Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6943566.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 { 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" 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_6943566.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6943566.pdb" } 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: 2.04, per 1000 atoms: 0.60 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: 0.39 Conformation dependent library (CDL) restraints added in 124.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 616 0.93 - 1.20: 1079 1.20 - 1.47: 792 1.47 - 1.74: 655 1.74 - 2.01: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 1.523 1.298 0.226 1.27e-02 6.20e+03 3.16e+02 bond pdb=" N VAL A 177 " pdb=" CA VAL A 177 " ideal model delta sigma weight residual 1.461 1.666 -0.206 1.19e-02 7.06e+03 2.99e+02 bond pdb=" CA VAL A 181 " pdb=" CB VAL A 181 " ideal model delta sigma weight residual 1.540 1.755 -0.215 1.25e-02 6.40e+03 2.96e+02 bond pdb=" N GLU A 147 " pdb=" CA GLU A 147 " ideal model delta sigma weight residual 1.455 1.248 0.207 1.21e-02 6.83e+03 2.93e+02 bond pdb=" N ASP A 60 " pdb=" CA ASP A 60 " ideal model delta sigma weight residual 1.458 1.673 -0.215 1.27e-02 6.20e+03 2.87e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.71: 3185 4.71 - 9.41: 1875 9.41 - 14.12: 592 14.12 - 18.82: 111 18.82 - 23.53: 14 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 115.47 5.60 3.60e-01 7.72e+00 2.42e+02 angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 109.44 13.16 1.00e+00 1.00e+00 1.73e+02 angle pdb=" O MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 122.12 135.79 -13.67 1.06e+00 8.90e-01 1.66e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 109.83 12.77 1.00e+00 1.00e+00 1.63e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.90 134.09 -13.19 1.07e+00 8.73e-01 1.52e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 1325 17.65 - 35.30: 103 35.30 - 52.95: 41 52.95 - 70.59: 8 70.59 - 88.24: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LYS A 188 " pdb=" N LYS A 188 " pdb=" CA LYS A 188 " pdb=" CB LYS A 188 " ideal model delta harmonic sigma weight residual -122.60 -99.14 -23.46 0 2.50e+00 1.60e-01 8.81e+01 dihedral pdb=" N BLYS A 93 " pdb=" C BLYS A 93 " pdb=" CA BLYS A 93 " pdb=" CB BLYS A 93 " ideal model delta harmonic sigma weight residual 122.80 143.61 -20.81 0 2.50e+00 1.60e-01 6.93e+01 dihedral pdb=" C BLYS A 93 " pdb=" N BLYS A 93 " pdb=" CA BLYS A 93 " pdb=" CB BLYS A 93 " ideal model delta harmonic sigma weight residual -122.60 -142.50 19.90 0 2.50e+00 1.60e-01 6.34e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 122 0.248 - 0.495: 81 0.495 - 0.742: 30 0.742 - 0.989: 9 0.989 - 1.237: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.35 -1.24 2.00e-01 2.50e+01 3.82e+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 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CG ALEU A 153 " pdb=" CB ALEU A 153 " pdb=" CD1ALEU A 153 " pdb=" CD2ALEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.017 2.00e-02 2.50e+03 6.32e-02 1.20e+02 pdb=" CG TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.121 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.071 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.080 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.092 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.016 2.00e-02 2.50e+03 6.74e-02 1.02e+02 pdb=" CG HIS A 115 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.103 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.053 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.125 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.057 