: 0.0983 0.1850 0.011 1.066 0.0 107.6 16.6 227 n/a 5_weight: 0.0983 0.1850 0.011 1.066 0.0 107.6 16.6 227 n/a 5_xyzrec: 0.0918 0.1866 0.010 1.142 0.0 107.6 16.6 227 n/a 5_adp: 0.0901 0.1873 0.010 1.142 0.0 111.1 16.8 227 n/a 5_regHadp: 0.0904 0.1876 0.010 1.142 0.0 111.1 16.8 227 n/a 5_occ: 0.0897 0.1875 0.010 1.142 0.0 111.1 16.8 227 n/a end: 0.0896 0.1870 0.010 1.142 0.0 111.1 16.8 227 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4426565_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4426565_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0200 Refinement macro-cycles (run) : 482.6100 Write final files (write_after_run_outputs) : 11.8500 Total : 498.4800 Total CPU time: 8.66 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:00 PST -0800 (1735492740.21 s) Start R-work = 0.1568, R-free = 0.1636 Final R-work = 0.0896, R-free = 0.1870 =============================================================================== Job complete usr+sys time: 526.54 seconds wall clock time: 9 minutes 7.85 seconds (547.85 seconds total)