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.012 2.00e-02 2.50e+03 5.62e-02 9.46e+01 pdb=" CG PHE A 162 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.105 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.077 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.091 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.015 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 854 2.29 - 2.87: 7943 2.87 - 3.45: 10608 3.45 - 4.02: 15268 4.02 - 4.60: 21947 Nonbonded interactions: 56620 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.715 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.785 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.800 2.270 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.825 2.100 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.843 2.450 ... (remaining 56615 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_6943566_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= 0.3609 r_free= 0.1972 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.476316 | | target function (ml) not normalized (work): 22068.238559 | | target function (ml) not normalized (free): 1143.679096 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3785 0.2157 4.858 4.9037| | 2: 3.78 - 3.00 1.00 2430 110 0.3393 0.1659 4.0836 4.0668| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.84 0.83 0.13 6614.76| | 2: 3.78 - 3.00 2430 110 0.93 11.55 1.48 0.26 459.10| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 391.43 max = 12076.13 mean = 3580.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.46| |phase err.(test): min = 0.00 max = 89.96 mean = 33.22| |-----------------------------------------------------------------------------| ----------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 0.249 1557 Z= 5.539 Angle : 5.281 19.516 2118 Z= 3.691 Chirality : 0.371 1.237 243 Planarity : 0.032 0.103 284 Dihedral : 13.797 88.242 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 27.57 % 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: -2.61 (0.47), residues: 224 helix: -2.85 (0.32), residues: 108 sheet: -1.43 (0.67), residues: 40 loop : 0.44 (0.70), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.030 ARG A 145 TYR 0.088 0.047 TYR A 141 PHE 0.120 0.035 PHE A 164 HIS 0.065 0.032 HIS A 115 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= 0.3609 r_free= 0.1972 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.476316 | | target function (ml) not normalized (work): 22068.238559 | | target function (ml) not normalized (free): 1143.679096 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3564 0.3640 0.2097 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3564 0.3640 0.2097 n_refl.: 5182 remove outliers: r(all,work,free)=0.2511 0.2536 0.2097 n_refl.: 5178 overall B=-2.47 to atoms: r(all,work,free)=0.2417 0.2439 0.2046 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1557 0.1557 0.1553 n_refl.: 5178 remove outliers: r(all,work,free)=0.1555 0.1555 0.1553 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 0.4062 445.191 406.101 0.627 1.069 0.388 11.894-9.307 99.02 97 4 0.1901 714.699 693.206 0.906 1.065 0.372 9.237-7.194 100.00 213 7 0.2205 584.482 575.931 0.939 1.057 0.364 7.162-5.571 100.00 427 22 0.2284 438.583 424.568 0.907 1.043 0.292 5.546-4.326 100.00 867 58 0.1353 602.112 595.091 0.950 1.021 0.215 4.315-3.360 100.00 1859 96 0.1297 572.615 567.006 1.032 0.983 0.188 3.356-3.002 100.00 1373 60 0.1618 441.052 432.511 1.052 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.3080 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1553 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1556 r_free=0.1557 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 20.606734 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.686979 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 0.1773 0.0616 0.010 1.0 3.2 0.5 0.0 0 10.303 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 17.73 6.16 3.013 16.386 1.687 0.018 10.18 17.81 7.62 4.841 16.586 1.687 0.015 Individual atomic B min max mean iso aniso Overall: 2.43 112.28 17.79 5.21 1785 0 Protein: 2.43 112.28 15.07 5.20 1519 0 Water: 4.39 111.83 33.59 N/A 258 0 Other: 17.08 34.45 24.43 N/A 8 0 Chain A: 2.43 112.28 17.79 N/A 1785 0 Histogram: Values Number of atoms 2.43 - 13.41 917 13.41 - 24.40 482 24.40 - 35.38 196 35.38 - 46.37 100 46.37 - 57.35 60 57.35 - 68.34 15 68.34 - 79.32 6 79.32 - 90.31 5 90.31 - 101.29 1 101.29 - 112.28 3 =========================== Idealize ADP of riding H ========================== r_work=0.1018 r_free=0.1781 r_work=0.1012 r_free=0.1789 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1012 r_free = 0.1789 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 = 0.1017 r_free = 0.1786 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 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= 0.1017 r_free= 0.1786 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014195 | | target function (ls_wunit_k1) not normalized (work): 69.910182 | | target function (ls_wunit_k1) not normalized (free): 10.348564 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1057 0.1017 0.1786 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2118 0.2116 0.2252 n_refl.: 5177 remove outliers: r(all,work,free)=0.2118 0.2116 0.2252 n_refl.: 5177 overall B=-0.94 to atoms: r(all,work,free)=0.2077 0.2074 0.2241 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1064 0.1025 0.1807 n_refl.: 5177 remove outliers: r(all,work,free)=0.1060 0.1020 0.1807 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 0.3274 314.839 291.455 0.629 1.002 0.360 11.894-9.307 99.02 97 4 0.1541 506.477 501.830 0.961 1.004 0.351 9.237-7.194 100.00 213 7 0.1669 414.197 415.019 0.999 1.004 0.341 7.162-5.571 100.00 427 22 0.1621 310.805 307.873 0.954 1.003 0.292 5.546-4.326 100.00 867 58 0.0920 426.691 423.577 0.968 1.002 0.202 4.315-3.360 100.00 1859 96 0.0776 405.788 405.818 1.015 1.000 0.193 3.356-3.002 100.00 1373 60 0.1012 312.555 310.810 0.989 0.997 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9174 b_overall=-4.2016 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1020 r_free=0.1807 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1022 r_free=0.1811 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1022 r_free=0.1811 | n_water=258 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1053 r_free=0.1809 | n_water=248 | time (s): 19.240 (total time: 19.860) Filter (q & B) r_work=0.1054 r_free=0.1810 | n_water=245 | time (s): 1.740 (total time: 21.600) Compute maps r_work=0.1054 r_free=0.1810 | n_water=245 | time (s): 0.550 (total time: 22.150) Filter (map) r_work=0.1349 r_free=0.1889 | n_water=148 | time (s): 1.390 (total time: 23.540) Find peaks r_work=0.1349 r_free=0.1889 | n_water=148 | time (s): 0.440 (total time: 23.980) Add new water r_work=0.1674 r_free=0.2153 | n_water=235 | time (s): 1.260 (total time: 25.240) Refine new water occ: r_work=0.1165 r_free=0.1636 adp: r_work=0.1137 r_free=0.1672 occ: r_work=0.1137 r_free=0.1642 adp: r_work=0.1121 r_free=0.1666 occ: r_work=0.1121 r_free=0.1650 adp: r_work=0.1118 r_free=0.1656 ADP+occupancy (water only), MIN, final r_work=0.1118 r_free=0.1656 r_work=0.1118 r_free=0.1656 | n_water=235 | time (s): 4.290 (total time: 29.530) Filter (q & B) r_work=0.1118 r_free=0.1656 | n_water=235 | time (s): 0.790 (total time: 30.320) Filter (dist only) r_work=0.1124 r_free=0.1662 | n_water=233 | time (s): 17.890 (total time: 48.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.813643 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.622212 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 0.1019 0.1774 0.0754 0.009 1.0 4.5 0.5 0.0 0 11.407 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.19 17.74 7.54 4.640 17.221 2.622 0.014 9.43 17.87 8.44 5.706 17.692 2.622 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.33 17.17 6.76 1760 0 Protein: 0.00 106.33 15.52 6.72 1519 0 Water: 0.00 63.16 27.39 N/A 233 0 Other: 21.71 48.99 33.87 N/A 8 0 Chain A: 0.00 106.33 16.31 N/A 1673 0 Chain S: 1.90 59.65 33.85 N/A 87 0 Histogram: Values Number of atoms 0.00 - 10.63 625 10.63 - 21.27 705 21.27 - 31.90 205 31.90 - 42.53 134 42.53 - 53.17 45 53.17 - 63.80 27 63.80 - 74.43 11 74.43 - 85.07 3 85.07 - 95.70 3 95.70 - 106.33 2 =========================== Idealize ADP of riding H ========================== r_work=0.0943 r_free=0.1787 r_work=0.0940 r_free=0.1788 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0940 r_free = 0.1788 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0933 r_free = 0.1772 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0933 r_free= 0.1772 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011805 | | target function (ls_wunit_k1) not normalized (work): 58.116308 | | target function (ls_wunit_k1) not normalized (free): 9.660532 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0976 0.0933 0.1772 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2058 0.2057 0.2164 n_refl.: 5175 remove outliers: r(all,work,free)=0.2058 0.2057 0.2164 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2058 0.2057 0.2164 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0971 0.0928 0.1778 n_refl.: 5175 remove outliers: r(all,work,free)=0.0971 0.0928 0.1778 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 0.3188 314.839 298.889 0.665 1.002 0.360 11.894-9.307 99.02 97 4 0.1469 506.477 501.073 0.982 1.005 0.325 9.237-7.194 100.00 213 7 0.1474 414.197 415.754 1.034 1.005 0.305 7.162-5.571 100.00 427 22 0.1400 310.805 308.794 0.999 1.004 0.300 5.546-4.326 100.00 867 58 0.0782 426.691 424.200 1.014 1.003 0.222 4.315-3.360 100.00 1859 96 0.0719 405.788 405.294 1.066 1.000 0.203 3.356-3.002 100.00 1373 60 0.0952 312.555 311.815 1.043 0.997 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.7334 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0928 r_free=0.1778 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0931 r_free=0.1782 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0931 r_free=0.1782 | n_water=233 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.0941 r_free=0.1783 | n_water=230 | time (s): 18.200 (total time: 18.820) Filter (q & B) r_work=0.0971 r_free=0.1805 | n_water=229 | time (s): 1.250 (total time: 20.070) Compute maps r_work=0.0971 r_free=0.1805 | n_water=229 | time (s): 0.490 (total time: 20.560) Filter (map) r_work=0.1257 r_free=0.1908 | n_water=157 | time (s): 1.430 (total time: 21.990) Find peaks r_work=0.1257 r_free=0.1908 | n_water=157 | time (s): 0.400 (total time: 22.390) Add new water r_work=0.1611 r_free=0.2258 | n_water=243 | time (s): 1.390 (total time: 23.780) Refine new water occ: r_work=0.1058 r_free=0.1773 adp: r_work=0.1058 r_free=0.1777 occ: r_work=0.1046 r_free=0.1763 adp: r_work=0.1046 r_free=0.1767 occ: r_work=0.1036 r_free=0.1752 adp: r_work=0.1037 r_free=0.1758 ADP+occupancy (water only), MIN, final r_work=0.1037 r_free=0.1758 r_work=0.1037 r_free=0.1758 | n_water=243 | time (s): 12.870 (total time: 36.650) Filter (q & B) r_work=0.1036 r_free=0.1758 | n_water=242 | time (s): 1.690 (total time: 38.340) Filter (dist only) r_work=0.1035 r_free=0.1761 | n_water=241 | time (s): 18.230 (total time: 56.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.131219 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.218285 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 0.0922 0.1853 0.0931 0.011 1.1 4.5 0.5 0.0 0 0.566 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.22 18.53 9.31 5.625 18.440 0.218 5.098 8.81 18.69 9.88 7.316 18.408 0.218 5.003 Individual atomic B min max mean iso aniso Overall: 0.00 104.85 16.95 8.96 1768 0 Protein: 0.00 104.85 15.58 8.93 1519 0 Water: 0.00 60.93 25.06 N/A 241 0 Other: 17.17 50.73 32.74 N/A 8 0 Chain A: 0.00 104.85 16.28 N/A 1661 0 Chain S: 0.00 60.93 27.27 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.48 609 10.48 - 20.97 691 20.97 - 31.45 250 31.45 - 41.94 132 41.94 - 52.42 43 52.42 - 62.91 20 62.91 - 73.39 13 73.39 - 83.88 5 83.88 - 94.36 3 94.36 - 104.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.0881 r_free=0.1869 r_work=0.0886 r_free=0.1876 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0886 r_free = 0.1876 target_work(ml) = 5.006 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0876 r_free = 0.1868 target_work(ml) = 5.001 | | occupancies: max = 1.00 min = 0.22 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= 0.0876 r_free= 0.1868 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.000678 | | target function (ml) not normalized (work): 24618.335383 | | target function (ml) not normalized (free): 1876.872364 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0927 0.0876 0.1868 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2037 0.2036 0.2171 n_refl.: 5175 remove outliers: r(all,work,free)=0.2037 0.2036 0.2171 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2037 0.2036 0.2171 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0917 0.0868 0.1856 n_refl.: 5175 remove outliers: r(all,work,free)=0.0917 0.0868 0.1856 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 0.3696 314.839 286.757 0.575 0.993 0.316 11.894-9.307 99.02 97 4 0.1906 506.477 491.461 0.952 0.996 0.313 9.237-7.194 100.00 213 7 0.1882 414.197 408.419 1.015 0.998 0.290 7.162-5.571 100.00 427 22 0.1766 310.805 303.895 0.987 0.999 0.290 5.546-4.326 100.00 867 58 0.0894 426.691 422.104 1.011 1.000 0.215 4.315-3.360 100.00 1859 96 0.0570 405.788 405.070 1.070 1.002 0.210 3.356-3.002 100.00 1373 60 0.0583 312.555 312.332 1.053 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.1746 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0868 r_free=0.1856 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=0.0868 r_free=0.1856 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0868 r_free=0.1856 | n_water=241 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.0883 r_free=0.1850 | n_water=238 | time (s): 18.300 (total time: 18.930) Filter (q & B) r_work=0.0936 r_free=0.1858 | n_water=235 | time (s): 1.550 (total time: 20.480) Compute maps r_work=0.0936 r_free=0.1858 | n_water=235 | time (s): 0.500 (total time: 20.980) Filter (map) r_work=0.1220 r_free=0.1906 | n_water=163 | time (s): 1.390 (total time: 22.370) Find peaks r_work=0.1220 r_free=0.1906 | n_water=163 | time (s): 0.420 (total time: 22.790) Add new water r_work=0.1529 r_free=0.2191 | n_water=239 | time (s): 1.250 (total time: 24.040) Refine new water occ: r_work=0.0991 r_free=0.1856 adp: r_work=0.0987 r_free=0.1868 occ: r_work=0.0979 r_free=0.1845 adp: r_work=0.0978 r_free=0.1855 occ: r_work=0.0971 r_free=0.1831 adp: r_work=0.0970 r_free=0.1840 ADP+occupancy (water only), MIN, final r_work=0.0970 r_free=0.1840 r_work=0.0970 r_free=0.1840 | n_water=239 | time (s): 8.860 (total time: 32.900) Filter (q & B) r_work=0.0970 r_free=0.1840 | n_water=239 | time (s): 0.770 (total time: 33.670) Filter (dist only) r_work=0.0970 r_free=0.1840 | n_water=239 | time (s): 16.110 (total time: 49.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.027768 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.194971 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 0.0878 0.1848 0.0970 0.011 1.1 5.4 0.5 0.0 0 0.514 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.78 18.48 9.70 7.002 18.465 0.195 4.958 8.58 18.92 10.34 8.057 18.569 0.195 4.893 Individual atomic B min max mean iso aniso Overall: 0.00 104.03 17.20 10.46 1766 0 Protein: 0.00 104.03 15.96 10.43 1519 0 Water: 0.00 57.81 24.63 N/A 239 0 Other: 16.98 49.23 31.80 N/A 8 0 Chain A: 0.00 104.03 16.56 N/A 1652 0 Chain S: 0.09 55.43 26.46 N/A 114 0 Histogram: Values Number of atoms 0.00 - 10.40 597 10.40 - 20.81 674 20.81 - 31.21 267 31.21 - 41.61 132 41.61 - 52.02 56 52.02 - 62.42 16 62.42 - 72.82 12 72.82 - 83.23 5 83.23 - 93.63 5 93.63 - 104.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.0858 r_free=0.1892 r_work=0.0861 r_free=0.1896 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0861 r_free = 0.1896 target_work(ml) = 4.899 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0852 r_free = 0.1880 target_work(ml) = 4.893 | | occupancies: max = 1.00 min = 0.23 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= 0.0852 r_free= 0.1880 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.892872 | | target function (ml) not normalized (work): 24087.608117 | | target function (ml) not normalized (free): 2223.230320 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0905 0.0852 0.1880 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2067 0.2064 0.2204 n_refl.: 5175 remove outliers: r(all,work,free)=0.2067 0.2064 0.2204 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2067 0.2064 0.2204 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0904 0.0853 0.1885 n_refl.: 5175 remove outliers: r(all,work,free)=0.0904 0.0853 0.1885 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 0.3880 314.839 284.863 0.569 0.988 0.318 11.894-9.307 99.02 97 4 0.1944 506.477 490.523 0.955 0.993 0.317 9.237-7.194 100.00 213 7 0.2118 414.197 404.817 1.016 0.995 0.290 7.162-5.571 100.00 427 22 0.1998 310.805 301.302 0.995 0.997 0.280 5.546-4.326 100.00 867 58 0.0932 426.691 422.020 1.021 0.999 0.215 4.315-3.360 100.00 1859 96 0.0528 405.788 405.197 1.084 1.002 0.210 3.356-3.002 100.00 1373 60 0.0423 312.555 312.534 1.068 1.004 0.058 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8094 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0852 r_free=0.1885 After: r_work=0.0856 r_free=0.1884 ================================== NQH flips ================================== r_work=0.0856 r_free=0.1884 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B A 80 GLN B Total number of N/Q/H flips: 3 r_work=0.0859 r_free=0.1879 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0859 r_free=0.1879 | n_water=239 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0879 r_free=0.1869 | n_water=234 | time (s): 20.090 (total time: 20.680) Filter (q & B) r_work=0.0986 r_free=0.1914 | n_water=231 | time (s): 1.400 (total time: 22.080) Compute maps r_work=0.0986 r_free=0.1914 | n_water=231 | time (s): 0.640 (total time: 22.720) Filter (map) r_work=0.1247 r_free=0.2010 | n_water=165 | time (s): 1.680 (total time: 24.400) Find peaks r_work=0.1247 r_free=0.2010 | n_water=165 | time (s): 0.540 (total time: 24.940) Add new water r_work=0.1528 r_free=0.2197 | n_water=237 | time (s): 2.050 (total time: 26.990) Refine new water occ: r_work=0.0983 r_free=0.1892 adp: r_work=0.0974 r_free=0.1887 occ: r_work=0.0967 r_free=0.1877 adp: r_work=0.0967 r_free=0.1880 occ: r_work=0.0960 r_free=0.1870 adp: r_work=0.0960 r_free=0.1873 ADP+occupancy (water only), MIN, final r_work=0.0960 r_free=0.1873 r_work=0.0960 r_free=0.1873 | n_water=237 | time (s): 13.230 (total time: 40.220) Filter (q & B) r_work=0.0960 r_free=0.1873 | n_water=237 | time (s): 1.140 (total time: 41.360) Filter (dist only) r_work=0.0960 r_free=0.1873 | n_water=237 | time (s): 16.830 (total time: 58.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.969745 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.212155 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 0.0912 0.1856 0.0944 0.011 1.2 8.0 0.5 0.0 0 0.485 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.12 18.56 9.44 7.994 18.798 0.212 4.965 8.87 18.79 9.91 9.139 18.943 0.212 4.900 Individual atomic B min max mean iso aniso Overall: 0.00 103.90 17.60 12.03 1764 0 Protein: 0.00 103.90 16.42 12.01 1519 0 Water: 0.00 59.68 24.71 N/A 237 0 Other: 14.94 50.51 30.55 N/A 8 0 Chain A: 0.00 103.90 16.95 N/A 1645 0 Chain S: 0.00 59.68 26.48 N/A 119 0 Histogram: Values Number of atoms 0.00 - 10.39 594 10.39 - 20.78 632 20.78 - 31.17 300 31.17 - 41.56 132 41.56 - 51.95 55 51.95 - 62.34 26 62.34 - 72.73 7 72.73 - 83.12 10 83.12 - 93.51 3 93.51 - 103.90 5 =========================== Idealize ADP of riding H ========================== r_work=0.0887 r_free=0.1879 r_work=0.0893 r_free=0.1887 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0893 r_free = 0.1887 target_work(ml) = 4.910 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0885 r_free = 0.1877 target_work(ml) = 4.903 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0885 r_free= 0.1877 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.903470 | | target function (ml) not normalized (work): 24139.782673 | | target function (ml) not normalized (free): 2341.982069 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1275 0.1836 5.5001 6.2598| | 2: 3.78 - 3.00 1.00 2430 110 0.0408 0.1947 4.2913 13.21| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.13 1.00 0.94 12362.99| | 2: 3.78 - 3.00 2430 110 0.99 1.81 1.00 0.96 818.34| |alpha: min = 0.93 max = 0.96 mean = 0.95| |beta: min = 521.27 max = 20814.72 mean = 6664.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.84 mean = 7.04| |phase err.(test): min = 0.00 max = 82.89 mean = 7.04| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0885 0.1877 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2114 0.2110 0.2284 n_refl.: 5175 remove outliers: r(all,work,free)=0.2114 0.2110 0.2284 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2114 0.2110 0.2284 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0935 0.0884 0.1882 n_refl.: 5175 remove outliers: r(all,work,free)=0.0935 0.0884 0.1882 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 0.3913 314.839 285.003 0.595 0.988 0.312 11.894-9.307 99.02 97 4 0.1968 506.477 491.523 0.998 0.994 0.307 9.237-7.194 100.00 213 7 0.2170 414.197 406.094 1.057 0.997 0.270 7.162-5.571 100.00 427 22 0.2059 310.805 301.215 1.040 0.998 0.270 5.546-4.326 100.00 867 58 0.1033 426.691 421.283 1.070 1.000 0.223 4.315-3.360 100.00 1859 96 0.0553 405.788 405.633 1.149 1.002 0.216 3.356-3.002 100.00 1373 60 0.0396 312.555 312.737 1.135 1.003 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.6376 ================= 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 : 0.3609 0.1972 0.083 5.281 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1553 0.083 5.281 6.4 116.8 17.4 258 0.000 1_settarget: 0.1555 0.1553 0.083 5.281 6.4 116.8 17.4 258 0.000 1_nqh: 0.1556 0.1557 0.083 5.281 6.4 116.8 17.4 258 0.006 1_weight: 0.1556 0.1557 0.083 5.281 6.4 116.8 17.4 258 0.006 1_xyzrec: 0.1158 0.1773 0.010 1.022 6.4 116.8 17.4 258 0.200 1_adp: 0.1018 0.1781 0.010 1.022 2.4 112.3 17.8 258 0.200 1_regHadp: 0.1012 0.1789 0.010 1.022 2.4 112.3 17.8 258 0.200 1_occ: 0.1017 0.1786 0.010 1.022 2.4 112.3 17.8 258 0.200 2_bss: 0.1020 0.1807 0.010 1.022 1.5 111.3 16.8 258 0.200 2_settarget: 0.1020 0.1807 0.010 1.022 1.5 111.3 16.8 258 0.200 2_updatecdl: 0.1020 0.1807 0.010 1.040 1.5 111.3 16.8 258 0.200 2_nqh: 0.1022 0.1811 0.010 1.040 1.5 111.3 16.8 258 0.200 2_sol: 0.1124 0.1662 0.010 1.040 1.0 111.3 16.3 233 n/a 2_weight: 0.1124 0.1662 0.010 1.040 1.0 111.3 16.3 233 n/a 2_xyzrec: 0.1019 0.1774 0.009 0.982 1.0 111.3 16.3 233 n/a 2_adp: 0.0943 0.1787 0.009 0.982 0.0 106.3 17.2 233 n/a 2_regHadp: 0.0940 0.1788 0.009 0.982 0.0 106.3 17.2 233 n/a 2_occ: 0.0933 0.1772 0.009 0.982 0.0 106.3 17.2 233 n/a 3_bss: 0.0928 0.1778 0.009 0.982 0.0 106.3 17.2 233 n/a 3_settarget: 0.0928 0.1778 0.009 0.982 0.0 106.3 17.2 233 n/a 3_updatecdl: 0.0928 0.1778 0.009 0.986 0.0 106.3 17.2 233 n/a 3_nqh: 0.0931 0.1782 0.009 0.986 0.0 106.3 17.2 233 n/a 3_sol: 0.1035 0.1761 0.009 0.986 0.0 106.3 17.0 241 n/a 3_weight: 0.1035 0.1761 0.009 0.986 0.0 106.3 17.0 241 n/a 3_xyzrec: 0.0922 0.1853 0.011 1.065 0.0 106.3 17.0 241 n/a 3_adp: 0.0881 0.1869 0.011 1.065 0.0 104.8 16.9 241 n/a 3_regHadp: 0.0886 0.1876 0.011 1.065 0.0 104.8 16.9 241 n/a 3_occ: 0.0876 0.1868 0.011 1.065 0.0 104.8 16.9 241 n/a 4_bss: 0.0868 0.1856 0.011 1.065 0.0 104.8 16.9 241 n/a 4_settarget: 0.0868 0.1856 0.011 1.065 0.0 104.8 16.9 241 n/a 4_updatecdl: 0.0868 0.1856 0.011 1.078 0.0 104.8 16.9 241 n/a 4_nqh: 0.0868 0.1856 0.011 1.078 0.0 104.8 16.9 241 n/a 4_sol: 0.0970 0.1840 0.011 1.078 0.0 104.8 17.0 239 n/a 4_weight: 0.0970 0.1840 0.011 1.078 0.0 104.8 17.0 239 n/a 4_xyzrec: 0.0878 0.1848 0.011 1.054 0.0 104.8 17.0 239 n/a 4_adp: 0.0858 0.1892 0.011 1.054 0.0 104.0 17.2 239 n/a 4_regHadp: 0.0861 0.1896 0.011 1.054 0.0 104.0 17.2 239 n/a 4_occ: 0.0852 0.1880 0.011 1.054 0.0 104.0 17.2 239 n/a 5_bss: 0.0852 0.1885 0.011 1.054 0.0 104.0 17.2 239 n/a 5_settarget: 0.0852 0.1885 0.011 1.054 0.0 104.0 17.2 239 n/a 5_updatecdl: 0.0852 0.1885 0.011 1.071 0.0 104.0 17.2 239 n/a 5_setrh: 0.0856 0.1884 0.011 1.071 0.0 104.0 17.2 239 n/a 5_nqh: 0.0859 0.1879 0.011 1.071 0.0 104.0 17.2 239 n/a 5_sol: 0.0960 0.1873 0.011 1.071 0.0 104.0 17.3 237 n/a 5_weight: 0.0960 0.1873 0.011 1.071 0.0 104.0 17.3 237 n/a 5_xyzrec: 0.0912 0.1856 0.011 1.202 0.0 104.0 17.3 237 n/a 5_adp: 0.0887 0.1879 0.011 1.202 0.0 103.9 17.6 237 n/a 5_regHadp: 0.0893 0.1887 0.011 1.202 0.0 103.9 17.6 237 n/a 5_occ: 0.0885 0.1877 0.011 1.202 0.0 103.9 17.6 237 n/a end: 0.0884 0.1882 0.011 1.202 0.0 103.9 17.6 237 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6943566_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6943566_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8400 Refinement macro-cycles (run) : 483.8300 Write final files (write_after_run_outputs) : 10.1900 Total : 497.8600 Total CPU time: 8.69 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:02 PST -0800 (1735492742.60 s) Start R-work = 0.1555, R-free = 0.1553 Final R-work = 0.0884, R-free = 0.1882 =============================================================================== Job complete usr+sys time: 529.03 seconds wall clock time: 9 minutes 10.64 seconds (550.64 seconds total)